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Manageiro V, Borges V, Rodrigues R, Bettencourt C, Silva C, Gomes JP, Gonçalves P. Recurrence, Microevolution, and Spatiotemporal Dynamics of Legionella pneumophila Sequence Type 1905, Portugal, 2014-2022. Emerg Infect Dis 2024; 30:1022-1025. [PMID: 38666647 PMCID: PMC11060437 DOI: 10.3201/eid3005.231383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
We investigated molecular evolution and spatiotemporal dynamics of atypical Legionella pneumophila serogroup 1 sequence type 1905 and determined its long-term persistence and linkage to human disease in dispersed locations, far beyond the large 2014 outbreak epicenter in Portugal. Our finding highlights the need for public health interventions to prevent further disease spread.
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Santos JD, Sobral D, Pinheiro M, Isidro J, Bogaardt C, Pinto M, Eusébio R, Santos A, Mamede R, Horton DL, Gomes JP, Borges V. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. Genome Med 2024; 16:61. [PMID: 38659008 PMCID: PMC11044337 DOI: 10.1186/s13073-024-01334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. RESULTS The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. CONCLUSIONS The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
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Affiliation(s)
- João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Carlijn Bogaardt
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rodrigo Eusébio
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - André Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rafael Mamede
- Faculdade de Medicina, Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel L Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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Mendonça R, Furtado R, Coelho A, Correia CB, Suyarko E, Borges V, Gomes JP, Pista A, Batista R. Raw milk cheeses from Beira Baixa, Portugal-A contributive study for the microbiological hygiene and safety assessment. Braz J Microbiol 2024:10.1007/s42770-024-01332-y. [PMID: 38622468 DOI: 10.1007/s42770-024-01332-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
Due to specific bacterial microbiota, raw milk cheeses have appreciated sensory properties. However, they may pose a threat to consumer safety due to potential pathogens presence. This study evaluated the microbiological contamination of 98 raw milk cheeses from Beira Baixa, Portugal. Presence and enumeration of Coagulase Positive Staphylococci (CPS), Listeria monocytogenes, Salmonella spp., pathogenic Escherichia coli, and indicator microorganisms (non-pathogenic E. coli and Listeria spp.) was attained. E. coli antimicrobial resistance (AMR) was also evaluated. PCR and/or Whole genome sequencing (WGS) was used to characterize E. coli, Salmonella spp. and L. monocytogenes isolates. Sixteen cheeses (16.3%) were classified as Satisfactory, 59 (60.2%) as Borderline and 23 (23.5%) as Unsatisfactory/Potential Injurious to Health. L. monocytogenes, CPS > 104 cfu g-1, Extraintestinal pathogenic E. coli (ExPEC) and Salmonella spp. were detected in 4.1%, 6.1%, 3.1% and 1.0% of the samples, respectively. Listeria innocua (4.1%) and E. coli > 104 cfu g-1 (16.3%) were also detected. AMR E. coli was detected in 23/98 (23.5%) of the cheese samples, of which two were multidrug resistant. WGS identified genotypes already associated to human disease and Listeria spp. cluster analysis indicated that cheese contamination might be related with noncompliance with Good Hygiene Practices during cheese production.
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Affiliation(s)
- Rita Mendonça
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal.
- Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
| | - Rosália Furtado
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Anabela Coelho
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Cristina Belo Correia
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Elena Suyarko
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- NOVA School of Science and Technology, 2829-516, Caparica, Portugal
| | - Vítor Borges
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - João Paulo Gomes
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Animal and Veterinary Research Center (CECAV), Faculty of Veterinary Medicine, Lusófona University-Lisbon University Centre, Lisbon, Portugal
| | - Angela Pista
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Rita Batista
- Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal.
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Rodrigues IC, Ribeiro-Almeida M, Silveira L, Prata JC, de Carvalho AP, Roque C, Gomes JP, Borges V, Pista Â, Martins da Costa P. Unveiling a Listeria monocytogenes Outbreak in a Rabbit Farm: Clinical Manifestation, Antimicrobial Resistance, Genomic Insights and Environmental Investigation. Microorganisms 2024; 12:785. [PMID: 38674729 PMCID: PMC11051769 DOI: 10.3390/microorganisms12040785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Listeria monocytogenes poses a threat to both human and animal health. This work describes an L. monocytogenes outbreak in a Portuguese rabbit farm, detailing the isolates' clinical manifestations, necropsy findings, and phenotypic and genomic profiles. Clinical signs, exclusively observed in does, included lethargy and reproductive signs. Post-mortem examination of does revealed splenomegaly, hepatomegaly with a reticular pattern, pulmonary congestion, and haemorrhagic lesions in the uterus, with thickening of the uterine wall and purulent greyish exudates. Positive L. monocytogenes samples were identified in fattening and maternity units across different samples, encompassing does and environmental samples. Core-genome Multi Locus Sequence Typing (cgMLST) analysis confirmed the outbreak, with the 16 sequenced isolates (lineage II, CC31, and ST325) clustering within a ≤2 allelic difference (AD) threshold. Antimicrobial susceptibility testing for five antibiotics revealed that 15 out of 19 outbreak isolates were resistant to sulfamethoxazole-trimethoprim (SXT). Concordantly, all SXT-resistant sequenced isolates were found to exclusively harbour a plasmid containing a trimethoprim-resistance gene (dfrD), along with loci linked to resistance to lincosamides (lnuG), macrolides (mphB), and polyether ionophores (NarAB operon). All sequenced outbreak isolates carried the antibiotic resistance-related genes tetM, fosX, lin, norB, lmrB, sul, and mprF. The outbreak cluster comprises isolates from does and the environment, which underscores the ubiquitous presence of L. monocytogenes and emphasizes the importance of biosecurity measures. Despite limited data on listeriosis in rabbit farming, this outbreak reveals its significant impact on animal welfare and production.
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Affiliation(s)
- Inês C. Rodrigues
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Marisa Ribeiro-Almeida
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4099-002 Porto, Portugal
| | - Leonor Silveira
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (C.R.); (Â.P.)
| | - Joana C. Prata
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- i4HB—Institute for Health and Bioeconomy, University Institute of Health Sciences, Advanced Polytechnic and University Cooperative (CESPU), 4585-116 Gandra, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Translational Toxicology Research Laboratory, University Institute of Health Sciences (1H-TOXRUN, IUCS-CESPU), 4585-116 Gandra, Portugal
| | - André Pinto de Carvalho
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- NANTA Portugal, S.A., Rua da Estação, N° 157, 4630-221 Marco de Canaveses, Portugal
| | - Carla Roque
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (C.R.); (Â.P.)
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (J.P.G.); (V.B.)
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (J.P.G.); (V.B.)
| | - Ângela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (C.R.); (Â.P.)
| | - Paulo Martins da Costa
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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Isidro J, Escudero R, Luque-Larena JJ, Pinto M, Borges V, González-Martín-Niño R, Duarte S, Vieira L, Mougeot F, Vidal D, Herrera-Rodríguez D, Rodríguez-Pastor R, Herrero-Cófreces S, Jubete-Tazo F, Gomes JP, Lopes de Carvalho I. Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples. Front Microbiol 2024; 14:1277468. [PMID: 38249473 PMCID: PMC10797068 DOI: 10.3389/fmicb.2023.1277468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the growth and isolation of this fastidious pathogen in culture, the availability of strains and subsequently WGS data is still limited. Methods To surpass these constraints, we aimed to implement a culture-free approach to capture and sequence F. tularensis genomes directly from complex samples. Biological samples obtained from 50 common voles and 13 Iberian hares collected in Spain were confirmed as positive for F. tularensis subsp. holarctica and subjected to a WGS target capture and enrichment protocol, using RNA oligonucleotide baits designed to cover F. tularensis genomic diversity. Results We obtained full genome sequences of F. tularensis from 13 animals (20.6%), two of which had mixed infections with distinct genotypes, and achieved a higher success rate when compared with culture-dependent WGS (only successful for two animals). The new genomes belonged to different clades commonly identified in Europe (B.49, B.51 and B.262) and subclades. Despite being phylogenetically closely related to other genomes from Spain, the detected clusters were often found in other countries. A comprehensive phylogenetic analysis, integrating 599 F. tularensis subsp. holarctica genomes, showed that most (sub)clades are found in both humans and animals and that closely related strains are found in different, and often geographically distant, countries. Discussion Overall, we show that the implemented culture-free WGS methodology yields timely, complete and high-quality genomic data of F. tularensis, being a highly valuable approach to promote and potentiate the genomic surveillance of F. tularensis and ultimately increase the knowledge on the genomics, ecology and epidemiology of this highly infectious pathogen.
