1
|
Castilho de Arruda LD, Giovanetti M, Fonseca V, Zardin MCSU, Lichs GGDC, Asato S, Esposito AOP, Tokeshi Müller M, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos EV, Maziero LDMA, Frias DFR, Ahad das Neves D, Ferreira da Silva L, Rodrigues Barretos EC, Tsuha Oshiro PE, Modafari Goday B, Lemos dos Santos JK, Kashima S, de Albuquerque CFC, Said RFDC, Rosewell A, Demarchi LHF, Croda J, Alcantara LCJ, Cavalheiro Maymone Gonçalves C. Dengue Fever Surveillance in Mato Grosso do Sul: Insights from Genomic Analysis and Implications for Public Health Strategies. Viruses 2023; 15:1790. [PMID: 37766197 PMCID: PMC10536684 DOI: 10.3390/v15091790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Since its discovery in early 1916, dengue fever, a common vector-borne illness in Brazil, has resulted in extensive urban outbreaks and poses a serious threat to the public's health. Understanding the dynamics of Dengue Virus (DENV) serotypes circulating in different regions of Brazil is essential for implementing effective disease control and prevention measures. In response to this urgent need, we conducted an on-site training program in genomic surveillance in collaboration with the Central Laboratory of Health and the Secretary of Health of the Mato Grosso do Sul state. This initiative resulted in the generation of 177 DENV genome sequences collected between May 2021 and May 2022, a period during which over 11,391 dengue fever cases were reported in the state. Through this approach, we were able to identify the co-circulation of two different dengue serotypes (DENV1 and DENV2) as well as the existence of diverse viral lineages within each genotype, suggesting that multiple introduction events of different viral strains occurred in the region. By integrating epidemiological data, our findings unveiled temporal fluctuations in the relative abundance of different serotypes throughout various epidemic seasons, highlighting the complex and changing dynamics of DENV transmission throughout time. These findings demonstrate the value of ongoing surveillance activities in tracking viral transmission patterns, monitoring viral evolution, and informing public health actions.
Collapse
Affiliation(s)
- Larissa Domingues Castilho de Arruda
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
- Universidade Federal do Estado do Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil; (J.X.); (H.F.); (M.L.)
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di, 00128 Roma, Italy
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasília 70312-970, DF, Brazil;
| | - Marina Castilhos Souza Umaki Zardin
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (M.C.S.U.Z.); (G.G.d.C.L.); (S.A.); (M.T.M.); (L.H.F.D.)
| | - Gislene Garcia de Castro Lichs
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (M.C.S.U.Z.); (G.G.d.C.L.); (S.A.); (M.T.M.); (L.H.F.D.)
| | - Silvia Asato
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (M.C.S.U.Z.); (G.G.d.C.L.); (S.A.); (M.T.M.); (L.H.F.D.)
| | - Ana Olivia Pascoto Esposito
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (M.C.S.U.Z.); (G.G.d.C.L.); (S.A.); (M.T.M.); (L.H.F.D.)
| | - Miriam Tokeshi Müller
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (M.C.S.U.Z.); (G.G.d.C.L.); (S.A.); (M.T.M.); (L.H.F.D.)
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil; (J.X.); (H.F.); (M.L.)
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil; (J.X.); (H.F.); (M.L.)
| | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil; (J.X.); (H.F.); (M.L.)
| | - Carla de Oliveira
- lnstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Elaine Vieira Santos
- Fundação Hemocentro de Ribeirão Preto, Ribeirão Preto 14051-140, SP, Brazil (S.K.)
| | - Livia de Mello Almeida Maziero
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
- Universidade Federal do Estado do Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Danila Fernanda Rodrigues Frias
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
| | - Danielle Ahad das Neves
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
| | - Liliane Ferreira da Silva
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
- Universidade Federal do Estado do Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Ellen Caroline Rodrigues Barretos
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
| | - Paulo Eduardo Tsuha Oshiro
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
| | - Bianca Modafari Goday
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
| | - Jéssica Klener Lemos dos Santos
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
| | - Simone Kashima
- Fundação Hemocentro de Ribeirão Preto, Ribeirão Preto 14051-140, SP, Brazil (S.K.)
| | - Carlos F. C. de Albuquerque
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília 70312-970, DF, Brazil; (C.F.C.d.A.); (R.F.d.C.S.); (A.R.)
| | - Rodrigo Fabiano do Carmo Said
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília 70312-970, DF, Brazil; (C.F.C.d.A.); (R.F.d.C.S.); (A.R.)
| | - Alexander Rosewell
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília 70312-970, DF, Brazil; (C.F.C.d.A.); (R.F.d.C.S.); (A.R.)
| | - Luiz Henrique Ferraz Demarchi
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (M.C.S.U.Z.); (G.G.d.C.L.); (S.A.); (M.T.M.); (L.H.F.D.)
| | - Julio Croda
- Fundação Oswaldo Cruz, Universidade Federal de Mato Grosso do Sul-UFMS, Campo Grande 79000-000, MS, Brazil;
| | | | - Crhistinne Cavalheiro Maymone Gonçalves
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 79031-350, MS, Brazil; (L.D.C.d.A.); (L.d.M.A.M.); (D.F.R.F.); (D.A.d.N.); (L.F.d.S.); (E.C.R.B.); (P.E.T.O.); (B.M.G.); (J.K.L.d.S.)
