1
|
Pipek OA, Medgyes-Horváth A, Stéger J, Papp K, Visontai D, Koopmans M, Nieuwenhuijse D, Oude Munnink BB, Csabai I. Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples. Nat Commun 2024; 15:517. [PMID: 38225254 PMCID: PMC10789779 DOI: 10.1038/s41467-023-43391-z] [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: 07/11/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.
Collapse
Affiliation(s)
- Orsolya Anna Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary.
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Krisztián Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| |
Collapse
|
2
|
Kandeel A, Fahim M, Deghedy O, BahaaEldin H, Roshdy WH, Khalifa MK, Kandeil A, El Shesheny R, Naguib A, AbdelFatah M, Afifi S, Abdel Ghaffar K. Comparative analysis of COVID-19 and influenza prevalence among Egyptian pilgrims returning from Hajj and Umrah in 2022: epidemiology, clinical characteristics, and genomic sequencing. Arch Public Health 2024; 82:6. [PMID: 38216978 PMCID: PMC10785524 DOI: 10.1186/s13690-023-01229-6] [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: 05/31/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024] Open
Abstract
PURPOSE To describe the changes that occurred in the SARS-CoV-2 and influenza Prevalence, epidemiology, clinical picture, and prevalent genotypes among the Egyptian pilgrims returning from Hajj and Umrah 2022 seasons. METHODS Pilgrims were contacted at the airport and invited to participate in the survey. Pilgrims who consented were interviewed using a standardized line list that included participant demographics, respiratory symptoms if any, previous COVID-19 infection, influenza vaccination whereas COVID-19 vaccination information were collected from vaccination cards. Participants were asked to provide throat and nasopharyngeal swabs for SARS-CoV-2 and influenza testing using RT-PCR and a subset of isolates were sequenced. Descriptive data analysis was performed to describe the epidemiology and clinical symptoms of SARS-CoV-2 and influenza. Prevalence rates of SARS-CoV-2 and influenza during Hajj were calculated and compared to Umrah surveys using chi2 and t-test with a significance level < 0.05. RESULTS Overall, 3,862 Egyptian pilgrims enrolled, their mean age was 50.5 ± 47 years, half of them were > 50 years of age and 58.2% were males. Of them, 384 (9.9%) tested positive for SARS-CoV-2 and 51 (1.3%) for influenza viruses. Prevalence of SARS-CoV-2 infections (vaccine breakthrough) increased significantly between the Umrah and Hajj surveys (6.7% vs. 9.9%, p < 0.001), and variants of the virus varied considerably. Whereas no significant difference was found in influenza prevalence, vaccine coverage and vaccine breakthrough infection rates (11.7 vs. 9.2%, 26.9 vs. 26.8%, and 1.4 vs. 1.1% respectively). CONCLUSIONS SARS-CoV-2 prevalence among Egyptian pilgrims returning from Hajj in July increased with reduced vaccine effectiveness compared to Umrah in March 2022 suggesting a possible wave of SARS-CoV-2 in the upcoming winter.
Collapse
Affiliation(s)
- Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Ola Deghedy
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Hala BahaaEldin
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt.
| | - Wael H Roshdy
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Mohamed Kamal Khalifa
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Ahmed Kandeil
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt
| | - Rabeh El Shesheny
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt
| | - Amel Naguib
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Mohamad AbdelFatah
- Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Salma Afifi
- Ministry of Health and Population Consultant, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Khaled Abdel Ghaffar
- Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| |
Collapse
|
3
|
Peñas-Utrilla D, Muñóz P, Pérez-Lago L, García de Viedma D. Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections. Microb Genom 2024; 10:001158. [PMID: 38226969 PMCID: PMC10868610 DOI: 10.1099/mgen.0.001158] [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: 08/31/2023] [Accepted: 11/30/2023] [Indexed: 01/17/2024] Open
Abstract
Recombination events between Delta and Omicron SARS-CoV-2 lineages highlight the need for co-infection research. Existing studies focus on late-phase co-infections, with few examining earlier pandemic stages. This new study aims to globally identify and characterize co-infections using a bioinformatic pipeline to analyse genomic data from diverse locations and pandemic phases. Among 26988 high-quality SARS-CoV-2 isolates from 11 diverse project databases, we identified 141 potential co-infection cases (0.52%), surpassing previous prevalence estimates. These co-infections were observed throughout the pandemic timeline, with an increase noted after the emergence of the Omicron variant. Co-infections involving the Omicron variant were the most prevalent, potentially influenced by the high level of diversity within this lineage and its impact on the viral landscape. Additionally, we found co-infections involving the pre-Alpha/Alpha lineages, which have been rarely described, raising possibilities of contributing to new lineage emergence through recombination events. The analysis revealed co-infection cases involving both different and the same lineages/sublineages. Our study showcases the potential of our pipeline to leverage valuable information stored in global sequence repositories, advancing our understanding of SARS-CoV-2 co-infections. The prevalence of co-infections highlights the importance of monitoring viral diversity and its potential implications on disease dynamics. Integrating clinical data with genomic findings can further shed light on the clinical implications and outcomes of co-infections.