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Affiliation(s)
- Joana Isidro
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Escudero
- Reference and Research Laboratory on Special Pathogens, National Centre for Microbiology (CNM), Carlos II Health Institute (ISCIII), Madrid, Spain
| | - Juan José Luque-Larena
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rosa González-Martín-Niño
- Reference and Research Laboratory on Special Pathogens, National Centre for Microbiology (CNM), Carlos II Health Institute (ISCIII), Madrid, Spain
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Dolors Vidal
- Área de Microbiología, Facultad de Medicina, Universidad de Catilla-La Mancha (UCLM), Ciudad Real, Spain
| | - Daniel Herrera-Rodríguez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
- Área de Microbiología, Facultad de Medicina, Universidad de Catilla-La Mancha (UCLM), Ciudad Real, Spain
| | - Ruth Rodríguez-Pastor
- Department of Parasitology, Veterinary Faculty, University of Zaragoza, Zaragoza, Spain, Zaragoza, Spain
- Departamento de Parasitología, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Silvia Herrero-Cófreces
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - Fernando Jubete-Tazo
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Center (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Isabel Lopes de Carvalho
- Emergency and Biopreparedness Unit, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Nunes A, Oleastro M, Alves F, Liassine N, Lowe DM, Benejat L, Ducounau A, Jehanne Q, Borges V, Gomes JP, Godbole G, Lehours P. Erratum for Nunes et al., "Recurrent Campylobacter jejuni Infections with In Vivo Selection of Resistance to Macrolides and Carbapenems: Molecular Characterization of Resistance Determinants". Microbiol Spectr 2023:e0312123. [PMID: 37815350 DOI: 10.1128/spectrum.03121-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
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Borges V, Duque MP, Martins JV, Vasconcelos P, Ferreira R, Sobral D, Pelerito A, de Carvalho IL, Núncio MS, Borrego MJ, Roemer C, Neher RA, O'Driscoll M, Rocha R, Lopo S, Neves R, Palminha P, Coelho L, Nunes A, Isidro J, Pinto M, Santos JD, Mixão V, Santos D, Duarte S, Vieira L, Martins F, Machado J, Veríssimo VC, Grau B, Peralta-Santos A, Neves J, Caldeira M, Pestana M, Fernandes C, Caria J, Pinto R, Póvoas D, Maltez F, Sá AI, Salvador MB, Teófilo E, Rocha M, Moneti V, Duque LM, E Silva FF, Baptista T, Vasconcelos J, Casanova S, Mansinho K, Alves JV, Alves J, Silva A, Alpalhão M, Brazão C, Sousa D, Filipe P, Pacheco P, Peruzzu F, de Jesus RP, Ferreira L, Mendez J, Jordão S, Duarte F, Gonçalves MJ, Pena E, Silva CN, Guimarães AR, Tavares M, Freitas G, Cordeiro R, Gomes JP. Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal. Nat Med 2023; 29:2509-2517. [PMID: 37696933 PMCID: PMC10579057 DOI: 10.1038/s41591-023-02542-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Pathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the highest impact on case numbers and fitted them into a global context, finding evidence that several international sublineages probably emerged or spread early in Portugal. We estimated a 62% infection reporting rate and that 1.3% of the population of men who have sex with men in Portugal were infected. We infer the critical role played by sexual networks and superspreader gatherings, such as sauna attendance, in the dissemination of mpox virus. Overall, our findings highlight genomic epidemiology as a tool for the real-time monitoring and control of mpox epidemics, and can guide future vaccine policy in a highly susceptible population.
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Affiliation(s)
- Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Mariana Perez Duque
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
- Pathogen Dynamics Group, Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - João Vieira Martins
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
| | - Paula Vasconcelos
- Public Health Emergency Centre, Directorate-General of Health, Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Pelerito
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Isabel Lopes de Carvalho
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria Sofia Núncio
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria José Borrego
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Megan O'Driscoll
- Pathogen Dynamics Group, Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Raquel Rocha
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Lopo
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Neves
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Paula Palminha
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Coelho
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Fátima Martins
- Technical Board, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Jorge Machado
- Department Coordination, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Cabral Veríssimo
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
- Public Health Unit, ACES Cascais, ARSLVT, Cascais, Portugal
| | - Berta Grau
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
- Public Health Emergency Centre, Directorate-General of Health, Lisbon, Portugal
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
- Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
| | - André Peralta-Santos
- Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
- Comprehensive Health Research Centre (CHRC), Escola Nacional de Saúde Pública, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - José Neves
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Margarida Caldeira
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Mafalda Pestana
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Cândida Fernandes
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - João Caria
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Raquel Pinto
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Diana Póvoas
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Ana Isabel Sá
- Unidade de Doenças Sexualmente Transmissíveis da Lapa, Lisbon, Portugal
| | | | - Eugénio Teófilo
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | - Miguel Rocha
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | - Virginia Moneti
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | - Luis Miguel Duque
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | | | - Teresa Baptista
- GAT - Grupo de Ativistas em Tratamentos, Intendente, Lisbon, Portugal
| | - Joana Vasconcelos
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Sara Casanova
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Kamal Mansinho
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - João Vaz Alves
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - João Alves
- Serviço de Dermatovenereologia, Hospital Garcia de Orta, Almada, Portugal
| | - António Silva
- Serviço de Dermatovenereologia, Hospital Garcia de Orta, Almada, Portugal
| | - Miguel Alpalhão
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
- Dermatology Research Unit (PFilipe Lab), Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, Lisbon, Portugal
- Dermatology University Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Cláudia Brazão
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
| | - Diogo Sousa
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
| | - Paulo Filipe
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
- Dermatology Research Unit (PFilipe Lab), Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, Lisbon, Portugal
- Dermatology University Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Patrícia Pacheco
- Serviço de Infeciologia, Hospital Professor Doutor Fernando Fonseca, Amadora, Portugal
| | - Francesca Peruzzu
- Serviço de Infeciologia, Hospital Professor Doutor Fernando Fonseca, Amadora, Portugal
| | | | - Luís Ferreira
- Serviço Infeciologia do CHUP, Largo Professor Abel Salazar, Porto, Portugal
| | - Josefina Mendez
- Serviço Infeciologia do CHUP, Largo Professor Abel Salazar, Porto, Portugal
| | - Sofia Jordão
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Frederico Duarte
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Maria João Gonçalves
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Eduarda Pena
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Claúdio Nunes Silva
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | | | - Margarida Tavares
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Graça Freitas
- National Health Authority, Directorate-General of Health, Lisbon, Portugal
| | - Rita Cordeiro
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal.
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Nunes A, Oleastro M, Alves F, Liassine N, Lowe DM, Benejat L, Ducounau A, Jehanne Q, Borges V, Gomes JP, Godbole G, Philippe L. Recurrent Campylobacter jejuni Infections with In Vivo Selection of Resistance to Macrolides and Carbapenems: Molecular Characterization of Resistance Determinants. Microbiol Spectr 2023; 11:e0107023. [PMID: 37358443 PMCID: PMC10434052 DOI: 10.1128/spectrum.01070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023] Open
Abstract
We present two independent cases of recurrent multidrug-resistant Campylobacter jejuni infection in immunocompromised hosts and the clinical challenges encountered due to the development of high-level carbapenem resistance. The mechanisms associated with this unusual resistance for Campylobacters were characterized. Initial macrolide and carbapenem-susceptible strains acquired resistance to erythromycin (MIC > 256mg/L), ertapenem (MIC > 32mg/L), and meropenem (MIC > 32mg/L) during treatment. Carbapenem-resistant isolates developed an in-frame insertion resulting in an extra Asp residue in the major outer membrane protein PorA, within the extracellular loop L3 that connects β-strands 5 and 6 and forms a constriction zone involved in Ca2+ binding. The isolates presenting the highest MIC to ertapenem exhibited an extra nonsynonymous mutation (G167A|Gly56Asp) at PorA's extracellular loop L1. IMPORTANCE Carbapenem susceptibility patterns suggest drug impermeability, related to either insertion and/or single nucleotide polymorphism (SNP) within porA. Similar molecular events occurring in two independent cases support the association of these mechanisms with carbapenem resistance in Campylobacter spp.
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Affiliation(s)
- Alexandra Nunes
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Mónica Oleastro
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Frederico Alves
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | | | | | - Lucie Benejat
- French National Reference Centre for Campylobacters and Helicobacters, Bordeaux Hospital University Centre, Bordeaux, France
| | - Astrid Ducounau
- French National Reference Centre for Campylobacters and Helicobacters, Bordeaux Hospital University Centre, Bordeaux, France
| | - Quentin Jehanne
- French National Reference Centre for Campylobacters and Helicobacters, Bordeaux Hospital University Centre, Bordeaux, France
| | - Vítor Borges
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | | | - Lehours Philippe
- French National Reference Centre for Campylobacters and Helicobacters, Bordeaux Hospital University Centre, Bordeaux, France
- University of Bordeaux, INSERM, Bordeaux Institute of Oncology, Bordeaux, France
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9
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Mixão V, Pinto M, Sobral D, Di Pasquale A, Gomes JP, Borges V. ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Med 2023; 15:43. [PMID: 37322495 DOI: 10.1186/s13073-023-01196-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time-consuming and difficult to reproduce. RESULTS We developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) or cluster stability regions and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography, or vaccination/clinical status. ReporTree is able to maintain cluster nomenclature in subsequent analyses and to generate a nomenclature code combining cluster information at different hierarchical levels, thus facilitating the active surveillance of clusters of interest. By handling several input formats and clustering methods, ReporTree is applicable to multiple pathogens, constituting a flexible resource that can be smoothly deployed in routine surveillance bioinformatics workflows with negligible computational and time costs. This is demonstrated through a comprehensive benchmarking of (i) the cg/wgMLST workflow with large datasets of four foodborne bacterial pathogens and (ii) the alignment-based SNP workflow with a large dataset of Mycobacterium tuberculosis. To further validate this tool, we reproduced a previous large-scale study on Neisseria gonorrhoeae, demonstrating how ReporTree is able to rapidly identify the main species genogroups and characterize them with key surveillance metadata, such as antibiotic resistance data. By providing examples for SARS-CoV-2 and the foodborne bacterial pathogen Listeria monocytogenes, we show how this tool is currently a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species. CONCLUSIONS In summary, ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters that contributes to a sustainable and efficient public health genomics-informed pathogen surveillance. ReporTree is implemented in python 3.8 and is freely available at https://github.com/insapathogenomics/ReporTree .