- Universidade Federal do Estado do Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| |
Collapse
|
2
|
Barreto FK, Santos LA, Giovanetti M, Fonseca V, Aburjaile F, Silva JA, Freitas C, Peterka CRL, Rico JM, Almiron M, Melo CFCDAE, Alcântara LCJ. Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical training course in Brazil. EPIDEMIOLOGIA E SERVIÇOS DE SAÚDE 2023; 32:e2022614. [PMID: 37610938 PMCID: PMC10443443 DOI: 10.1590/s2237-96222023000200017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 06/06/2023] [Indexed: 08/25/2023] Open
Abstract
MAIN RESULTS Technology transfer can take place at large events, as long as safety protocols are strictly enforced. It is important to disseminate, at these events, the concepts of the Responsible Research and Innovation (RRI). Implications for services: Face-to-face training course is fundamental for training public health professionals. Technology transfer between research institutions and health services results in updating and improving health system performance. PERSPECTIVES Based on the success of the reported technology transfer, a new module will be incorporated into the next edition of VEME (Panama 2022), entitled Virus Evolution to Public Health Policy Makers. The objective of this report was to describe the first face-to-face course aimed at training public health professionals in performing real-time genomic surveillance during the pandemic period. Experience report on a theoretical-practical course focusing on genomic research and surveillance, including mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological modeling. There were 162 participants in the event and it was the first major face-to-face training course conducted during the COVID-19 epidemic in Brazil. No cases of SARS-CoV-2 infection was detected among the participants at the end of the event, suggesting the safety and effectiveness of all safety measures adopted. The results of this experience suggest that it is possible to conduct professional training safely during pandemics, as long as all safety protocols are followed.
Collapse
Affiliation(s)
- Fernanda Khouri Barreto
- Universidade Federal da Bahia, Instituto Multidisciplinar em Saúde, Vitória da Conquista, BA, Brazil
| | | | - Marta Giovanetti
- Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
| | - Flavia Aburjaile
- Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Joscelio Aguiar Silva
- Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil
| | - Carla Freitas
- Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública, Brasília, DF, Brazil
| | - Cassio Roberto Leonel Peterka
- Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil
| | - Jairo Mendez Rico
- Pan American Health Organization, Health Emergencies Department, Washington, DC, United States
| | - Maria Almiron
- Pan American Health Organization, Health Emergencies Department, Washington, DC, United States
| | | | - Luiz Carlos Júnior Alcântara
- Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG, Brazil
| |
Collapse
|
3
|
Braley LE, Jewell JB, Figueroa J, Humann JL, Main D, Mora-Romero GA, Moroz N, Woodhall JW, White RA, Tanaka K. Nanopore Sequencing with GraphMap for Comprehensive Pathogen Detection in Potato Field Soil. PLANT DISEASE 2023; 107:2288-2295. [PMID: 36724099 DOI: 10.1094/pdis-01-23-0052-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Early detection of causal pathogens is important to prevent crop loss from diseases. However, some diseases, such as soilborne diseases, are difficult to diagnose due to the absence of visible or characteristic symptoms. In the present study, the use of the Oxford Nanopore MinION sequencer as a molecular diagnostic tool was assessed due to its long-read sequencing capabilities and portability. Nucleotide samples (DNA or RNA) from potato field soils were sequenced and analyzed using a locally curated pathogen database, followed by identification via sequence mapping. We performed computational speed tests of three commonly used mapping/annotation tools (BLAST, BWA-BLAST, and BWA-GraphMap) and found BWA-GraphMap to be the fastest tool for local searching against our curated pathogen database. The data collected demonstrate the high potential of Nanopore sequencing as a minimally biased diagnostic tool for comprehensive pathogen detection in soil from potato fields. Our GraphMap-based MinION sequencing method could be useful as a predictive approach for disease management by identifying pathogens present in field soil prior to planting. Although this method still needs further experimentation with a larger sample size for practical use, the data analysis pipeline presented can be applied to other cropping systems and diagnostics for detecting multiple pathogens.
Collapse
Affiliation(s)
- Lauren E Braley
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Jeremy B Jewell
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Jose Figueroa
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, U.S.A
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, U.S.A
| | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, U.S.A
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, U.S.A
| | - Guadalupe A Mora-Romero
- Unidad de Investigación en Ambiente y Salud, Universidad Autónoma de Occidente, Los Mochis, Sinaloa 81223, México
| | - Natalia Moroz
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - James W Woodhall
- Parma Research and Extension Center, University of Idaho, Parma, ID 83660-6699, U.S.A
| | - Richard Allen White
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, U.S.A
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, U.S.A
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| |
Collapse
|
4
|
de Moraes L, Portilho MM, Vrancken B, Van den Broeck F, Santos LA, Cucco M, Tauro LB, Kikuti M, Silva MMO, Campos GS, Reis MG, Barral A, Barral-Netto M, Boaventura VS, Vandamme AM, Theys K, Lemey P, Ribeiro GS, Khouri R. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas. Viruses 2023; 15:1236. [PMID: 37376536 DOI: 10.3390/v15061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We performed a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA, and the Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.