Collapse
Affiliation(s)
- Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Plaza de San Diego, s/n, 28801 Alcalá de Henares, Madrid, Spain
| | - Patricia Muñóz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, 28029 Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, 28029 Madrid, Spain
| |
Collapse
|
4
|
Alexiev I, Ivanov I, Giovanetti M, Cella E, Stoikov I, Donchev D, Grigorova L, Gancheva A, Dimitrova R, Scarpa F, Korsun N, Trifonova I, Dobrinov V, Kantardjiev T, Christova I, Ciccozzi M. Early Detection of the Recombinant SARS-CoV-2 XAN Variant in Bulgaria: Initial Genomic Insights into Yet Another Piece of the Growing Puzzle of Recombinant Clades. Microorganisms 2023; 11:2041. [PMID: 37630601 PMCID: PMC10457977 DOI: 10.3390/microorganisms11082041] [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: 06/17/2023] [Revised: 07/29/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The first recombinant SARS-CoV-2 variants were identified in 2022, causing public health concerns. The importance of recombinant variants has increased especially since the WHO designated the recombinant variant XBB and its lineages as subvariants that require monitoring on 20 November 2022. In this study, we provide the first insights into the new SARS-CoV-2 variant named XAN, a recombinant composed of Omicron sub-lineages BA.2 and BA.5. To our knowledge, this is the first report on the recombinant SARS-CoV-2 XAN variant identified in Bulgaria.
Collapse
Affiliation(s)
- Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Ivan Ivanov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Marta Giovanetti
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA;
| | - Ivan Stoikov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Deyan Donchev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Lyubomira Grigorova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Anna Gancheva
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Reneta Dimitrova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Neli Korsun
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Ivelina Trifonova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Veselin Dobrinov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Todor Kantardjiev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Iva Christova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
| |
Collapse
|
5
|
Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
Collapse
Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| |
Collapse
|
6
|
Peñas-Utrilla D, Pérez-Lago L, Molero-Salinas A, Estévez A, Sanz A, Herranz M, Martínez-Laperche C, Andrés-Zayas C, Veintimilla C, Catalán P, Alonso R, Muñoz P, García de Viedma D. Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved. Genome Med 2023; 15:57. [PMID: 37488638 PMCID: PMC10367318 DOI: 10.1186/s13073-023-01198-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/30/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages. METHODS We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned. RESULTS Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection. CONCLUSIONS Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.
Collapse
Affiliation(s)
- Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Plaza de San Diego, S/N, Alcalá de Henares, Madrid, 28801, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Agustín Estévez
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Amadeo Sanz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
7
|
Kun Á, Hubai AG, Král A, Mokos J, Mikulecz BÁ, Radványi Á. Do pathogens always evolve to be less virulent? The virulence–transmission trade-off in light of the COVID-19 pandemic. Biol Futur 2023:10.1007/s42977-023-00159-2. [PMID: 37002448 PMCID: PMC10066022 DOI: 10.1007/s42977-023-00159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
AbstractThe direction the evolution of virulence takes in connection with any pathogen is a long-standing question. Formerly, it was theorized that pathogens should always evolve to be less virulent. As observations were not in line with this theoretical outcome, new theories emerged, chief among them the transmission–virulence trade-off hypotheses, which predicts an intermediate level of virulence as the endpoint of evolution. At the moment, we are very much interested in the future evolution of COVID-19’s virulence. Here, we show that the disease does not fulfill all the assumptions of the hypothesis. In the case of COVID-19, a higher viral load does not mean a higher risk of death; immunity is not long-lasting; other hosts can act as reservoirs for the virus; and death as a consequence of viral infection does not shorten the infectious period. Consequently, we cannot predict the short- or long-term evolution of the virulence of COVID-19.
Collapse
|
8
|
He Y, Dang S, Ma W, Chen L, Zhang R, Mei S, Wei X, Lv Q, Peng B, Sun Y, Kong D, Chen J, Li S, Tang X, Lu Q, Zhu C, Chen Z, Wan J, Zou X, Li M, Feng T, Ren L, Wang J. Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft. BIOSAFETY AND HEALTH 2023; 5:62-67. [PMID: 36320662 PMCID: PMC9613807 DOI: 10.1016/j.bsheal.2022.10.004] [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: 07/26/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3-31 days later. All 47 nasopharyngeal swabs were deep-sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n = 31), Beta (n = 1), and C.1.2 (n = 1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95% CI]: 2.77-10.22) than did the first samples (T1; median: 2; 95% CI: 1.63-3.74; Wilcoxon test, P = 0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. Intra-host diversity increased gradually with time, and new site mutations occurred in vivo without a population transmission bottleneck. Therefore, we could not determine the generational relationship from the mutation site changes alone.