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Affiliation(s)
- Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Adriano Di Pasquale
- National Reference Centre (NRC) for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale Dell'Abruzzo E del Molise "Giuseppe Caporale" (IZSAM), Teramo, Italy
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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10
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Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLoS Biol 2023; 21:e3002151. [PMID: 37310918 PMCID: PMC10263305 DOI: 10.1371/journal.pbio.3002151] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
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Affiliation(s)
- Nicholas F. G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Luc Gagne
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Matthew Doucette
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Erika Buzby
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Joshua Hall
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Stephanie Ash
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Rachel Harrington
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Seana Cofsky
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Selina Clancy
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Curtis J. Kapsak
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Joel Sevinsky
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Kevin Libuit
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Daniel J. Park
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Jacob M. Garrigues
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Kristin Carpenter-Azevedo
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Kutluhan Incekara
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Christina Nishimura
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Anthony Muyombwe
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carly Aquino
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Isabella M. Savino
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Karinda Felton
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Nyjil Hayward
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Allison Naumann
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, Minnesota, United States of America
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, Minnesota, United States of America
| | - Regina Bones Barcellos
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda M. S. Godinho
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Richard Steiner Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Aimee Ceniseros
- Idaho Bureau of Laboratories, Boise, Idaho, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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11
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Kislaya I, Peralta‐Santos A, Borges V, Vieira L, Sousa C, Ferreira B, Pelerito A, Gomes JP, Leite PP, Nunes B. Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants: A case-case study based on electronic health records. Influenza Other Respir Viruses 2023; 17:e13121. [PMID: 36935845 PMCID: PMC10014519 DOI: 10.1111/irv.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Background Information on vaccine effectiveness in a context of novel variants of concern (VOC) emergence is of key importance to inform public health policies. This study aimed to estimate a measure of comparative vaccine effectiveness between Omicron (BA.1) and Delta (B.1.617.2 and sub-lineages) VOC according to vaccination exposure (primary or booster). Methods We developed a case-case study using data on RT-PCR SARS-CoV-2-positive cases notified in Portugal during Weeks 49-51, 2021. To obtain measure of comparative vaccine effectiveness, we compared the odds of vaccination in Omicron cases versus Delta using logistic regression adjusted for age group, sex, region, week of diagnosis, and laboratory of origin. Results Higher odds of vaccination were observed in cases infected by Omicron VOC compared with Delta VOC cases for both complete primary vaccination (odds ratio [OR] = 2.1; 95% confidence interval [CI]: 1.8 to 2.4) and booster dose (OR = 5.2; 95% CI: 3.1 to 8.8), equivalent to reduction of vaccine effectiveness from 44.7% and 92.8%, observed against infection with Delta, to -6.0% (95% CI: 29.2% to 12.7%) and 62.7% (95% CI: 35.7% to 77.9%), observed against infection with Omicron, for complete primary vaccination and booster dose, respectively. Conclusion Consistent reduction in vaccine-induced protection against infection with Omicron was observed. Complete primary vaccination may not be protective against SARS-CoV-2 infection in regions where Omicron variant is dominant.
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Affiliation(s)
- Irina Kislaya
- Department of EpidemiologyNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
- Public Health Research Centre, NOVA National School of Public HealthUniversidade NOVA de LisboaLisbonPortugal
- Comprehensive Health Research Centre (CHRC)Universidade NOVA de LisboaLisbonPortugal
| | - André Peralta‐Santos
- Public Health Research Centre, NOVA National School of Public HealthUniversidade NOVA de LisboaLisbonPortugal
- Comprehensive Health Research Centre (CHRC)Universidade NOVA de LisboaLisbonPortugal
- Direção de Serviços de Informação e AnáliseDireção‐Geral da SaúdeLisbonPortugal
| | - Vítor Borges
- Genomic and Bioinformatics Unit, Department of Infectious DiseasesNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
| | - Luís Vieira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo JorgeUnidade de Tecnologia e InovaçãoLisbonPortugal
| | | | - Bibiana Ferreira
- Algarve Biomedical Center Research Institute (ABC‐RI)FaroPortugal
- Faculty of Medicine and Biomedical Sciences (FMCB), Campus de GambelasUniversity of AlgarveFaroPortugal
| | | | - João Paulo Gomes
- Genomic and Bioinformatics Unit, Department of Infectious DiseasesNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
| | - Pedro Pinto Leite
- Direção de Serviços de Informação e AnáliseDireção‐Geral da SaúdeLisbonPortugal
| | - Baltazar Nunes
- Department of EpidemiologyNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
- Public Health Research Centre, NOVA National School of Public HealthUniversidade NOVA de LisboaLisbonPortugal
- Comprehensive Health Research Centre (CHRC)Universidade NOVA de LisboaLisbonPortugal
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Kislaya I, Casaca P, Borges V, Sousa C, Ferreira BI, Fonte A, Fernandes E, Dias CM, Duarte S, Almeida JP, Grenho I, Coelho L, Ferreira R, Ferreira PP, Borges CM, Isidro J, Pinto M, Menezes L, Sobral D, Nunes A, Santos D, Gonçalves AM, Vieira L, Gomes JP, Leite PP, Nunes B, Machado A, Peralta-Santos A. Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal. Emerg Infect Dis 2023; 29:569-575. [PMID: 36737101 PMCID: PMC9973705 DOI: 10.3201/eid2903.221367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We estimated comparative primary and booster vaccine effectiveness (VE) of SARS-CoV-2 Omicron BA.5 and BA.2 lineages against infection and disease progression. During April-June 2022, we implemented a case-case and cohort study and classified lineages using whole-genome sequencing or spike gene target failure. For the case-case study, we estimated the adjusted odds ratios (aORs) of vaccination using a logistic regression. For the cohort study, we estimated VE against disease progression using a penalized logistic regression. We observed no reduced VE for primary (aOR 1.07 [95% CI 0.93-1.23]) or booster (aOR 0.96 [95% CI 0.84-1.09]) vaccination against BA.5 infection. Among BA.5 case-patients, booster VE against progression to hospitalization was lower than that among BA.2 case-patients (VE 77% [95% CI 49%-90%] vs. VE 93% [95% CI 86%-97%]). Although booster vaccination is less effective against BA.5 than against BA.2, it offers substantial protection against progression from BA.5 infection to severe disease.
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Affiliation(s)
| | | | - Vítor Borges
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Carlos Sousa
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Bibiana I. Ferreira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Ana Fonte
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Eugénia Fernandes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Carlos Matias Dias
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Sílvia Duarte
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - José Pedro Almeida
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Inês Grenho
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Luís Coelho
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Rita Ferreira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Patrícia Pita Ferreira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Cláudia Medeiros Borges
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Joana Isidro
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Miguel Pinto
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Luís Menezes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Daniel Sobral
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Alexandra Nunes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Daniela Santos
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - António Maia Gonçalves
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Luís Vieira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - João Paulo Gomes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Pedro Pinto Leite
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Baltazar Nunes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
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Macedo R, Isidro J, Ferreira R, Pinto M, Borges V, Duarte S, Vieira L, Gomes JP. Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. Int J Mol Sci 2023; 24:ijms24032912. [PMID: 36769230 PMCID: PMC9918089 DOI: 10.3390/ijms24032912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n = 100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, Santa Clara, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Moreover, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, 9, and 1 samples were 3+, 2+, and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance prediction, essentially in settings when culture is not routinely performed or for samples that fail to grow.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
- Correspondence:
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14
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Chen NF, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FM, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CB. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. medRxiv 2023:2022.10.14.22280783. [PMID: 36299420 PMCID: PMC9603838 DOI: 10.1101/2022.10.14.22280783] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
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Affiliation(s)
- Nicholas F.G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Luc Gagne
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Erika Buzby
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Joshua Hall
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Stephanie Ash
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Seana Cofsky
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Selina Clancy
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | | | | | | | | | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, CA, USA
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | | | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | | | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal,Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carly Aquino
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | | | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,School of Medicine, University of St Andrews, St Andrews, UK
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Regina Bones Barcellos
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda M.S. Godinho
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Richard Steiner Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Boston, MA, USA,Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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15
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Pista A, Silveira L, Ribeiro S, Fontes M, Castro R, Coelho A, Furtado R, Lopes T, Maia C, Mixão V, Borges V, Sá A, Soeiro V, Correia CB, Gomes JP, Saraiva M, Oleastro M, Batista R. Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization. Microorganisms 2022; 10:microorganisms10112132. [PMID: 36363724 PMCID: PMC9694878 DOI: 10.3390/microorganisms10112132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/30/2022] Open
Abstract
Human–wildlife coexistence may increase the potential risk of direct transmission of emergent or re-emergent zoonotic pathogens to humans. Intending to assess the occurrence of three important foodborne pathogens in wild animals of two wildlife conservation centers in Portugal, we investigated 132 fecal samples for the presence of Escherichia coli (Shiga toxin-producing E. coli (STEC) and non-STEC), Salmonella spp. and Campylobacter spp. A genotypic search for genes having virulence and antimicrobial resistance (AMR) was performed by means of PCR and Whole-Genome Sequencing (WGS) and phenotypic (serotyping and AMR profiles) characterization. Overall, 62 samples tested positive for at least one of these species: 27.3% for STEC, 11.4% for non-STEC, 3.0% for Salmonella spp. and 6.8% for Campylobacter spp. AMR was detected in four E. coli isolates and the only Campylobacter coli isolated in this study. WGS analysis revealed that 57.7% (30/52) of pathogenic E. coli integrated genetic clusters of highly closely related isolates (often involving different animal species), supporting the circulation and transmission of different pathogenic E. coli strains in the studied areas. These results support the idea that the health of humans, animals and ecosystems are interconnected, reinforcing the importance of a One Health approach to better monitor and control public health threats.