Collapse
Affiliation(s)
- Laise de Moraes
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Moyra M Portilho
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Department of Biomedical Sciences, Antwerp Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Luciane Amorim Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador 41150-100, Brazil
| | - Marina Cucco
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Laura B Tauro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Misiones, Puerto Iguazú N3370, Argentina
| | - Mariana Kikuti
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Monaise M O Silva
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Gúbio S Campos
- Laboratório de Virologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador 40231-300, Brazil
| | - Mitermayer G Reis
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Patologia e Medicina Legal, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Aldina Barral
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Manoel Barral-Netto
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Viviane Sampaio Boaventura
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Hospital Santa Izabel, Salvador 40050-410, Brazil
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Guilherme S Ribeiro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Medicina Preventiva e Social, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Ricardo Khouri
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
5
|
Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
Collapse
|
6
|
Kipp EJ, Lindsey LL, Milstein MS, Blanco CM, Baker JP, Faulk C, Oliver JD, Larsen PA. Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects. Parasit Vectors 2023; 16:68. [PMID: 36788607 PMCID: PMC9930342 DOI: 10.1186/s13071-023-05679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/19/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Blood-feeding insects are important vectors for an array of zoonotic pathogens. While previous efforts toward generating molecular resources have largely focused on major vectors of global medical and veterinary importance, molecular data across a large number of hematophagous insect taxa remain limited. Advancements in long-read sequencing technologies and associated bioinformatic pipelines provide new opportunities for targeted sequencing of insect mitochondrial (mt) genomes. For engorged hematophagous insects, such technologies can be leveraged for both insect mitogenome genome assembly and identification of vertebrate blood-meal sources. METHODS We used nanopore adaptive sampling (NAS) to sequence genomic DNA from four species of field-collected, blood-engorged mosquitoes (Aedes and Culex spp.) and one deer fly (Chrysops sp.). NAS was used for bioinformatical enrichment of mtDNA reads of hematophagous insects and potential vertebrate blood-meal hosts using publically available mt genomes as references. We also performed an experimental control to compare results of traditional non-NAS nanopore sequencing to the mt genome enrichment by the NAS method. RESULTS Complete mitogenomes were assembled and annotated for all five species sequenced with NAS: Aedes trivittatus, Aedes vexans, Culex restuans, Culex territans and the deer fly, Chrysops niger. In comparison to data generated during our non-NAS control experiment, NAS yielded a substantially higher proportion of reference-mapped mtDNA reads, greatly streamlining downstream mitogenome assembly and annotation. The NAS-assembled mitogenomes ranged in length from 15,582 to 16,045 bp, contained between 78.1% and 79.0% A + T content and shared the anticipated arrangement of 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Maximum likelihood phylogenies were generated to further characterize each insect species. Additionally, vertebrate blood-meal analysis was successful in three samples sequenced, with mtDNA-based phylogenetic analyses revealing that blood-meal sources for Chrysops niger, Culex restuans and Aedes trivittatus were human, house sparrow (Passer domesticus) and eastern cottontail rabbit (Sylvilagus floridanus), respectively. CONCLUSIONS Our findings show that NAS has dual utility to simultaneously molecularly identify hematophagous insects and their blood-meal hosts. Moreover, our data indicate NAS can facilitate a wide array of mitogenomic systematic studies through novel 'phylogenetic capture' methods. We conclude that the NAS approach has great potential for broadly improving genomic resources used to identify blood-feeding insects, answer phylogenetic questions and elucidate complex pathways for the transmission of vector-borne pathogens.
Collapse
Affiliation(s)
- Evan J. Kipp
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Laramie L. Lindsey
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Marissa S. Milstein
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Cristina M. Blanco
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Julia P. Baker
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, St. Paul, MN USA
| | - Jonathan D. Oliver
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| |
Collapse
|
7
|
Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach. JOURNAL OF TROPICAL ECOLOGY 2023. [DOI: 10.1017/s0266467423000019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Abstract
During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.
Collapse
|
8
|
Grimaldi A, Panariello F, Annunziata P, Giuliano T, Daniele M, Pierri B, Colantuono C, Salvi M, Bouché V, Manfredi A, Cuomo MC, Di Concilio D, Tiberio C, Fiorenza M, Portella G, Cimmino I, Sorrentino A, Fusco G, Granata MR, Cerino P, Limone A, Atripaldi L, Ballabio A, Cacchiarelli D. Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients. Genome Med 2022; 14:90. [PMID: 35962405 PMCID: PMC9372932 DOI: 10.1186/s13073-022-01098-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred by vaccination strategies or previous virus exposure. It is also becoming clear now that efficient genomic surveillance would require monitoring of the host gene expression to identify prognostic biomarkers of treatment efficacy and disease progression. Here we propose an integrative workflow to both generate thousands of SARS-CoV-2 genome sequences per week and analyze host gene expression upon infection. Methods In this study we applied an integrated workflow for RNA extracted from nasal swabs to obtain in parallel the full genome of SARS-CoV-2 and transcriptome of host respiratory epithelium. The RNA extracted from each sample was reverse transcribed and the viral genome was specifically enriched through an amplicon-based approach. The very same RNA was then used for patient transcriptome analysis. Samples were collected in the Campania region, Italy, for viral genome sequencing. Patient transcriptome analysis was performed on about 700 samples divided into two cohorts of patients, depending on the viral variant detected (B.1 or delta). Results We sequenced over 20,000 viral genomes since the beginning of the pandemic, producing the highest number of sequences in Italy. We thus reconstructed the pandemic dynamics in the regional territory from March 2020 to December 2021. In addition, we have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients’ metadata and isolated patient-specific signatures of SARS-CoV-2 infection. This allowed us to (i) identify three new viral variants that specifically originated in the Campania region, (ii) map SARS-CoV-2 intrahost variability during long-term infections and in one case identify an increase in the number of mutations in the viral genome, and (iii) identify host gene expression signatures correlated with viral load in upper respiratory ways. Conclusion In conclusion, we have successfully generated an optimized and cost-effective strategy to monitor SARS-CoV-2 genetic variability, without the need of automation. Thus, our approach is suitable for any lab with a benchtop sequencer and a limited budget, allowing an integrated genomic surveillance on premises. Finally, we have also identified a gene expression signature defining SARS-CoV-2 infection in real-world patients’ upper respiratory ways. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01098-8.