Collapse
Affiliation(s)
- Yaqing He
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Wentai Ma
- University of Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Long Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Renli Zhang
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shujiang Mei
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xinyi Wei
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Qiuying Lv
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Bo Peng
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Ying Sun
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Dongfeng Kong
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jiancheng Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shimin Li
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xiujuan Tang
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Qingju Lu
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Can Zhu
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Zhigao Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jia Wan
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xuan Zou
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Tiejiang Feng
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
9
|
Goya S, Sosa E, Nabaes Jodar M, Torres C, König G, Acuña D, Ceballos S, Distéfano AJ, Dopazo H, Dus Santos M, Fass M, Fernández Do Porto D, Fernández A, Gallego F, Gismondi MI, Gramundi I, Lusso S, Martí M, Mazzeo M, Mistchenko AS, Muñoz Hidalgo M, Natale M, Nardi C, Ousset J, Peralta AV, Pintos C, Puebla AF, Pianciola L, Rivarola M, Turjanski A, Valinotto L, Vera PA, Zaiat J, Zubrycki J, Aulicino P, Viegas M. Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations. Virus Res 2023; 325:199035. [PMID: 36586487 PMCID: PMC9795804 DOI: 10.1016/j.virusres.2022.199035] [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: 11/07/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological importance is unknown. MATERIAL AND METHODS We developed VICOS (Viral COinfection Surveillance), a new bioinformatic algorithm for variant calling, filtering and statistical analysis to identify samples suspected of being mixed SARS-CoV-2 populations from a large dataset in the framework of a community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August 2021 in Argentina. RESULTS We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS's results together with additional phylogenetic analysis revealed 3 cases of coinfections by two viruses of the same lineage, 2 cases by viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were likely a product of laboratory contamination. DISCUSSION Intra-sample viral diversity provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hidden diversity of SARS-CoV-2.
Collapse
Affiliation(s)
- Stephanie Goya
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina
| | - Ezequiel Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mercedes Nabaes Jodar
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Guido König
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Dolores Acuña
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Santiago Ceballos
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego (UNTDF), Ushuaia, Argentina.; Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
| | - Ana J Distéfano
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Hernán Dopazo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.; Laboratorio de Genómica. Biocódices S.A., Buenos Aires, Argentina
| | - María Dus Santos
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina.; Instituto de Virología/Instituto de Virologia e Innovaciones Tecnologicas (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Mónica Fass
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Darío Fernández Do Porto
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ailen Fernández
- Laboratorio Central ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Fernando Gallego
- Laboratorio de Hospital Regional de Ushuaia. Provincia de Tierra del Fuego
| | - María I Gismondi
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Ivan Gramundi
- Laboratorio de Hospital Regional de Ushuaia. Provincia de Tierra del Fuego
| | - Silvina Lusso
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina
| | - Marcelo Martí
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Melina Mazzeo
- Laboratorio Central ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Alicia S Mistchenko
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina.; Comisión de Investigaciones Científicas de la provincia de Buenos Aires, Argentina
| | - Marianne Muñoz Hidalgo
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Mónica Natale
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina
| | - Cristina Nardi
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego (UNTDF), Ushuaia, Argentina
| | - Julia Ousset
- Laboratorio Central ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Andrea V Peralta
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Carolina Pintos
- Laboratorio Central ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Andrea F Puebla
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Luis Pianciola
- Laboratorio Central ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Máximo Rivarola
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Adrian Turjanski
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura Valinotto
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo A Vera
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina
| | - Jonathan Zaiat
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jeremías Zubrycki
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.; Laboratorio de Genómica. Biocódices S.A., Buenos Aires, Argentina
| | - Paula Aulicino
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.; Laboratorio de Biología Celular y Retrovirus. Unidad de Virología y Epidemiología Molecular.Hospital de Pediatría "Prof. Juan P. Garrahan", CABA, Argentina..
| | - Mariana Viegas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina..
| |
Collapse
|
10
|
Shatizadeh Malekshahi S, Farahmand M, Choobin H. SARS-CoV-2 Related Viral Respiratory Co-Infections: A Narrative Review. TANAFFOS 2023; 22:19-26. [PMID: 37920316 PMCID: PMC10618585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 09/05/2022] [Indexed: 11/04/2023]
Abstract
Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the new coronavirus originating from Wuhan, China, responsible for the illness known as coronavirus disease 2019 (COVID-19). Early experience and the recent literature have shown that co-infection of SARS-CoV-2 with another respiratory virus might occur. Similar symptoms of acute respiratory infections (ARIs) and COVID-19 represent a challenge for diagnostic and therapeutic efficacy and may modify COVID-19 outcomes. Materials and Methods We reviewed the literature on the epidemic pattern and major learning points on important aspects of SARS-CoV-2-related viral respiratory co-infections during the COVID-19 pandemic. Databases such as PubMed, Scopus, Science Direct, and Google Scholar were used to conduct a comprehensive search. Results The circulation of respiratory viruses changed as the COVID-19 epidemic continues. Phenomena like viral interference, resource competition, and differences in virus-host range might explain why simultaneous viral respiratory infections have seemed to vanish with the spread of SARS-CoV-2. Conclusion Key research to be conducted during this pandemic should include the simultaneous screening of other respiratory pathogens with many available commercial platforms for transmission containment and appropriate clinical management.