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Affiliation(s)
- Angela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
- Correspondence:
| | - Leonor Silveira
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Sofia Ribeiro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Mariana Fontes
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Rita Castro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Anabela Coelho
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Rosália Furtado
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Teresa Lopes
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Rua Alexandre Herculano 321, 4000-055 Porto, Portugal
| | - Carla Maia
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Ana Sá
- Tapada Nacional de Mafra, Portão do Codeçal, 2640-602 Mafra, Portugal
| | - Vanessa Soeiro
- Centro de Recuperação do Parque Biológico de Gaia, Rua da Cunha, Avintes, 4430-812 Vila Nova de Gaia, Portugal
| | - Cristina Belo Correia
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Campo Grande 376, 1749-024 Lisbon, Portugal
| | - Margarida Saraiva
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Rua Alexandre Herculano 321, 4000-055 Porto, Portugal
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Rita Batista
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
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16
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Štefánek M, Wenner S, Borges V, Pinto M, Gomes JP, Rodrigues J, Faria I, Pessanha MA, Martins F, Sabino R, Veríssimo C, Nogueira ID, Carvalho PA, Bujdáková H, Jordao L. Antimicrobial Resistance and Biofilms Underlying Catheter-Related Bloodstream Coinfection by Enterobacter cloacae Complex and Candida parapsilosis. Antibiotics (Basel) 2022; 11:antibiotics11091245. [PMID: 36140024 PMCID: PMC9495738 DOI: 10.3390/antibiotics11091245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Biofilm-associated infections are a public health concern especially in the context of healthcare-associated infections such as catheter-related bloodstream infections (CRBSIs). We evaluated the biofilm formation and antimicrobials resistance (AMR) of Enterobacter cloacae complex and Candida parapsilosis co-isolated from a CRBSI patient. Antimicrobial susceptibility of central venous catheters (CVCs) and hemoculture (HC) isolates was evaluated, including whole genome sequencing (WGS) resistome analysis and evaluation of gene expression to obtain insight into their AMR determinants. Crystal violet assay was used to assess dual biofilm biomass and microscopy was used to elucidate a microorganism’s distribution within biofilms assembled on different materials. Bacteria were multidrug-resistant including resistance to colistin and beta-lactams, likely linked to the mcr-9-like phosphoethanolamine transferase and to an ACT family cephalosporin-hydrolyzing class C beta-lactamase, respectively. The R398I and Y132F mutations in the ERG11 gene and its differential expression might account for C. parapsilosis resistance to fluconazole. The phenotype of dual biofilms assembled on glass, polystyrene and polyurethane depends on the material and how biofilms were initiated by one or both pathogens. Biofilms assembled on polyurethane were denser and richer in the extracellular polymeric matrix, and microorganisms were differently distributed on the inner/outer surface of the CVC.
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Affiliation(s)
- Matúš Štefánek
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | | | - Vítor Borges
- Genomics and Bioinformatic Unit, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatic Unit, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatic Unit, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - João Rodrigues
- Unidade Laboratorial Integrada de Microbiologia, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisboa, Portugal
| | - Isabel Faria
- Laboratório de Microbiologia e Biologia Molecular do Serviço de Patologia Clínica, Centro Hospitalar de lisboa Ocidental (CHLO), 1349-019 Lisboa, Portugal
| | - Maria Ana Pessanha
- Laboratório de Microbiologia e Biologia Molecular do Serviço de Patologia Clínica, Centro Hospitalar de lisboa Ocidental (CHLO), 1349-019 Lisboa, Portugal
| | - Filomena Martins
- Direção do Programa de Prevenção e Controlo de Infeção e Resistência aos Antimicrobianos, Centro Hospitalar de lisboa Ocidental (CHLO), 1349-019 Lisboa, Portugal
| | - Raquel Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisboa, Portugal
- Institute of Environmental Health, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
| | - Cristina Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisboa, Portugal
| | | | | | - Helena Bujdáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | - Luisa Jordao
- Unidade de Investigação & Desenvolvimento, Departamento de Saúde Ambiental, Instituto Nacional de Saude Dr. Ricardo Jorge (INSA),1649-016 Lisboa, Portugal
- Correspondence:
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17
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Ribeiro M, Sousa M, Borges V, Gomes JP, Duarte S, Isidro J, Vieira L, Torres C, Santos H, Capelo JL, Poeta P, Igrejas G. Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples. J Proteomics 2022; 268:104714. [PMID: 36058542 DOI: 10.1016/j.jprot.2022.104714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
One of the most important livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) genetic lineages is the clonal complex (CC) 398, which can cause typical S. aureus-associated infections in people. In this work, whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics were applied to study the genetic characteristics of three MRSA CC398 isolates recovered from humans (strains C5621 and C9017), and from an animal (strain OR418). Of the three strains, C9017 presented the broadest resistance genotype, including resistance to fluroquinolone, clindamycin, tiamulin, macrolide and aminoglycoside antimicrobial classes. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains. For example, the immunoglobulin-binding protein Sbi was more abundant in OR418. Considering that Sbi is a multifunctional immune evasion factor in S. aureus, the results point to OR418 strain having high zoonotic potential. Overall, multiomics biomarker signatures can assume an important role to advance precision medicine in the years to come. SIGNIFICANCE: MRSA is one of the most representative drug-resistant pathogens and its dissemination is increasing due to MRSA capability of establishing new reservoirs. LA-MRSA is considered an emerging problem worldwide and CC398 is one of the most important genetic lineages. In this study, three MRSA CC398 isolates recovered from humans and from a wild animal were analyzed through whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics in order to gather systems-wide omics data and better understand the genetic characteristics of this lineage to identify distinctive markers and genomic features of relevance to public health. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains.
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Affiliation(s)
- Miguel Ribeiro
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Margarida Sousa
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal; Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Carmen Torres
- Biochemistry and Molecular Biology Unit, Faculty of Science and Technology, University of La Rioja, 26006 Logroño, Spain
| | - Hugo Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - José Luís Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Patrícia Poeta
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal; Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real 5000-801, Portugal; CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal.
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18
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Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O’Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biol 2022; 20:e3001769. [PMID: 35998195 PMCID: PMC9451062 DOI: 10.1371/journal.pbio.3001769] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/07/2022] [Indexed: 11/30/2022] Open
Abstract
The current nomenclature for monkeypox virus is stigmatising and misleading. This Perspective article proposes a practical and neutral system of nomenclature that will allow efficient communication without the risk of further misconceptions, discrimination and stigmatisation.
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Affiliation(s)
- Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University; Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- * E-mail: (CH); (TO)
| | | | - Placide Mbala
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo; University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Richard Njouom
- Virology Unit, Centre Pasteur of Cameroon, Yaoundé, Cameroon
| | | | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University; Ede, Osun State, Nigeria
| | | | | | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Richard A. Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emma Hodcroft
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Geneva Center of Emerging Viral Diseases, HUG, University of Geneva, Geneva, Switzerland
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Áine O’Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Moritz U. G. Kraemer
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Lucas Freitas
- GISAID at Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola C. Resende
- GISAID at Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Raphael T. C. Lee
- GISAID at Bioinformatics Institute and ID labs A*STAR, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Department of Biological Sciences and YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Ahmed E. Ogwell
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Yenew Kebede
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail: (CH); (TO)
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Isidro J, Borges V, Pinto M, Sobral D, Santos JD, Nunes A, Mixão V, Ferreira R, Santos D, Duarte S, Vieira L, Borrego MJ, Núncio S, de Carvalho IL, Pelerito A, Cordeiro R, Gomes JP. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat Med 2022; 28:1569-1572. [PMID: 35750157 PMCID: PMC9388373 DOI: 10.1038/s41591-022-01907-y] [Citation(s) in RCA: 342] [Impact Index Per Article: 171.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/20/2022] [Indexed: 12/17/2022]
Abstract
The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. 1-6). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered with 2018-2019 cases linked to an endemic country, it segregates in a divergent phylogenetic branch, likely reflecting continuous accelerated evolution. An in-depth mutational analysis suggests the action of host APOBEC3 in viral evolution as well as signs of potential MPXV human adaptation in ongoing microevolution. Our findings also indicate that genome sequencing may provide resolution to track the spread and transmission of this presumably slow-evolving double-stranded DNA virus.
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Affiliation(s)
- Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria José Borrego
- National Reference Laboratory of Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sofia Núncio
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Isabel Lopes de Carvalho
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Pelerito
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Cordeiro
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal.
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Silvestre I, Borges V, Duarte S, Nunes A, Sobral R, Vieira L, Gomes JP, Borrego MJ. Global gene expression analysis of Streptococcus agalactiae at exponential growth phase. Cell Mol Biol (Noisy-le-grand) 2022; 68:1-8. [PMID: 36495527 DOI: 10.14715/cmb/2022.68.7.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 12/13/2022]
Abstract
A comparative overview of the global gene expression levels of S. agalactiae reference strain NEM316 at the exponential growth phase was done through RNA-sequencing. The expression levels of 47 genes potentially linked to virulence evidenced that: i) the major nuclease, GBS_RS03720/gbs0661, presented higher mean expression values than the remainder of DNase genes; ii) the genetic pilus island PI-2a genes presented higher mean expression values than PI-1 coding genes; and, iii) three virulence-associated genes ranked among the top-100 most expressed genes (GBS_RS07760, GBS_RS09445 and GBS_RS03485). Among this top-100, genes encoding proteins involved in "Translation, ribosomal structure and biogenesis" represented 46%. Curiously, genes with no assigned function were grouped in the category of highly expressed genes. As very little is known about the molecular mechanisms behind the release of DNases, preliminary assays were developed to understand whether direct DNA exposure would affect gene expression at the exponential growth phase. No differentially expressed genes were detected, indicating that follow-up studies are needed to disclose the complex molecular pathways (and stimuli) triggering the release of DNases. In general, our insights on the global expression levels of NEM316 at exponential growth phase with and without DNA exposure should open novel research lines to decipher S. agalactiae puzzling adaptation and virulence mechanisms, such as DNase production.
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Affiliation(s)
- Inês Silvestre
- Department of Life Sciences, UCIBIO, Nova School of Science and Technology, Caparica, Portugal.
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal.
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Rita Sobral
- Department of Life Sciences, UCIBIO, Nova School of Science and Technology, Caparica, Portugal.
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal.