Collapse
Affiliation(s)
- Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Patrizia Annunziata
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Teresa Giuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Michela Daniele
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Biancamaria Pierri
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Marcello Salvi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Valentina Bouché
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Claudia Tiberio
- UOC Microbiologia e Virologia, P.O. Cotugno A.O. dei Colli, Naples, Italy
| | - Mariano Fiorenza
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Portella
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Ilaria Cimmino
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy.,UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Antonio Sorrentino
- UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Giovanna Fusco
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Maria Rosaria Granata
- UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Antonio Limone
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Luigi Atripaldi
- UOC Microbiologia e Virologia, P.O. Cotugno A.O. dei Colli, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Department of Translational Medicine, University of Naples Federico II, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,SSM School for Advanced Studies, University of Naples Federico II, Naples, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy. .,Department of Translational Medicine, University of Naples Federico II, Naples, Italy. .,SSM School for Advanced Studies, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
9
|
de Figueiredo MLG, Williams EP, Jonsson CB, Khan MJ, Nunes MRT, de Lima CPS, Figueiredo LTM, Costa MRF, Mourão MPG, Lacerda MVG, Aquino VH. Screening of febrile patients with suspected malaria from the Brazilian Amazon for virus infection. Arch Virol 2022; 167:2151-2162. [PMID: 35841448 DOI: 10.1007/s00705-022-05514-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 05/12/2022] [Indexed: 11/25/2022]
Abstract
Arthropod-borne viruses (arboviruses) are a significant public health threat, especially in tropical and subtropical regions. More than 150 arboviruses can cause febrile illness following infection in humans. The Brazilian Amazon region has the highest number of arboviruses detected worldwide. In addition to arboviruses, malaria, caused by Plasmodium vivax, is endemic in the Amazon. Patients with malaria and arboviral disease frequently show similar clinical presentation and laboratory findings, making the diagnosis of the cause of the infection challenging. The aim of this study was to evaluate the potential for viral infections in patients with suspected malaria but without Plasmodium infection in the Brazilian Amazon. We recruited 200 subjects with suspected malaria in Manaus, Brazil. First, we tested for arboviruses in serum samples from 124 of the 200 participants using an arbovirus DNA microarray platform, which did not detect any virus. Then, we mixed the serum samples of the other 76 participants in 10 pools and subjected them to next-generation sequencing. Analysis of the sequencing data revealed the presence of only one arbovirus (Zika virus) in one sample pool. This analysis also detected the presence of primate erythroparvovirus 1 and pegivirus C. These results suggest that arboviruses are not the most frequent viral infections in patients with suspected malaria but without Plasmodium infection in the metropolitan region of Manaus. Implementation of specific viral surveillance tests will help in the early detection of viruses with epidemic potential.
Collapse
Affiliation(s)
- Mario Luis Garcia de Figueiredo
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Evan P Williams
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mohd Jaseem Khan
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | | | - Luiz Tadeu Moraes Figueiredo
- Ribeirao Preto Medical School, Virology Research Center, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | - Maria Paula Gomes Mourão
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Marcus Vinícius Guimarães Lacerda
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Amazonas, Brazil.
- Instituto Leônidas and Maria Deane (FIOCRUZ-Amazonas), Fundação Oswaldo Cruz, Manaus, Amazonas, Brazil.
| | - Victor Hugo Aquino
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil.
| |
Collapse
|
10
|
Featherstone LA, Zhang JM, Vaughan TG, Duchene S. Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications. Virus Evol 2022; 8:veac045. [PMID: 35775026 PMCID: PMC9241095 DOI: 10.1093/ve/veac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/23/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and statistical inference. It has also experienced more intense application than ever before amid the SARS-CoV-2 pandemic. In light of this, we present a review of phylodynamic models beginning with foundational models and assumptions. Our target audience is public health researchers, epidemiologists, and biologists seeking a working knowledge of the links between epidemiology, evolutionary models, and resulting epidemiological inference. We discuss the assumptions linking evolutionary models of pathogen population size to epidemiological models of the infected population size. We then describe statistical inference for phylodynamic models and list how output parameters can be rearranged for epidemiological interpretation. We go on to cover more sophisticated models and finish by highlighting future directions.