Collapse
Affiliation(s)
| | - Mohammad Farahmand
- Research Center for Emergency and Disaster Resilience, Red Crescent Society of the Islamic Republic of Iran, Tehran, Iran
| | - Hamzeh Choobin
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
11
|
Al-Khalaifah H, Alotaibi M, Al-Nasser A. The relation between avian coronaviruses and SARS-CoV-2 coronavirus. Front Microbiol 2022; 13:976462. [PMID: 36312988 PMCID: PMC9608149 DOI: 10.3389/fmicb.2022.976462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/20/2022] [Indexed: 01/04/2023] Open
Abstract
The coronaviruses (CoVs) are a family of ribonucleic acid viruses that are present in both mammals and birds. SARS-CoV and MERS-CoV originated in bats, and there is a possibility that this could be the case for SARS-CoV-2 as well. There is already evidence that a probable intermediary host is responsible for the emergence of viruses in humans as was the case for SARS-CoVs and MERS-CoV. As the SARS-CoV-2 originated from a live animal market, there is always the question if domestic animals are susceptible to these viruses and the possible risk of zoonotic transmission with mammals, including humans. This uncertainty of the transmission of the COVID-19 virus between humans and animals is of great significance worldwide. Hence, this paper focuses on the avian CoVs and their possible relation and interaction with SARS-CoV-2.
Collapse
|
12
|
Braga-Paz I, Ferreira de Araújo JL, Alves HJ, de Ávila RE, Resende GG, Teixeira MM, de Aguiar RS, de Souza RP, Bahia D. Negative correlation between ACE2 gene expression levels and loss of taste in a cohort of COVID-19 hospitalized patients: New clues to long-term cognitive disorders. Front Cell Infect Microbiol 2022; 12:905757. [PMID: 36250059 PMCID: PMC9556632 DOI: 10.3389/fcimb.2022.905757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
In early 2020, one of the most prevalent symptoms of SARS-CoV-2 infection was the loss of smell (anosmia), found in 60-70% of all cases. Anosmia used to occur early, concomitantly with other symptoms, and often persisted after recovery for an extended period, sometimes for months. In addition to smell disturbance, COVID-19 has also been associated with loss of taste (ageusia). The latest research suggests that SARS-CoV-2 could spread from the respiratory system to the brain through receptors in sustentacular cells localized to the olfactory epithelium. The virus invades human cells via the obligatory receptor, angiotensin-converting enzyme II (ACE2), and a priming protease, TMPRSS2, facilitating viral penetration. There is an abundant expression of both ACE2 and TMPRSS2 in sustentacular cells. In this study, we evaluated 102 COVID-19 hospitalized patients, of which 17.60% presented anosmia and 9.80% ageusia. ACE1, ACE2, and TMPRSS2 gene expression levels in nasopharyngeal tissue were obtained by RT-qPCR and measured using ΔCT analysis. ACE1 Alu287bp association was also evaluated. Logistic regression models were generated to estimate the effects of variables on ageusia and anosmia Association of ACE2 expression levels with ageusia. was observed (OR: 1.35; 95% CI: 1.098-1.775); however, no association was observed between TMPRSS2 and ACE1 expression levels and ageusia. No association was observed among the three genes and anosmia, and the Alu287bp polymorphism was not associated with any of the outcomes. Lastly, we discuss whetherthere is a bridge linking these initial symptoms, including molecular factors, to long-term COVID-19 health consequences such as cognitive dysfunctions.