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Maria José Borrego
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
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21
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Pereira IS, Pais SV, Borges V, Borrego MJ, Gomes JP, Mota LJ. The Type III Secretion Effector CteG Mediates Host Cell Lytic Exit of Chlamydia trachomatis. Front Cell Infect Microbiol 2022; 12:902210. [PMID: 35903198 PMCID: PMC9318579 DOI: 10.3389/fcimb.2022.902210] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Chlamydia trachomatis is an obligate intracellular bacterium causing ocular and urogenital infections in humans that are a significant burden worldwide. The completion of its characteristic infectious cycle relies on the manipulation of several host cell processes by numerous chlamydial type III secretion effector proteins. We previously identified the C. trachomatis CteG effector and showed it localizes at the host cell plasma membrane at late stages of infection. Here, we showed that, from 48 h post-infection, mammalian cells infected by wild-type C. trachomatis contained more infectious chlamydiae in the culture supernatant than cells infected by a CteG-deficient strain. This phenotype was CteG-dependent as it could be complemented in cells infected by the CteG-deficient strain carrying a plasmid encoding CteG. Furthermore, we detected a CteG-dependent defect on host cell cytotoxicity, indicating that CteG mediates chlamydial lytic exit. Previous studies showed that Pgp4, a global regulator of transcription encoded in the C. trachomatis virulence plasmid, also mediates chlamydial lytic exit. However, by using C. trachomatis strains encoding or lacking Pgp4, we showed that production and localization of CteG are not regulated by Pgp4. A C. trachomatis strain lacking both CteG and Pgp4 was as defective in promoting host cell cytotoxicity as mutant strains lacking only CteG or Pgp4. Furthermore, CteG overproduction in a plasmid suppressed the host cell cytotoxic defect of CteG- and Pgp4-deficient chlamydiae. Overall, we revealed the first chlamydial type III secretion effector involved in host cell lytic exit. Our data indicates that CteG and Pgp4 participate in a single cascade of events, but involving multiple layers of regulation, leading to lysis of host cells and release of the infectious chlamydiae.
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Affiliation(s)
- Inês Serrano Pereira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Sara Vilela Pais
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria José Borrego
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Jaime Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- *Correspondence: Luís Jaime Mota,
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22
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Monteiro IP, Sousa S, Borges V, Gonçalves P, Gomes JP, Mota LJ, Franco IS. A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector. Front Cell Infect Microbiol 2022; 12:864626. [PMID: 35711665 PMCID: PMC9195298 DOI: 10.3389/fcimb.2022.864626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Legionella pneumophila is an accidental human pathogen that causes the potentially fatal Legionnaires’ disease, a severe type of pneumonia. The main virulence mechanism of L. pneumophila is a Type 4B Secretion System (T4SS) named Icm/Dot that transports effector proteins into the host cell cytosol. The concerted action of effectors on several host cell processes leads to the formation of an intracellular Legionella-containing vacuole that is replication competent and avoids phagolysosomal degradation. To date over 300 Icm/Dot substrates have been identified. In this study, we searched the genome of a L. pneumophila strain (Pt/VFX2014) responsible for the second largest L. pneumophila outbreak worldwide (in Vila Franca de Xira, Portugal, in 2014) for genes encoding potential novel Icm/Dot substrates. This strain Pt/VFX2014 belongs to serogroup 1 but phylogenetically segregates from all other serogroup 1 strains previously sequenced, displaying a unique mosaic genetic backbone. The ability of the selected putative effectors to be delivered into host cells by the T4SS was confirmed using the TEM-1 β-lactamase reporter assay. Two previously unknown Icm/Dot effectors were identified, VFX05045 and VFX10045, whose homologs Lpp1450 and Lpp3070 in clinical strain L. pneumophila Paris were also confirmed as T4SS substrates. After delivery into the host cell cytosol, homologs VFX05045/Lpp1450 remained diffused in the cell, similarly to Lpp3070. In contrast, VFX10045 localized to the host cell nucleus. To understand how VFX10045 and Lpp3070 (94% of identity at amino acid level) are directed to distinct sites, we carried out a comprehensive site-directed mutagenesis followed by analyses of the subcellular localization of the mutant proteins. This led to the delineation of region in the C-terminal part (residues 380 to 534) of the 583 amino acid-long VFX10045 as necessary and sufficient for nuclear targeting and highlighted the fundamental function of the VFX10045-specific R440 and I441 residues in this process. These studies revealed a strain-specific nucleotropism for new effector VFX10045/Lpp3070, which anticipates distinct functions between these homologs.
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Affiliation(s)
- Inês P. Monteiro
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Sofia Sousa
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Vítor Borges
- Núcleo de Bioinformática, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Paulo Gonçalves
- Laboratório Nacional de Referência de Legionella, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - João Paulo Gomes
- Núcleo de Bioinformática, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Luís Jaime Mota
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Irina S. Franco
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- *Correspondence: Irina S. Franco,
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Sá R, Isidro J, Borges V, Duarte S, Vieira L, Gomes JP, Tedim S, Matias J, Leite A. Unravelling the hurdles of a large COVID-19 epidemiological investigation by viral genomics. J Infect 2022; 85:64-74. [PMID: 35609706 PMCID: PMC9123803 DOI: 10.1016/j.jinf.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/16/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
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Greil R, Lin NU, Murthy RK, Abramson V, Anders C, Bachelot T, Bedard PL, Borges V, Cameron D, Carey L, Chien AJ, Curigliano G, DiGiovanna MP, Gelmon K, Hortobagyi G, Hurvitz S, Krop I, Loi S, Loibl S, Mueller V, Oliveira M, Paplomata E, Pegram M, Slamon D, Zelnak A, Ramos J, Feng W, Winer E. Aktualisierte Ergebnisse von Tucatinib versus Placebo in Kombination
mit Trastuzumab und Capecitabin bei Patienten mit vorbehandeltem, metastasierten
HER2-positiven Brustkrebs mit ZNS-Metastasen (HER2CLIMB). Geburtshilfe Frauenheilkd 2022. [DOI: 10.1055/s-0042-1746156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- R Greil
- Dritte medizinische Abteilung, Paracelsus Medizinische
Universität Salzburg, Salzburger Krebsforschungsinstitut –
Zentrum für Klinische Krebs- und Immunologiestudien und Cancer Cluster
Salzburg, Salzburg. Österreich
| | - N U Lin
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - R K Murthy
- MD Anderson Cancer Center, Houston, Texas, USA
| | - V Abramson
- Vanderbilt University Medical Center, Nashville, Tennessee,
USA
| | - C Anders
- Duke Cancer Institute, Durham, North Carolina, USA
| | | | - P L Bedard
- University Health Network, Princess Margaret Cancer Centre, Toronto,
Ontario, Kanada
| | - V Borges
- University of Colorado Cancer Center, Aurora, Colorado,
USA
| | - D Cameron
- Edinburgh Cancer Research Centre, Edinburgh, Vereinigtes
Königreich
| | - L Carey
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North
Carolina, USA
| | - A J Chien
- University of California at San Francisco, San Francisco, Kalifornien,
USA
| | - G Curigliano
- Istituto Europeo di Oncologia, IRCCS, University of Milano, Mailand,
Italien
| | | | - K Gelmon
- British Columbia Cancer – Vancouver Centre, British Columbia,
Kanada
| | | | - S Hurvitz
- UCLA Medical Center/Jonsson Comprehensive Cancer Center, Los
Angeles, Kalifornien, USA
| | - I Krop
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - S Loi
- Peter MacCallum Cancer Centre, Melbourne, Australien
| | - S Loibl
- Deutsche Brust-Gruppe, Neu-Isenburg. Deutschland
| | - V Mueller
- Universitätsklinikum Hamburg-Eppendorf, Hamburg,
Deutschland
| | - M Oliveira
- Hospital Universitario Vall D‘Hebron, Barcelona,
Spanien
| | - E Paplomata
- Carbone Cancer Center University of Wisconsin, Madison, Wisconsin,
USA
| | - M Pegram
- Stanford Comprehensive Cancer Institute Palo Alto, Kalifornien,
USA
| | - D Slamon
- UCLA Medical Center/Jonsson Comprehensive Cancer Center, Los
Angeles, Kalifornien, USA
| | - A Zelnak
- Northside Hospital, Sandy Springs, Georgia, USA
| | - J Ramos
- Seagen Inc., Bothell, Washington, USA
| | - W Feng
- Seagen Inc., Bothell, Washington, USA
| | - E. Winer
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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25
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Amicone M, Borges V, Alves MJ, Isidro J, Zé-Zé L, Duarte S, Vieira L, Guiomar R, Gomes JP, Gordo I. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evol Med Public Health 2022; 10:142-155. [PMID: 35419205 PMCID: PMC8996265 DOI: 10.1093/emph/eoac010] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/08/2022] [Indexed: 01/13/2023] Open
Abstract
Background and objectives To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures. Methodology We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains. Results From the frequencies of the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.3 × 10 -6 ± 0.2 × 10-6 per-base per-infection cycle (mean across both lineages of SARS-CoV-2 ± 2SEM). We further show that mutation accumulation is larger in the CoV-2-D lineage and heterogeneous along the genome, consistent with the action of positive selection on the spike protein, which accumulated five times more mutations than the corresponding genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. Conclusions and implications These results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome toward adaptation to new environments. Lay Summary: Each time a virus replicates inside a cell, errors (mutations) occur. Here, via laboratory propagation in cells originally isolated from the kidney epithelium of African green monkeys, we estimated the rate at which the SARS-CoV-2 virus mutates-an important parameter for understanding how it can evolve within and across humans. We also confirm the potential of its Spike protein to adapt to a new environment and report the emergence of mutators-viral populations where mutations occur at a significantly faster rate.