Collapse
Affiliation(s)
- Leo A Featherstone
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Joshua M Zhang
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Timothy G Vaughan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
- Swiss Institute of Bioinformatics, Geneva 1015, Switzerland
| | - Sebastian Duchene
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| |
Collapse
|
11
|
Giovanetti M, Pereira LA, Adelino TÉR, Fonseca V, Xavier J, de Araújo Fabri A, Slavov SN, da Silva Lemos P, de Almeida Marques W, Kashima S, Lourenço J, de Oliveira T, Campelo de Albuquerque CF, Freitas C, Peterka CRL, da Cunha RV, Mendonça AF, Lemes da Silva V, Alcantara LCJ. A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil. Microbiol Spectr 2022; 10:e0015522. [PMID: 35254139 PMCID: PMC9045127 DOI: 10.1128/spectrum.00155-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022] Open
Abstract
Since the introduction of the Zika virus (ZIKV) into Brazil in 2015, its transmission dynamics have been intensively studied in many parts of the country, although much is still unknown about its circulation in the midwestern states. Here, using nanopore technology, we obtained 23 novel partial and near-complete ZIKV genomes from the state of Goiás, located in the Midwest of Brazil. Genomic, phylogenetic, and epidemiological approaches were used to retrospectively explore the spatiotemporal evolution of the ZIKV-Asian genotype in this region. As a likely consequence of a gradual accumulation of herd immunity, epidemiological data revealed a decline in the number of reported cases over 2018 to 2021. Phylogenetic reconstructions revealed that multiple independent introductions of the Asian lineage have occurred in Goiás over time and revealed a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics. IMPORTANCE Despite the considerable morbidity and mortality of arboviral infections in Brazil, such as Zika, chikungunya, dengue fever, and yellow fever, our understanding of these outbreaks is hampered by the limited availability of genomic data to track and control the epidemic. In this study, we provide a retrospective reconstruction of the Zika virus transmission dynamics in the state of Goiás by analyzing genomic data from areas in Midwest Brazil not covered by other previous studies. Our study provides an understanding of how ZIKV initiates transmission in this region and reveals a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics, revealing how this toolkit can be used to help policymakers prioritize areas to be targeted, especially in the context of finite public health resources.
Collapse
Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Augusto Pereira
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Talita Émile Ribeiro Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Allison de Araújo Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Svetoslav Nanev Slavov
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Poliana da Silva Lemos
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Brazil
| | - William de Almeida Marques
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK
| | - Tulio de Oliveira
- School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | | | - Carla Freitas
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS), Brasília, Brazil
| | - Cassio Roberto Leonel Peterka
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Brazil
| | | | - Ana Flávia Mendonça
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | | | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
12
|
Steinig E, Duchêne S, Aglua I, Greenhill A, Ford R, Yoannes M, Jaworski J, Drekore J, Urakoko B, Poka H, Wurr C, Ebos E, Nangen D, Manning L, Laman M, Firth C, Smith S, Pomat W, Tong SYC, Coin L, McBryde E, Horwood P. Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing. Mol Biol Evol 2022; 39:msac040. [PMID: 35171290 PMCID: PMC8963328 DOI: 10.1093/molbev/msac040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance surveillance and outbreak response in communities without access to sequencing infrastructure. Here, we adapt random forest models for single nucleotide polymorphism (SNP) polishing developed by Sanderson and colleagues (2020. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing. Genome Res. 30(9):1354-1363) to estimate divergence and effective reproduction numbers (Re) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (PNG; n = 159). Successive barcoded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low coverage (>5× to 10×) provided sufficient data to accurately infer genotypes with high recall when compared with Illumina references. Random forest models achieved high resolution on ST93 outbreak sequence types (>90% accuracy and precision) and enabled phylodynamic inference of epidemiological parameters using birth-death skyline models. Our method reproduced phylogenetic topology, origin of the outbreaks, and indications of epidemic growth (Re > 1). Nextflow pipelines implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks on portable nanopore platforms. Our study shows that nanopore technology can be used for bacterial outbreak reconstruction at competitive costs, providing opportunities for infection control in hospitals and communities without access to sequencing infrastructure, such as in remote northern Australia and PNG.
Collapse
Affiliation(s)
- Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia
| | - Sebastián Duchêne
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Izzard Aglua
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea
| | - Andrew Greenhill
- Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea
| | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea
| | - Mition Yoannes
- Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea
| | - Jan Jaworski
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea
| | - Jimmy Drekore
- Simbu Children's Foundation, Kundiawa, Papua New Guinea
| | - Bohu Urakoko
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea
| | - Harry Poka
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea
| | - Clive Wurr
- Surgical Department, Goroka General Hospital, Goroka, Papua New Guinea
| | - Eri Ebos
- Surgical Department, Goroka General Hospital, Goroka, Papua New Guinea
| | - David Nangen
- Surgical Department, Goroka General Hospital, Goroka, Papua New Guinea
| | - Laurens Manning
- Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Australia
- Medical School, University of Western Australia, Harry Perkins Research Institute, Fiona Stanley Hospital, Murdoch, Australia
| | - Moses Laman
- Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea
| | - Cadhla Firth
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia
| | - Simon Smith
- Cairns Hospital and Hinterland Health Service, Queensland Health, Cairns, Australia
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lachlan Coin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Emma McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia
| | - Paul Horwood
- Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, Australia
| |
Collapse
|
13
|
Abstract
It is unclear whether West Nile virus (WNV) circulates endemically in Portugal. Despite the country’s adequate climate for transmission, Portugal has only reported four human WNV infections so far. We performed a review of WNV-related data (1966–2020), explored mosquito (2016–2019) and land type distributions (1992–2019), and used climate data (1981–2019) to estimate WNV transmission suitability in Portugal. Serological and molecular evidence of WNV circulation from animals and vectors was largely restricted to the south. Land type and climate-driven transmission suitability distributions, but not the distribution of WNV-capable vectors, were compatible with the North-South divide present in serological and molecular evidence of WNV circulation. Our study offers a comprehensive, data-informed perspective and review on the past epidemiology, surveillance and climate-driven transmission suitability of WNV in Portugal, highlighting the south as a subregion of importance. Given the recent WNV outbreaks across Europe, our results support a timely change towards local, active surveillance. Lourenço et al. review historical data and quantify the transmission potential of West Nile virus in Portugal. They report a North-South divide in infection patterns, a higher ecological capacity in the south, and an increasing positive effect of climate change over the last 40 years.