Collapse
Affiliation(s)
- Isabela Braga-Paz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - João Locke Ferreira de Araújo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Hugo José Alves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Gustavo Gomes Resende
- Hospital das Clínicas, Universidade Federal de Minas Gerais (HC-UFMG/EBSERH), Belo Horizonte, Brazil
| | - Mauro Martins Teixeira
- Departamento de Bioquimica e imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Renato Santana de Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Instituto D’Or de Pesquisa e Ensino, Instituto D'OR (IDOR), Rio de Janeiro, Brazil
| | - Renan Pedra de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- *Correspondence: Renan Pedra de Souza, ; Diana Bahia,
| | - Diana Bahia
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- *Correspondence: Renan Pedra de Souza, ; Diana Bahia,
| |
Collapse
|
13
|
SARS-CoV-2 dual infection with Delta and Omicron variants in an immunocompetent host: a case report. Int J Infect Dis 2022; 124:41-44. [PMID: 36075374 PMCID: PMC9444311 DOI: 10.1016/j.ijid.2022.08.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the high number of SARS-CoV-2 infections, only a few cases of dual infection have been reported. Here, we describe a case of COVID-19 caused simultaneously by Delta and Omicron variants in an immunocompetent individual during the early emergence of Omicron variant. A 73-year-old man was hospitalized with suspected acute coronary syndrome and a positive test result for SARS-CoV-2 RNA was received during routine testing at the hospital. He experienced mild symptoms of COVID-19 and was discharged on the ninth day. We sequenced the SARS-CoV-2 whole genome from the sample obtained on admission. The viral sequence was classified as PANGO lineage B.1.1.10 by the Galaxy pipeline; however, on detailed manual analysis, we identified the presence of both Delta and Omicron variants. After excluding the possibilities of a recombinant virus or contamination in the sample, we confirmed the presence of dual infection in this patient. We highlight that dual infections with SARS-CoV-2 may be more common than expected but are difficult to detect during the waves of one dominant variant.
Collapse
|
14
|
Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
Collapse
Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
| |
Collapse
|
15
|
Modelling the interplay of SARS-CoV-2 variants in the United Kingdom. Sci Rep 2022; 12:12372. [PMID: 35859100 PMCID: PMC9296900 DOI: 10.1038/s41598-022-16147-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/05/2022] [Indexed: 12/28/2022] Open
Abstract
Many COVID-19 vaccines are proving to be highly effective to prevent severe disease and to diminish infections. Their uneven geographical distribution favors the appearance of new variants of concern, as the highly transmissible Delta variant, affecting particularly non-vaccinated people. It is important to device reliable models to analyze the spread of the different variants. A key factor is to consider the effects of vaccination as well as other measures used to contain the pandemic like social behaviour. The stochastic geographical model presented here, fulfills these requirements. It is based on an extended compartmental model that includes various strains and vaccination strategies, allowing to study the emergence and dynamics of the new COVID-19 variants. The model conveniently separates the parameters related to the disease from the ones related to social behavior and mobility restrictions. We applied the model to the United Kingdom by using available data to fit the recurrence of the currently prevalent variants. Our computer simulations allow to describe the appearance of periodic waves and the features that determine the prevalence of certain variants. They also provide useful predictions to help planning future vaccination boosters. We stress that the model could be applied to any other country of interest.
Collapse
|
16
|
de Oliveira CM, Romano CM, Sussuchi L, Cota BDCV, Levi JE. SARS-CoV-2 BA.1 and BA.2 coinfection detected by genomic surveillance in Brazil, January 2022. Arch Virol 2022; 167:2271-2273. [PMID: 35841447 PMCID: PMC9287692 DOI: 10.1007/s00705-022-05532-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
Abstract
In January 2022, our genomic surveillance network identified a SARS-CoV-2 BA.1 and BA.2 coinfection in a sample from a patient residing in Brazil. Our results suggest that the true number of SARS-CoV-2 coinfections remains largely underestimated.
Collapse
Affiliation(s)
| | - Camila Malta Romano
- Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil
| | - Luciane Sussuchi
- Research and Development, Dasa, Av. Juruá, 434, Barueri, São Paulo, 06455-01, Brazil
| | | | - José Eduardo Levi
- Research and Development, Dasa, Av. Juruá, 434, Barueri, São Paulo, 06455-01, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil
| |
Collapse
|
17
|
Fernandez-Cadena JC, Carvajal M, Muñoz E, Prado-Vivar B, Marquez S, Proaño S, Bayas R, Guadalupe JJ, Becerra-Wong M, Gutierrez B, Morey-Leon G, Trueba G, Grunauer M, Barragán V, Rojas-Silva P, Andrade-Molina D, Cárdenas P. First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador. New Microbes New Infect 2022; 48:101001. [PMID: 35818397 PMCID: PMC9259011 DOI: 10.1016/j.nmni.2022.101001] [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: 01/29/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
Background COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.
Collapse
Affiliation(s)
| | - M Carvajal
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - E Muñoz
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - B Prado-Vivar
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - S Marquez
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - S Proaño
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - R Bayas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - J J Guadalupe
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal, Ecuador
| | - M Becerra-Wong
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - B Gutierrez
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal, Ecuador.,Departament of Zoology, University of Oxford, UK
| | | | - G Trueba
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - M Grunauer
- Universidad San Francisco de Quito, COCSA, Escuela de Medicina, Ecuador.,Unidad de Cuidados Intensivos, Hospital de los Valles, Quito, Ecuador
| | - V Barragán
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - P Rojas-Silva
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | | | - P Cárdenas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| |
Collapse
|
18
|
Vatteroni ML, Capria AL, Spezia PG, Frateschi S, Pistello M. Co-infection with SARS-CoV-2 omicron BA.1 and BA.2 subvariants in a non-vaccinated woman. THE LANCET. MICROBE 2022; 3:e478. [PMID: 35623374 PMCID: PMC9129255 DOI: 10.1016/s2666-5247(22)00119-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/26/2022] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Pietro Giorgio Spezia
- Virology Unit, University of Pisa, I-56127 Pisa, Italy; Retrovirus Centre and Virology Section, University of Pisa, I-56127 Pisa, Italy
| | | | - Mauro Pistello
- Virology Unit, University of Pisa, I-56127 Pisa, Italy; Retrovirus Centre and Virology Section, University of Pisa, I-56127 Pisa, Italy.