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Affiliation(s)
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria João Alves
- Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Líbia Zé-Zé
- Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School|Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Corresponding authors. Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal. E-mail: ; Instituto Gulbenkian de Ciência, Oeiras, Portugal. E-mail:
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Corresponding authors. Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal. E-mail: ; Instituto Gulbenkian de Ciência, Oeiras, Portugal. E-mail:
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26
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Gamelas V, Saraiva R, Duarte Santos J, Borges V, Saiote J, Costa Simões J. Gastrointestinal: Diarrhea and bowel thickening in elderly patients: A diagnosis to keep in mind. J Gastroenterol Hepatol 2022; 37:418. [PMID: 34414596 DOI: 10.1111/jgh.15655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/09/2022]
Affiliation(s)
- V Gamelas
- Gastroenterology Department, Central Lisbon University Hospital Center, Lisbon, Portugal
| | - R Saraiva
- Gastroenterology Department, Central Lisbon University Hospital Center, Lisbon, Portugal
| | - J Duarte Santos
- Pathology Department, Central Lisbon University Hospital Center, Lisbon, Portugal
| | - V Borges
- Gastroenterology Department, Central Lisbon University Hospital Center, Lisbon, Portugal
| | - J Saiote
- Gastroenterology Department, Central Lisbon University Hospital Center, Lisbon, Portugal
| | - J Costa Simões
- Gastroenterology Department, Central Lisbon University Hospital Center, Lisbon, Portugal
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27
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Pinto M, Borges V, Nascimento M, Martins F, Pessanha MA, Faria I, Rodrigues J, Matias R, Gomes JP, Jordao L. Insights on catheter-related bloodstream infections: a prospective observational study on the catheter colonization and multi-drug resistance. J Hosp Infect 2022; 123:43-51. [DOI: 10.1016/j.jhin.2022.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
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28
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Kislaya I, Rodrigues EF, Borges V, Gomes JP, Sousa C, Almeida JP, Peralta-Santos A, Nunes B. Comparative Effectiveness of Coronavirus Vaccine in Preventing Breakthrough Infections among Vaccinated Persons Infected with Delta and Alpha Variants. Emerg Infect Dis 2022; 28:331-337. [PMID: 34876242 PMCID: PMC8798697 DOI: 10.3201/eid2802.211789] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We developed a case-case study to compare mRNA vaccine effectiveness against Delta versus Alpha coronavirus variants. We used data on 2,097 case-patients with PCR-positive severe acute respiratory syndrome coronavirus 2 infections reported in Portugal during May-July 2021. We estimated the odds of vaccine breakthrough infection in Delta-infected versus Alpha-infected patients by using conditional logistic regression adjusted for age group and sex and matched by the week of diagnosis. We compared reverse-transcription PCR cycle threshold values by vaccination status and variant as an indirect measure of viral load. We found significantly higher odds of vaccine breakthrough infection in Delta-infected patients than in Alpha-infected patients (odds ratio 1.96 [95% CI 1.22-3.14]), suggesting lower effectiveness of the mRNA vaccines in preventing infection with the Delta variant. We estimated lower mean cycle threshold values for the Delta cases (mean difference -2.10 [95% CI -2.74 to -1.47]), suggesting higher infectiousness than the Alpha variant.
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Affiliation(s)
| | | | - Vítor Borges
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - João P. Gomes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - Carlos Sousa
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - José P. Almeida
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - André Peralta-Santos
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - Baltazar Nunes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - PT-COVID-19 Group2
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
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29
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Moura A, Lefrancq N, Wirth T, Leclercq A, Borges V, Gilpin B, Dallman TJ, Frey J, Franz E, Nielsen EM, Thomas J, Pightling A, Howden BP, Tarr CL, Gerner-Smidt P, Cauchemez S, Salje H, Brisse S, Lecuit M. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Sci Adv 2021; 7:eabj9805. [PMID: 34851675 PMCID: PMC8635441 DOI: 10.1126/sciadv.abj9805] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering Lm-CC1 first isolation to present days, to define its evolutionary history and population dynamics. We show that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming and food industrialization in the 20th century. In sharp contrast to its global spread over the past century, transmission chains are now mostly local, with limited inter- and intra-country spread. This study provides an unprecedented insight into L. monocytogenes phylogeography and population dynamics and highlights the importance of genome analyses for a better control of pathogen transmission.
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Affiliation(s)
- Alexandra Moura
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Noémie Lefrancq
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Thierry Wirth
- Institut Systématique Evolution Biodiversité (ISYEB),Museum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, Paris, France
- PSL University, EPHE, Paris, France
| | - Alexandre Leclercq
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Vítor Borges
- Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Brent Gilpin
- Christchurch Science Centre, Institute of Environmental Science and Research Limited, Christchurch, New Zealand
| | | | - Joachim Frey
- Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Juno Thomas
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arthur Pightling
- Biostatistics and Bioinformatics, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia
| | - Cheryl L. Tarr
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Simon Cauchemez
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Henrik Salje
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
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30
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Correia AM, Borges V, Isidro J, Lima AR, Fernandes A, Godinho ML, Duarte S, Ferrão J, Vieira L, Gomes JP. Potential recurrence of COVID-19 in a healthcare professional: SARS-CoV-2 genome sequencing confirms contagiousness after re-positivity. Int J Infect Dis 2021; 112:318-320. [PMID: 34547489 PMCID: PMC8450161 DOI: 10.1016/j.ijid.2021.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/01/2021] [Accepted: 09/15/2021] [Indexed: 11/15/2022] Open
Abstract
Re-positivity of SARS-CoV-2 tests is widely reported, raising discussion about guidance for patient discharge and ending isolation. The unsuccessful recovery of replication-competent virus and/or absence of secondary cases has suggested that re-positive patients are not contagious. This study reports SARS-CoV-2 re-positivity in a healthcare professional 16 days after three negative tests, with viral genome sequencing supporting contagiousness leading to secondary cases.
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Affiliation(s)
- Ana M Correia
- Northern Regional Health Administration, Cávado I - Braga Primary Healthcare Centres Group, Public Health Unit, Braga, Portugal.
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Ana R Lima
- Northern Regional Health Administration, Cávado I - Braga Primary Healthcare Centres Group, Public Health Unit, Braga, Portugal
| | - Alberto Fernandes
- Northern Regional Health Administration, Cávado I - Braga Primary Healthcare Centres Group, Public Health Unit, Braga, Portugal
| | - Maria Leonor Godinho
- Northern Regional Health Administration, Cávado I - Braga Primary Healthcare Centres Group, Public Health Unit, Braga, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - José Ferrão
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
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31
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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32
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Silvestre I, Nunes A, Borges V, Isidro J, Silva C, Vieira L, Gomes JP, Borrego MJ. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. Infect Genet Evol 2021; 93:104969. [PMID: 34147652 DOI: 10.1016/j.meegid.2021.104969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.
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Affiliation(s)
- Inês Silvestre
- Department of Life Sciences, UCIBIO, Nova School of Science and Technology, 2829-516 Caparica, Portugal; National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; CBIOS - Research Center for Biosciences & Health Technologies, Lusófona University of Humanities and Technologies, Campo Grande 376, 1749-024 Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Catarina Silva
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), Nova Medical School
- Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), Nova Medical School
- Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal.
| | - Maria José Borrego
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal.
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33
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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34
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Hurvitz S, Harbeck N, Vahdat L, Wolff A, Tolaney S, Loi S, Masuda N, O'Shaughnessy J, Xie D, Walker L, Rustia E, Borges V. 126TiP HER2CLIMB-02: Tucatinib or placebo with T-DM1 for unresectable locally-advanced or metastatic HER2+ breast cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.03.140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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35
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Gamelas V, Borges V, Santos S, Santos J, Silva MJ, Bernardes C, Ramos J. Gastrointestinal: Olmesartan-induced enterocolopathy: A new presentation of a known entity. J Gastroenterol Hepatol 2021; 36:1150. [PMID: 33305434 DOI: 10.1111/jgh.15332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/07/2020] [Accepted: 11/03/2020] [Indexed: 12/09/2022]
Affiliation(s)
- V Gamelas
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - V Borges
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - S Santos
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - J Santos
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - M J Silva
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - C Bernardes
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - J Ramos
- Gastroenterology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
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36
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Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, Gonzalez G, Garcia-Leon A, Crispie F, O'Connor L, Murphy N, Mossong J, Vergison A, Wienecke-Baldacchino AK, Abdelrahman T, Riccardo F, Stefanelli P, Di Martino A, Bella A, Lo Presti A, Casaca P, Moreno J, Borges V, Isidro J, Ferreira R, Gomes JP, Dotsenko L, Suija H, Epstein J, Sadikova O, Sepp H, Ikonen N, Savolainen-Kopra C, Blomqvist S, Möttönen T, Helve O, Gomes-Dias J, Adlhoch C. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Euro Surveill 2021; 26:2100348. [PMID: 33890566 PMCID: PMC8063589 DOI: 10.2807/1560-7917.es.2021.26.16.2100348] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).
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Affiliation(s)
- Tjede Funk
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Anastasia Pharris
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Gianfranco Spiteri
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Nick Bundle
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Angeliki Melidou
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Michael Carr
- National Virus Reference Laboratory (NVRL), University College Dublin, Dublin, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Gabriel Gonzalez
- National Virus Reference Laboratory (NVRL), University College Dublin, Dublin, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Alejandro Garcia-Leon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland on behalf of the All Ireland Infectious Diseases (AIID) Cohort
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland on behalf of the Irish Coronavirus Sequencing Consortium (ICSC)
| | - Lois O'Connor
- Health Service Executive - Health Protection Surveillance Centre (HPSC), Dublin, Ireland
| | - Niamh Murphy
- Health Service Executive - Health Protection Surveillance Centre (HPSC), Dublin, Ireland
| | | | | | | | | | | | | | | | | | | | - Pedro Casaca
- Directorate of Analysis and Information, Directorate-General of Health, Lisbon, Portugal
| | - Joana Moreno
- Directorate of Analysis and Information, Directorate-General of Health, Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Rita Ferreira
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | | | | | | | | | | | - Niina Ikonen
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Carita Savolainen-Kopra
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Soile Blomqvist
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Teemu Möttönen
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Otto Helve
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Joana Gomes-Dias
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Cornelia Adlhoch
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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37
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Borges V, Isidro J, Macedo F, Neves J, Silva L, Paiva M, Barata J, Catarino J, Ciobanu L, Duarte S, Vieira L, Guiomar R, Gomes JP. Nosocomial Outbreak of SARS-CoV-2 in a "Non-COVID-19" Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission. Viruses 2021; 13:v13040604. [PMID: 33916205 PMCID: PMC8065743 DOI: 10.3390/v13040604] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/15/2022] Open
Abstract
Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a "non-COVID-19" hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (J.I.); (J.P.G.)