Collapse
|
14
|
de Matos SMS, Hennigen AF, Wachholz GE, Rengel BD, Schuler-Faccini L, Roehe PM, Varela APM, Fraga LR. Possible Emergence of Zika Virus of African Lineage in Brazil and the Risk for New Outbreaks. Front Cell Infect Microbiol 2021; 11:680025. [PMID: 34368011 PMCID: PMC8342935 DOI: 10.3389/fcimb.2021.680025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sophia Martins Simon de Matos
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - André Ferreira Hennigen
- Laboratory of Virology, Department of Microbiology, Immunology and Parasitology, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gabriela Elis Wachholz
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruna Duarte Rengel
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lavinia Schuler-Faccini
- Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Paulo Michel Roehe
- Laboratory of Virology, Department of Microbiology, Immunology and Parasitology, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Postgraduate Program in Bioscience, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
15
|
Gräf T, Vazquez C, Giovanetti M, de Bruycker-Nogueira F, Fonseca V, Claro IM, de Jesus JG, Gómez A, Xavier J, de Mendonça MCL, Villalba S, Torales J, Gamarra ML, Thézé J, de Filippis AMB, Azevedo V, de Oliveira T, Franco L, de Albuquerque CFC, Irala S, Holmes EC, Méndez Rico JA, Alcantara LCJ. Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay. Emerg Infect Dis 2021; 27:1393-1404. [PMID: 33900172 PMCID: PMC8084490 DOI: 10.3201/eid2705.204244] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Paraguay has been severely affected by emergent Zika and chikungunya viruses, and dengue virus is endemic. To learn more about the origins of genetic diversity and epidemiologic history of these viruses in Paraguay, we deployed portable sequencing technologies to strengthen genomic surveillance and determine the evolutionary and epidemic history of arthropod-borne viruses (arboviruses). Samples stored at the Paraguay National Central Laboratory were sequenced and subjected to phylogenetic analysis. Among 33 virus genomes generated, we identified 2 genotypes of chikungunya and 2 serotypes of dengue virus that circulated in Paraguay during 2014–2018; the main source of these virus lineages was estimated to be Brazil. The evolutionary history inferred by our analyses precisely matched the available travel history of the patients. The genomic surveillance approach used was valuable for describing the epidemiologic history of arboviruses and can be used to determine the origins and evolution of future arbovirus outbreaks.
Collapse
|
16
|
High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Sci Rep 2021; 11:13669. [PMID: 34211026 PMCID: PMC8249533 DOI: 10.1038/s41598-021-93145-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 06/21/2021] [Indexed: 01/18/2023] Open
Abstract
COVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients' Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.
Collapse
|
17
|
Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WDA, Junior Franca de Barros J, Adelino TER, Tosta S, Fritsch H, Iani FCDM, Mares-Guia MA, Salgado A, Fonseca V, Xavier J, Lopes EN, Soares GC, de Castro Amarante MF, Azevedo V, Kruger A, Correa Matta G, Paineiras-Domingos LL, Colonnello C, Bispo de Filippis AM, Montesano C, Colizzi V, Barreto FK. Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses. Front Public Health 2021; 9:693743. [PMID: 34277552 PMCID: PMC8282202 DOI: 10.3389/fpubh.2021.693743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/07/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Qesya Rodrigues Ferreira
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | | | | | - Talita Emile Ribeiro Adelino
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hegger Fritsch
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | | | - Alvaro Salgado
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Elisson Nogueira Lopes
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gilson Carlos Soares
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Alícia Kruger
- Departamento Nacional de IST/AIDS/Hepatites Virais, Brasília, Brazil
| | - Gustavo Correa Matta
- Escola Nacional de Saúde Pública Sergio Arouca, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | - Carla Montesano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Vittorio Colizzi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Fernanda Khouri Barreto
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| |
Collapse
|
18
|
Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF, Costa AVB, Silva EC, Mendes MCO, Filippis AMB, Albuquerque CFC, Abreu AL, Oliveira MAA, Alcantara LCJ, Faria NR. Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil. INFECTION GENETICS AND EVOLUTION 2021; 91:104785. [PMID: 33652117 DOI: 10.1016/j.meegid.2021.104785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022]
Abstract
Autochthonous Zika virus (ZIKV) transmission in Brazil was first identified in April 2015 in Brazil, with the first ZIKV-associated microcephaly cases detected in October 2015. Despite efforts on understanding ZIKV transmission in Brazil, little is known about the virus epidemiology and genetic diversity in Minas Gerais (MG), the second most populous state in the country. We report molecular and genomic findings from the main public health laboratory in MG. Until January 2020, 26,817 ZIKV suspected infections and 86 congenital syndrome cases were reported in MG state. We tested 8552 ZIKV and microcephaly suspected cases. Ten genomes were generated on-site directly from clinical samples. A total of 1723 confirmed cases were detected in Minas Gerais, with two main epidemic waves; the first and larger epidemic wave peaked in March 2016, with the second smaller wave that peaked in March 2017. Dated molecular clock analysis revealed that multiple introductions occurred in Minas Gerais between 2014 and 2015, suggesting that the virus was circulating unnoticed for at least 16 months before the first confirmed laboratory case that we retrospectively identified in December 2015. Our findings highlight the importance of continued genomic surveillance strategies combined with traditional epidemiology to assist public health laboratories in monitoring and understanding the diversity of circulating arboviruses, which might help attenuate the public health impact of infectious diseases.