| |
Collapse
|
19
|
Combes P, Bisseux M, Bal A, Marin P, Latour J, Archimbaud C, Brebion A, Chabrolles H, Regagnon C, Lafolie J, Destras G, Simon B, Izopet J, Josset L, Henquell C, Mirand A. Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing. Clin Microbiol Infect 2022; 28:1503.e5-1503.e8. [PMID: 35792280 PMCID: PMC9250411 DOI: 10.1016/j.cmi.2022.06.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022]
Abstract
Objectives To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients. Methods Since December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets. Results Between weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3831 respiratory samples, of which 3237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected. Conclusions This work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.
Collapse
|
20
|
Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron. Sci Rep 2022; 12:9377. [PMID: 35672431 PMCID: PMC9172093 DOI: 10.1038/s41598-022-13113-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/03/2022] [Indexed: 01/04/2023] Open
Abstract
AbstractConcomitant infection or co-infection with distinct SARS-CoV-2 genotypes has been reported as part of the epidemiological surveillance of the COVID-19 pandemic. In the context of the spread of more transmissible variants during 2021, co-infections are not only important due to the possible changes in the clinical outcome, but also the chance to generate new genotypes by recombination. However, a few approaches have developed bioinformatic pipelines to identify co-infections. Here we present a metagenomic pipeline based on the inference of multiple fragments similar to amplicon sequence variant (ASV-like) from sequencing data and a custom SARS-CoV-2 database to identify the concomitant presence of divergent SARS-CoV-2 genomes, i.e., variants of concern (VOCs). This approach was compared to another strategy based on whole-genome (metagenome) assembly. Using single or pairs of sequencing data of COVID-19 cases with distinct SARS-CoV-2 VOCs, each approach was used to predict the VOC classes (Alpha, Beta, Gamma, Delta, Omicron or non-VOC and their combinations). The performance of each pipeline was assessed using the ground-truth or expected VOC classes. Subsequently, the ASV-like pipeline was used to analyze 1021 cases of COVID-19 from Costa Rica to investigate the possible occurrence of co-infections. After the implementation of the two approaches, an accuracy of 96.2% was revealed for the ASV-like inference approach, which contrasts with the misclassification found (accuracy 46.2%) for the whole-genome assembly strategy. The custom SARS-CoV-2 database used for the ASV-like analysis can be updated according to the appearance of new VOCs to track co-infections with eventual new genotypes. In addition, the application of the ASV-like approach to all the 1021 sequenced samples from Costa Rica in the period October 12th–December 21th 2021 found that none corresponded to co-infections with VOCs. In conclusion, we developed a metagenomic pipeline based on ASV-like inference for the identification of co-infection with distinct SARS-CoV-2 VOCs, in which an outstanding accuracy was achieved. Due to the epidemiological, clinical, and molecular relevance of the concomitant infection with distinct genotypes, this work represents another piece in the process of the surveillance of the COVID-19 pandemic in Costa Rica and worldwide.
Collapse
|
21
|
Focosi D, Maggi F. Recombination in Coronaviruses, with a Focus on SARS-CoV-2. Viruses 2022; 14:1239. [PMID: 35746710 PMCID: PMC9228924 DOI: 10.3390/v14061239] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence for recombination in SARS-CoV-2 and reconcile nomenclature for recombinants, discuss their origin and fitness, and speculate how recombinants could make a difference in the future of the COVID-19 pandemics.
Collapse
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| |
Collapse
|
22
|
Rockett RJ, Draper J, Gall M, Sim EM, Arnott A, Agius JE, Johnson-Mackinnon J, Fong W, Martinez E, Drew AP, Lee C, Ngo C, Ramsperger M, Ginn AN, Wang Q, Fennell M, Ko D, Hueston L, Kairaitis L, Holmes EC, O'Sullivan MN, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance. Nat Commun 2022; 13:2745. [PMID: 35585202 PMCID: PMC9117272 DOI: 10.1038/s41467-022-30518-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data. Here, using genomic approaches, Rockett et al. identify Omicron and Delta SARS-CoV-2 co-infections in two adults, highlighting the usefulness of genomic surveillance for the timely recognition of co-infections in situations when different variants of the virus are circulating in the community.