- Correspondence:
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (J.I.); (J.P.G.)
| | - Filipe Macedo
- Local Coordination Group for the Prevention and Control of Infections and Antimicrobial Resistance Program, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal; (F.M.); (J.N.)
| | - José Neves
- Local Coordination Group for the Prevention and Control of Infections and Antimicrobial Resistance Program, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal; (F.M.); (J.N.)
| | - Luís Silva
- Clinical Pathology Department, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal;
| | - Mário Paiva
- Clinical Department, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal;
| | - José Barata
- Internal Medicine Department, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal;
| | - Judite Catarino
- Public Health Authority, Regional Health Administration of Lisbon and Tagus Valley, Health Centers Groups of Tagus Valley, 2615-042 Alverca do Ribatejo, Portugal; (J.C.); (L.C.)
| | - Liliana Ciobanu
- Public Health Authority, Regional Health Administration of Lisbon and Tagus Valley, Health Centers Groups of Tagus Valley, 2615-042 Alverca do Ribatejo, Portugal; (J.C.); (L.C.)
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.D.); (L.V.)
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.D.); (L.V.)
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School|Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1649-016 Lisbon, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal;
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (J.I.); (J.P.G.)
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38
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Borges V, Sousa C, Menezes L, Gonçalves AM, Picão M, Almeida JP, Vieita M, Santos R, Silva AR, Costa M, Carneiro L, Casaca P, Pinto-Leite P, Peralta-Santos A, Isidro J, Duarte S, Vieira L, Guiomar R, Silva S, Nunes B, Gomes JP. Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021. Euro Surveill 2021; 26:2100131. [PMID: 33706862 PMCID: PMC7953529 DOI: 10.2807/1560-7917.es.2021.26.10.2100130] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022] Open
Abstract
We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83-95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
- These authors contributed equally to this work
| | - Carlos Sousa
- These authors contributed equally to this work
- Molecular Diagnostics Laboratory, Unilabs, Oporto, Portugal
| | | | | | | | | | | | | | - Ana Rita Silva
- Molecular Diagnostics Laboratory, Unilabs, Oporto, Portugal
| | - Mariana Costa
- Molecular Diagnostics Laboratory, Unilabs, Oporto, Portugal
| | - Luís Carneiro
- Molecular Diagnostics Laboratory, Unilabs, Oporto, Portugal
| | - Pedro Casaca
- Division of Epidemiology and Statistics, Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
| | - Pedro Pinto-Leite
- Division of Epidemiology and Statistics, Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
| | - André Peralta-Santos
- Division of Epidemiology and Statistics, Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics; National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics; National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases; National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Susana Silva
- Epidemiological Research Unit Department of Epidemiology, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Baltazar Nunes
- Epidemiological Research Unit Department of Epidemiology, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
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Pinto M, Borges V, Isidro J, Rodrigues JC, Vieira L, Borrego MJ, Gomes JP. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microb Genom 2021; 7:000481. [PMID: 33245688 PMCID: PMC8208699 DOI: 10.1099/mgen.0.000481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Neisseria gonorrhoeae, the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.
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Affiliation(s)
- Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Carlos Rodrigues
- Laboratory of Microbiology, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School/Faculty of Medical Sciences, New University of Lisbon, Lisbon, Portugal
| | - Maria José Borrego
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
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Borges V, Isidro J, Correia C, Cordeiro D, Vieira L, Lodhia Z, Fernandes C, Rodrigues AM, Azevedo J, Alves J, Roxo J, Rocha M, Côrte-Real R, Toscano C, Pessanha MA, Nissan I, Pilo S, Rorman E, Dveyrin Z, Paitan Y, Paran H, Wagner-Kolasko G, Beirnes J, Gibbons S, Severini A, Borrego MJ, Gomes JP. Transcontinental Dissemination of the L2b/D-Da Recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) Strain: Need of Broad Multi-Country Molecular Surveillance. Clin Infect Dis 2021; 73:e1004-e1007. [PMID: 33512482 DOI: 10.1093/cid/ciab067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Previously, we identified a Chlamydia trachomatis lymphogranuloma venereum (LGV) recombinant strain possessing a non-LGV ompA genotype. Here, culture-independent genome sequencing confirms its circulation in Europe, Middle East, and North America, and unveils emergence of antibiotic resistance. Broad surveillance is needed.
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Affiliation(s)
- Vítor Borges
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Joana Isidro
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Cristina Correia
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Dora Cordeiro
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Zohra Lodhia
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Cândida Fernandes
- Centro Hospitalar e Universitário de Lisboa Central, Lisbon, Portugal
| | | | | | | | - João Roxo
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisbon, Portugal
| | - Miguel Rocha
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisbon, Portugal
| | - Rita Côrte-Real
- Centro Hospitalar e Universitário de Lisboa Central, Lisbon, Portugal
| | | | | | - Israel Nissan
- National Public Health Laboratories, Tel Aviv, Israel
| | - Shlomo Pilo
- National Public Health Laboratories, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratories, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratories, Tel Aviv, Israel
| | - Yossi Paitan
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine & Tel Aviv University, Tel Aviv, Israel.,Clinical Microbiology Lab, Meir Medical Center, Kfar Saba, Israel
| | - Haim Paran
- Department of General Surgery A, Meir Medical Center, Kfar Saba, Israel
| | - Gal Wagner-Kolasko
- Department of Family Medicine, Clalit Gan-Meir LGBT Clinic, Tel Aviv, Israel
| | | | | | - Alberto Severini
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - João Paulo Gomes
- National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
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41
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Borges V, Isidro J, Cortes-Martins H, Duarte S, Vieira L, Leite R, Gordo I, Caetano CP, Nunes B, Sá R, Oliveira A, Guiomar R, Gomes JP. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerg Microbes Infect 2020; 9:2488-2496. [PMID: 33131453 PMCID: PMC7717510 DOI: 10.1080/22221751.2020.1844552] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 01/02/2023]
Abstract
Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Helena Cortes-Martins
- Reference and Surveillance Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ricardo Leite
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Constantino P. Caetano
- Department of Epidemiology, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Baltazar Nunes
- Department of Epidemiology, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Centro de Investigação em Saúde Pública, Escola Nacional de Saúde Pública, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Regina Sá
- Public Health Unit, Primary Care Cluster of Baixo Vouga, Central Regional Health Administration, Aveiro, Portugal
| | - Ana Oliveira
- Public Health Unit, Primary Care Cluster of Baixo Vouga, Central Regional Health Administration, Aveiro, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | | | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
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Pinto L, Torres C, Gil C, Santos HM, Capelo JL, Borges V, Gomes JP, Silva C, Vieira L, Poeta P, Igrejas G. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain. OMICS 2020; 24:81-95. [PMID: 32073998 DOI: 10.1089/omi.2019.0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.
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Affiliation(s)
- Luís Pinto
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Concha Gil
- Departamento de Microbiologia II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Hugo M Santos
- LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - José Luís Capelo
- LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Catarina Silva
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Patrícia Poeta
- Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
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43
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Zé-Zé L, Borges V, Osório HC, Machado J, Gomes JP, Alves MJ. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal. PLoS Negl Trop Dis 2020; 14:e0008657. [PMID: 32997656 PMCID: PMC7549828 DOI: 10.1371/journal.pntd.0008657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 10/12/2020] [Accepted: 07/28/2020] [Indexed: 12/29/2022] Open
Abstract
Aedes albopictus, along with Ae. aegypti, are key arbovirus vectors that have been expanding their geographic range over the last decades. In 2017, Ae. albopictus was detected for the first time at two distinct locations in Portugal. In order to understand how the Ae. albopictus populations recently introduced in Portugal are genetically related and which is their likely route of invasion, we performed an integrative cytochrome C oxidase I gene (COI)- and mitogenome-based phylogeographic analysis of mosquitoes samples collected in Portugal in 2017 and 2018 in the context of the global Ae. albopictus diversity. COI-based analysis (31 partial sequences obtained from 83 mosquitoes) revealed five haplotypes (1 to 5), with haplotype 1 (which is widely distributed in temperate areas worldwide) being detected in both locations. Haplotypes 2 and 3 were exclusively found in Southern region (Algarve), while haplotype 4 and 5 were only detected in the North of Portugal (Penafiel, Oporto region). Subsequent high discriminatory analyses based on Ae. albopictus mitogenome (17 novel sequences) not only confirmed a high degree of genetic variability within and between populations at both geographic locations (compatible with the Ae. albopictus mosquito populations circulating in Europe), but also revealed two mitogenome mutational signatures not previously reported at worldwide level. While our results generally sustain the occurrence of multiple introduction events, fine mitogenome sequence inspection further indicates a possible Ae. albopictus migration within the country, from the Northern introduction locality to the Southern region. In summary, the observed scenario of high Ae. albopictus genetic diversity in Portugal, together with the detection of mosquitoes in successive years since 2017 in Algarve and Penafiel, points that both Ae. albopictus populations seem to be already locally established, as its presence has been reported for three consecutive years, raising the public health awareness for future mosquito-borne diseases outbreaks. In 2017, Aedes albopictus was reported for the first time in Portugal at two distinct locations, in the premises of a tire company in Penafiel, in the North, and nearby a golf course in Algarve, a tourism destination in the southernmost country region. The geographical spread of this species is promoted by egg and larvae transport in aquatic trade goods, as tires and aquatic plants, and adult anthropophilic behavior that favors passive land transportation. In Portugal, especially in the Southern region, temperate climate conditions are adequate for adult mosquitoes to survive most of the year. In a way to understand the genetic variability of Ae. albopictus populations introduced in Portugal, we analyzed 31 cytochrome C oxidase I gene (COI) partial sequences and 17 mitogenome sequences, integrating them in the context of the global Ae. albopictus phylogeographic diversity (i.e., 183 COI and 26 mitogenome sequences previously reported at worldwide level). Although COI haplotype 1 predominated, four additional haplotypes (2 to 5) were detected in Portugal. Subsequent in-depth mitogenome analysis revealed considerable genetic diversity, including not only sequences relating to mitogenomes reported mainly from Italy, Japan and China, but also two novel mitogenome mutational signatures. Our study indicates that Ae. albopictus is locally established in Portugal and intra-country dispersal may have already happened, highlighting the challenges for vector surveillance and control programs aiming at restraining arbovirus disease burden in the future.