Collapse
Affiliation(s)
- Felipe C M Iani
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil; Department of Zoology, University of Oxford, United Kingdom; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban 4001, South Africa; Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - William M Souza
- Department of Zoology, University of Oxford, United Kingdom; Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Talita E R Adelino
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jaqueline G Jesus
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maira A Pereira
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Marcos V F Silva
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Alana V B Costa
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Erniria C Silva
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Brazil
| | - Márcia C O Mendes
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Brazil
| | - Ana M B Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - André L Abreu
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Marluce A A Oliveira
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
| | - Luiz C J Alcantara
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
| |
Collapse
|
19
|
Lourenço J, Thompson RN, Thézé J, Obolski U. Characterising West Nile virus epidemiology in Israel using a transmission suitability index. ACTA ACUST UNITED AC 2021; 25. [PMID: 33213688 PMCID: PMC7678037 DOI: 10.2807/1560-7917.es.2020.25.46.1900629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Climate is a major factor in the epidemiology of West Nile virus (WNV), a pathogen increasingly pervasive worldwide. Cases increased during 2018 in Israel, the United States and Europe. Aim We set to retrospectively understand the spatial and temporal determinants of WNV transmission in Israel, as a case study for the possible effects of climate on virus spread. Methods We employed a suitability index to WNV, parameterising it with prior knowledge pertaining to a bird reservoir and Culex species, using local time series of temperature and humidity as inputs. The predicted suitability index was compared with confirmed WNV cases in Israel (2016–2018). Results The suitability index was highly associated with WNV cases in Israel, with correlation coefficients of 0.91 (p value = 4 × 10− 5), 0.68 (p = 0.016) and 0.9 (p = 2 × 10− 4) in 2016, 2017 and 2018, respectively. The fluctuations in the number of WNV cases between the years were explained by higher area under the index curve. A new WNV seasonal mode was identified in the south-east of Israel, along the Great Rift Valley, characterised by two yearly peaks (spring and autumn), distinct from the already known single summer peak in the rest of Israel. Conclusions By producing a detailed geotemporal estimate of transmission potential and its determinants in Israel, our study promotes a better understanding of WNV epidemiology and has the potential to inform future public health responses. The proposed approach further provides opportunities for retrospective and prospective mechanistic modelling of WNV epidemiology and its associated climatic drivers.
Collapse
Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Robin N Thompson
- Christ Church, University of Oxford, Oxford, United Kingdom.,Mathematical Institute, University of Oxford, Oxford, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Julien Thézé
- Joint Research Unit Epidemiology of Animal and Zoonotic Diseases (EPIA), INRA, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Uri Obolski
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel.,School of Public Health, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
20
|
Li SL, Messina JP, Pybus OG, Kraemer MUG, Gardner L. A review of models applied to the geographic spread of Zika virus. Trans R Soc Trop Med Hyg 2021; 115:956-964. [PMID: 33570155 PMCID: PMC8417088 DOI: 10.1093/trstmh/trab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/13/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
In recent years, Zika virus (ZIKV) has expanded its geographic range and in 2015–2016 caused a substantial epidemic linked to a surge in developmental and neurological complications in newborns. Mathematical models are powerful tools for assessing ZIKV spread and can reveal important information for preventing future outbreaks. We reviewed the literature and retrieved modelling studies that were developed to understand the spatial epidemiology of ZIKV spread and risk. We classified studies by type, scale, aim and applications and discussed their characteristics, strengths and limitations. We examined the main objectives of these models and evaluated the effectiveness of integrating epidemiological and phylogeographic data, along with socioenvironmental risk factors that are known to contribute to vector–human transmission. We also assessed the promising application of human mobility data as a real-time indicator of ZIKV spread. Lastly, we summarised model validation methods used in studies to ensure accuracy in models and modelled outcomes. Models are helpful for understanding ZIKV spread and their characteristics should be carefully considered when developing future modelling studies to improve arbovirus surveillance.
Collapse
Affiliation(s)
- Sabrina L Li
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK
| | - Jane P Messina
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK.,School of Global and Area Studies, University of Oxford, 12 Bevington Road, Oxford, OX2 6LH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2682, USA.,Center for Systems Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2682, USA
| |
Collapse
|
21
|
New Insights on the Zika Virus Arrival in the Americas and Spatiotemporal Reconstruction of the Epidemic Dynamics in Brazil. Viruses 2020; 13:v13010012. [PMID: 33374816 PMCID: PMC7824532 DOI: 10.3390/v13010012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 12/20/2022] Open
Abstract
Zika virus (ZIKV) became a worldwide public health emergency after its introduction in the Americas. Brazil was implicated as central in the ZIKV dispersion, however, a better understanding of the pathways the virus took to arrive in Brazil and the dispersion within the country is needed. An updated genome dataset was assembled with publicly available data. Bayesian phylogeography methods were applied to reconstruct the spatiotemporal history of ZIKV in the Americas and with more detail inside Brazil. Our analyses reconstructed the Brazilian state of Pernambuco as the likely point of introduction of ZIKV in Brazil, possibly during the 2013 Confederations Cup. Pernambuco played an important role in spreading the virus to other Brazilian states. Our results also underscore the long cryptic circulation of ZIKV in all analyzed locations in Brazil. Conclusions: This study brings new insights about the early moments of ZIKV in the Americas, especially regarding the Brazil-Haiti cluster at the base of the American clade and describing for the first time migration patterns within Brazil.