Collapse
Affiliation(s)
- Rebecca J Rockett
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Jenny Draper
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Eby M Sim
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Alicia Arnott
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Jessica E Agius
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia
| | - Jessica Johnson-Mackinnon
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Winkie Fong
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Elena Martinez
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Alexander P Drew
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Clement Lee
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Christine Ngo
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Marc Ramsperger
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Andrew N Ginn
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Qinning Wang
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Michael Fennell
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Danny Ko
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Linda Hueston
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Lukas Kairaitis
- Renal Services Blacktown Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Matthew N O'Sullivan
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Sharon C-A Chen
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Jen Kok
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia. .,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia. .,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia. .,School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
| |
Collapse
|
23
|
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] [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]
|
24
|
First Identification of Reinfection by a Genetically Different Variant of SARS-CoV-2 in a Homeless Person from the Metropolitan Area of Santiago, Chile. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2022; 2022:3859071. [PMID: 35528635 PMCID: PMC9068328 DOI: 10.1155/2022/3859071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/05/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023]
Abstract
The identification and tracking of SARS-CoV-2 infected patients in the general population are essential components of the global strategy to limit the COVID-19 viral spread, specifically for maintaining traceability and suppressing the resurgence of local outbreaks. Public health programs that include continuous RT-qPCR testing for COVID-19 in the general population, viral sequencing, and genomic surveillance for highly contagious forms of the virus have allowed for the identification of SARS-CoV-2 infections and reinfections. This work identified SARS-CoV-2 reinfection in a homeless person, which occurred 58 days after the first COVID-19 diagnosis. Genomic sequencing identified a different Nextstrain classification clade (20A and 20B) and PANGO lineage, with a divergence of 4 single nucleotide variants (SNVs) in S and ORF1ab genes, suggesting reinfection by different viral variants. This study is the first from the great metropolitan area of Santiago, Chile, one of the top ten countries in the world to live during the COVID-19 pandemic. We support the importance of performing intensive genomic surveillance programs in the whole population and high-risk groups, such as homeless people, nearly 20 thousand people in Chile, and have limited access to health care services and poor viral traceability.
Collapse
|
25
|
Magalhães AC, Ricardo S, Moreira AC, Nunes M, Tavares M, Pinto RJ, Gomes MS, Pereira L. InfectionCMA: A Cell MicroArray Approach for Efficient Biomarker Screening in In Vitro Infection Assays. Pathogens 2022; 11:pathogens11030313. [PMID: 35335638 PMCID: PMC8955223 DOI: 10.3390/pathogens11030313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023] Open
Abstract
The recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the scientific community to acquire knowledge in real-time, when total lockdowns and the interruption of flights severely limited access to reagents as the global pandemic became established. This unique reality made researchers aware of the importance of designing efficient in vitro set-ups to evaluate infectious kinetics. Here, we propose a histology-based method to evaluate infection kinetics grounded in cell microarray (CMA) construction, immunocytochemistry and in situ hybridization techniques. We demonstrate that the chip-like organization of the InfectionCMA has several advantages, allowing side-by-side comparisons between diverse cell lines, infection time points, and biomarker expression and cytolocalization evaluation in the same slide. In addition, this methodology has the potential to be easily adapted for drug screening.
Collapse
Affiliation(s)
- Ana C. Magalhães
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- Ipatimup–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Sara Ricardo
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- Ipatimup–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, Advanced Polytechnic and University Cooperative (CESPU), 4585-116 Gandra, Portugal
| | - Ana C. Moreira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-319 Porto, Portugal
| | - Mariana Nunes
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- Ipatimup–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Margarida Tavares
- Department of Infectious Diseases and Emerging Infectious Disease Unit, CHUSJ–Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal;
- Public Health and Forensic Sciences and Medical Education Department, FMUP–Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- EPIUnit–Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Ricardo J. Pinto
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- Ipatimup–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Maria Salomé Gomes
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-319 Porto, Portugal
| | - Luisa Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (S.R.); (A.C.M.); (M.N.); (R.J.P.); (M.S.G.)