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Affiliation(s)
- Líbia Zé-Zé
- Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- * E-mail:
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Hugo Costa Osório
- Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Jorge Machado
- Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Maria João Alves
- Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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Schäfer W, Schmidt T, Cordsmeier A, Borges V, Beare PA, Pechstein J, Schulze-Luehrmann J, Holzinger J, Wagner N, Berens C, Heydel C, Gomes JP, Lührmann A. The anti-apoptotic Coxiella burnetii effector protein AnkG is a strain specific virulence factor. Sci Rep 2020; 10:15396. [PMID: 32958854 PMCID: PMC7506536 DOI: 10.1038/s41598-020-72340-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 08/26/2020] [Indexed: 11/24/2022] Open
Abstract
The ability to inhibit host cell apoptosis is important for the intracellular replication of the obligate intracellular pathogen Coxiella burnetii, as it allows the completion of the lengthy bacterial replication cycle. Effector proteins injected into the host cell by the C. burnetii type IVB secretion system (T4BSS) are required for the inhibition of host cell apoptosis. AnkG is one of these anti-apoptotic effector proteins. The inhibitory effect of AnkG requires its nuclear localization, which depends on p32-dependent intracellular trafficking and importin-α1-mediated nuclear entry of AnkG. Here, we compared the sequences of ankG from 37 C. burnetii isolates and classified them in three groups based on the predicted protein size. The comparison of the three different groups allowed us to identify the first 28 amino acids as essential and sufficient for the anti-apoptotic activity of AnkG. Importantly, only the full-length protein from the first group is a bona fide effector protein injected into host cells during infection and has anti-apoptotic activity. Finally, using the Galleria mellonella infection model, we observed that AnkG from the first group has the ability to attenuate pathology during in vivo infection, as it allows survival of the larvae despite bacterial replication.
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Affiliation(s)
- Walter Schäfer
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany
| | - Teresa Schmidt
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany
| | - Arne Cordsmeier
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany
| | - Vítor Borges
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Paul A Beare
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Julian Pechstein
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany
| | - Jan Schulze-Luehrmann
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany
| | - Jonas Holzinger
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany
| | - Nicole Wagner
- Institut für Molekulare Pathogenese, Friedrich-Loeffler-Institut, 07743, Jena, Germany
| | - Christian Berens
- Institut für Molekulare Pathogenese, Friedrich-Loeffler-Institut, 07743, Jena, Germany
| | - Carsten Heydel
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus Liebig Universität Gießen, Frankfurter Straße 85-89, 35392, Gießen, Germany
| | - João Paulo Gomes
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Anja Lührmann
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054, Erlangen, Germany.
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45
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Sousa M, Silva N, Borges V, P Gomes J, Vieira L, Caniça M, Torres C, Igrejas G, Poeta P. MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant. Sci Total Environ 2020; 722:137845. [PMID: 32199375 DOI: 10.1016/j.scitotenv.2020.137845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
A methicillin-resistant Staphylococcus aureus CC398 was recovered from a wild female boar (Sus scrofa) in the north of Portugal, in 2013 (Sousa et al. 2017). Whole genome sequencing (WGS) revealed this strain carries a new variant of a mecA-containing staphylococcal chromosomal gene cassette (SCCmec) type IV with an uncommon J3 region. WGS studies can facilitate surveillance and provide more detailed characterization of bacterial clones circulating in the wild, reinforcing the need for a one health perspective to better understand and control antimicrobial resistance.
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Affiliation(s)
- Margarida Sousa
- MicroART - Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Veterinary and Animal Science Research Center (CECAV), UTAD, Vila Real, Portugal; Functional Genomics and Proteomics Unit, UTAD, Vila Real, Portugal; National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AR-HAI), National Institute of Health Dr. Ricardo Jorge (NIH), Lisbon, Portugal; Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Nuno Silva
- Moredun Research Institute (MRI), Pentlands Science Park, Bush Loan, Penicuik, Scotland, UK
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AR-HAI), National Institute of Health Dr. Ricardo Jorge (NIH), Lisbon, Portugal; Centre for the Study of Animal Sciences (CECA/ICETA), University of Oporto, Oporto, Portugal
| | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, UTAD, Vila Real, Portugal; Department of Genetics and Biotechnology, UTAD, Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Caparica, Portugal
| | - Patrícia Poeta
- MicroART - Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Caparica, Portugal.
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46
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Curigliano G, Murthy R, Loi S, Okines A, Paplomata E, Hamilton E, Hurvitz S, Cameron D, Borges V, Bedard P, Oliveira M, Jakobsen E, Bachelot T, Shachar S, Mueller V, Carey L, Loibl S, Feng W, Walker L, Winer E. 137O Tucatinib vs placebo added to trastuzumab and capecitabine in previously treated HER2+ metastatic breast cancer with and without brain metastases (HER2CLIMB). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.03.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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47
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Borges V, Cordeiro D, Salas AI, Lodhia Z, Correia C, Isidro J, Fernandes C, Rodrigues AM, Azevedo J, Alves J, Roxo J, Rocha M, Côrte-Real R, Vieira L, Borrego MJ, Gomes JP. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microb Genom 2020; 5. [PMID: 31697227 PMCID: PMC6927300 DOI: 10.1099/mgen.0.000313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Dora Cordeiro
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Ana Isabel Salas
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Zohra Lodhia
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Cristina Correia
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Cândida Fernandes
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Ana Maria Rodrigues
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Jacinta Azevedo
- Sexually Transmitted Diseases Clinic, Lapa Health Centre, Lisbon, Portugal
| | - João Alves
- Sexually Transmitted Diseases Clinic, Lapa Health Centre, Lisbon, Portugal
| | - João Roxo
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisboa, Portugal
| | - Miguel Rocha
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisboa, Portugal
| | - Rita Côrte-Real
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Maria José Borrego
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
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48
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Isidro J, Ferreira S, Pinto M, Domingues F, Oleastro M, Gomes JP, Borges V. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen. Infect Genet Evol 2020; 80:104213. [PMID: 32006709 DOI: 10.1016/j.meegid.2020.104213] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023]
Abstract
Arcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome with 1165 genes. It presents a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a type I secretion system (T1SS) harboring another agglutinin and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) and other antibiotic resistant determinants. We unprecedentedly describe a genetic mechanism of A. butzleri macrolides resistance, (inactivation of a TetR repressor likely regulating an EP). Fluoroquinolones resistance correlated with Thr-85-Ile in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the main antigen PorA, we show that A. butzleri is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats indicates that phase variation likely modulates A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast and diverse virulence and antibiotic resistance arsenals that open a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.
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Affiliation(s)
- Joana Isidro
- Bioinformatics Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Susana Ferreira
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal.
| | - Miguel Pinto
- Bioinformatics Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Fernanda Domingues
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.
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49
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Vilares A, Borges V, Sampaio D, Ferreira I, Martins S, Vieira L, Gargaté MJ, Gomes JP. Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii. Parasitol Res 2020; 119:587-599. [PMID: 31897784 DOI: 10.1007/s00436-019-06523-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/23/2019] [Indexed: 11/30/2022]
Abstract
Advances in molecular epidemiology of Toxoplasma gondii are hampered by technical and cost-associated hurdles underlying the acquisition of genomic data from parasites. In order to implement an enhanced genotyping approach for molecular surveillance of T. gondii, we applied a multi-locus amplicon-based sequencing strategy to samples associated with human infection. This approach, targeting genome-dispersed polymorphic loci potentially involved in adaptation and virulence, genetically discriminated almost all 68 studied strains and revealed a scenario of marked genomic mosaicism. Two-thirds (n = 43) of all strains were classified as recombinant, although recombination seemed to be linked to the classical archetypal lineage. While 92% of the Sag2 archetype I strains revealed genetic mosaicism, only 45% of Sag2 archetype II strains were identified as recombinant. Contrarily to the virulence-associated archetype I, most type II strains (regardless of their recombination background) were non-virulent in mouse. Besides Sag2, some of the newly studied loci (namely the type I/I-like alleles of Sag1, B17, PK1, and Sag3 and type III/III-like alleles of TgM-A) constitute promising candidates to rapidly infer T. gondii mouse virulence. Our successful attempt to capture microsatellite length variation launches good perspectives for the straightforward transition from the laborious intensive historical method to more informative next-generation sequencing (NGS)/bioinformatics-based methodologies. Overall, while T. gondii whole-genome sequencing will be hardly feasible in most laboratories, this study shows that a discrete loci panel has the potential to improve the molecular epidemiology of T. gondii towards a better monitoring of circulating genotypes with clinical importance.
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Affiliation(s)
- Anabela Vilares
- National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal. .,Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal.
| | - Vítor Borges
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Daniel Sampaio
- Innovation and Technology Unit, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Idalina Ferreira
- National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Susana Martins
- National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Luis Vieira
- Innovation and Technology Unit, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.,Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Maria João Gargaté
- National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
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50
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Brinkmann A, Andrusch A, Belka A, Wylezich C, Höper D, Pohlmann A, Nordahl Petersen T, Lucas P, Blanchard Y, Papa A, Melidou A, Oude Munnink BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Marcacci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A. Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets. J Clin Microbiol 2019; 57:e00466-19. [PMID: 31167846 PMCID: PMC6663916 DOI: 10.1128/jcm.00466-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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Affiliation(s)
- Annika Brinkmann
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Andreas Andrusch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Ariane Belka
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas Nordahl Petersen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pierrick Lucas
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Yannick Blanchard
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Anna Papa
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Angeliki Melidou
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | | | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Erhard van der Vries
- Department of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands
| | | | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Annelies Kroneman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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