Collapse
|
22
|
Lamb HJ, Hayes BJ, Nguyen LT, Ross EM. The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock. Genes (Basel) 2020; 11:E1478. [PMID: 33317066 PMCID: PMC7763041 DOI: 10.3390/genes11121478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.
Collapse
Affiliation(s)
- Harrison J. Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4067, Australia; (B.J.H.); (L.T.N.); (E.M.R.)
| | | | | | | |
Collapse
|
23
|
Palatnick A, Zhou B, Ghedin E, Schatz MC. iGenomics: Comprehensive DNA sequence analysis on your Smartphone. Gigascience 2020; 9:giaa138. [PMID: 33284326 PMCID: PMC7720420 DOI: 10.1093/gigascience/giaa138] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/29/2020] [Accepted: 11/10/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is on a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available. RESULTS iGenomics is the first comprehensive mobile genome analysis application, with capabilities to align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets of viral and bacterial genomes and show that iGenomics has performance comparable to the popular BWA-MEM/SAMtools/IGV suite, without necessitating a laptop or server cluster. CONCLUSIONS iGenomics is available open source (https://github.com/stuckinaboot/iGenomics) and for free on Apple's App Store (https://apple.co/2HCplzr).
Collapse
Affiliation(s)
- Aspyn Palatnick
- Cold Spring Harbor High School, 82 Turkey Lane, Cold Spring Harbor, NY 11724, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Networked and Social Systems Engineering, University of Pennsylvania, 220 South 33rd Street, Philadelphia, PA 19104, USA
| | - Bin Zhou
- Department of Biology, New York University, 100 Washington Square, New York, NY 10003, USA
| | - Elodie Ghedin
- Department of Biology, New York University, 100 Washington Square, New York, NY 10003, USA
- Department of Epidemiology, New York University School of Global Public Health, 665 Broadway St, New York, NY 10003, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Departments of Computer Science and Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21211, USA
| |
Collapse
|
24
|
Joonlasak K, Batty EM, Kochakarn T, Panthan B, Kümpornsin K, Jiaranai P, Wangwiwatsin A, Huang A, Kotanan N, Jaru-Ampornpan P, Manasatienkij W, Watthanachockchai T, Rakmanee K, Jones AR, Fernandez S, Sensorn I, Sungkanuparph S, Pasomsub E, Klungthong C, Chookajorn T, Chantratita W. Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a. Virus Res 2020; 292:198233. [PMID: 33227343 PMCID: PMC7679658 DOI: 10.1016/j.virusres.2020.198233] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/07/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
There were multiple introduction events of SARS-CoV-2 into Thailand. One lineage, designated A/Thai-1, has expanded and has become a predominant and unique lineage in Thailand. A major frame-shift mutation was found at the gene encoding ORF7a, a putative host antagonizing factor of the virus.
Coronavirus Disease 2019 (COVID-19) is a global public health threat. Genomic surveillance of SARS-CoV-2 was implemented in March of 2020 at a major diagnostic hub in Bangkok, Thailand. Several virus lineages supposedly originated in many countries were found, and a Thai-specific lineage, designated A/Thai-1, has expanded to be predominant in Thailand. A virus sample in the SARS-CoV-2 A/Thai-1 lineage contains a frame-shift deletion at ORF7a, encoding a putative host antagonizing factor of the virus.
Collapse
Affiliation(s)
- Khajohn Joonlasak
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Elizabeth M Batty
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Theerarat Kochakarn
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Bhakbhoom Panthan
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Krittikorn Kümpornsin
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Poramate Jiaranai
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arporn Wangwiwatsin
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Huang
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Namfon Kotanan
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wudtichai Manasatienkij
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Treewat Watthanachockchai
- Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kingkan Rakmanee
- Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Anthony R Jones
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Insee Sensorn
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Somnuek Sungkanuparph
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Ekawat Pasomsub
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chonticha Klungthong
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Thanat Chookajorn
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Wasun Chantratita
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
25
|
Tümmler B. Molecular epidemiology in current times. Environ Microbiol 2020; 22:4909-4918. [PMID: 32945108 DOI: 10.1111/1462-2920.15238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023]
Abstract
Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence-based exploration of variable genomic sites. Multilocus sequence typing of housekeeping genes and allele profiling of the core genome have become standard techniques of bacterial strain typing that may be supplemented by whole genome sequencing to explore all single nucleotide variants and/or the composition of the accessory genome. Next, novel protocols to investigate host and microbiome based upon smart third generation sequencing technologies are being developed for an effective surveillance, rapid diagnosis and real-time tracking of infectious diseases.
Collapse
Affiliation(s)
- Burkhard Tümmler
- Clinical Research Group, Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| |
Collapse
|