- Ipatimup–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence:
| |
Collapse
|
26
|
Li Y, Jiang Y, Li Z, Yu Y, Chen J, Jia W, Kaow Ng Y, Ye F, Cheng Li S, Shen B. Both Simulation and Sequencing Data Reveal Coinfections with Multiple SARS-CoV-2 Variants in the COVID-19 Pandemic. Comput Struct Biotechnol J 2022; 20:1389-1401. [PMID: 35342534 PMCID: PMC8930779 DOI: 10.1016/j.csbj.2022.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/13/2022] [Accepted: 03/13/2022] [Indexed: 01/16/2023] Open
|
27
|
SARS-CoV-2 reinfection in a healthcare worker: First case in Portugal confirmed by viral genome sequencing. Porto Biomed J 2022; 7:e171. [PMID: 35146178 PMCID: PMC8824399 DOI: 10.1097/j.pbj.0000000000000171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/26/2022] Open
|
28
|
D'Agostino Y, Rocco T, Ferravante C, Porta A, Tosco A, Cappa VM, Lamberti J, Alexandrova E, Memoli D, Terenzi I, Pironti C, Motta O, Weisz A, Giurato G, Rizzo F. Rapid and sensitive detection of SARS-CoV-2 variants in nasopharyngeal swabs and wastewaters. Diagn Microbiol Infect Dis 2022; 102:115632. [PMID: 35074623 PMCID: PMC8719921 DOI: 10.1016/j.diagmicrobio.2021.115632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 virus is continuously evolving, with appearance of new variants characterized by multiple genomic mutations, some of which can affect functional properties, including infectivity, interactions with host immunity, and disease severity. The rapid spread of new SARS-CoV-2 variants has highlighted the urgency to trace the virus evolution, to help limit its diffusion, and to assess effectiveness of containment strategies. We propose here a PCR-based rapid, sensitive and low-cost allelic discrimination assay panel for the identification of SARS-CoV-2 genotypes, useful for detection in different sample types, such as nasopharyngeal swabs and wastewater. The tests carried out demonstrate that this in-house assay, whose results were confirmed by SARS-CoV-2 whole-genome sequencing, can detect variations in up to 10 viral genome positions at once and is specific and highly sensitive for identification of all tested SARS-CoV-2 clades, even in the case of samples very diluted and of poor quality, particularly difficult to analyze.
Collapse
Affiliation(s)
- Ylenia D'Agostino
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Medical Genomics Program, AOU 'SS. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy
| | - Teresa Rocco
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Medical Genomics Program, AOU 'SS. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy
| | - Carlo Ferravante
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, Salerno, Italy
| | - Amalia Porta
- Department of Farmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Alessandra Tosco
- Department of Farmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Valeria Mirici Cappa
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, Salerno, Italy
| | - Jessica Lamberti
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy
| | - Elena Alexandrova
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Medical Genomics Program, AOU 'SS. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy
| | - Ilaria Terenzi
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy
| | - Concetta Pironti
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy
| | - Oriana Motta
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Medical Genomics Program, AOU 'SS. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy; Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, Salerno, Italy.
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Medical Genomics Program, AOU 'SS. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy; Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, Salerno, Italy.
| | - Francesca Rizzo
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Salerno, Italy; Medical Genomics Program, AOU 'SS. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy; Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, Salerno, Italy.
| |
Collapse
|
29
|
Mobile RZ, Warnawin SVSC, Kojo TK, Rodrigues JAP, Cavilha AMDQ, Zerbinati RM, Adamoski D, Oliveira JCD, Conzentino MS, Huergo LF, Gradia DF, Braz-Silva PH, Schussel JL. SARS-CoV-2 in saliva, viremia and seroprevalence for COVID-19 surveillance at a single hematopoietic stem cell transplantation center: a prospective cohort study. Rev Inst Med Trop Sao Paulo 2022; 64:e39. [PMID: 35674637 PMCID: PMC9173687 DOI: 10.1590/s1678-9946202264039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/02/2022] [Indexed: 11/27/2022] Open
Abstract
This prospective cohort study aims to analyze the surveillance of COVID-19 at a single hematopoietic stem cell transplantation (HSCT) center in Brazil, in 29 patients undergoing allogeneic HSCT and 57 healthcare workers (nurses and dentists), through viral shedding of SARS-CoV-2 in saliva and plasma and seroprevalence of anti-SARS-CoV-2 IgG. In addition, we report two cases with prolonged persistent detection of SARS-CoV-2 without seroconversion. The sample collection was performed seven times for patients and five times for healthcare workers. Only two patients tested positive for SARS-CoV-2 in their saliva and plasma samples (6.9%) without seroconversion. All healthcare workers were asymptomatic and none tested positive. Two patients (6.9%) and four nurses (8%) had positive serology. No dentists had positive viral detection or positive serology. Our results reflect a low prevalence of positive RT-PCR and seroprevalence of SARS-CoV-2 in patients and healthcare workers at a single HSCT center. Results have also corroborated how the rigorous protocols adopted in transplant centers were even more strengthened in this pandemic scenario.
Collapse
|
30
|
Mingaleeva RN, Nigmatulina NA, Sharafetdinova LM, Romozanova AM, Gabdoulkhakova AG, Filina YV, Shavaliyev RF, Rizvanov AA, Miftakhova RR. Biology of the SARS-CoV-2 Coronavirus. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1662-1678. [PMID: 36717455 PMCID: PMC9839213 DOI: 10.1134/s0006297922120215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
New coronavirus infection causing COVID-19, which was first reported in late 2019 in China, initiated severe social and economic crisis that affected the whole world. High frequency of the errors in replication of RNA viruses, zoonotic nature of transmission, and high transmissibility allowed betacoronaviruses to cause the third pandemic in the world since the beginning of 2003: SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019. The latest pandemic united scientific community and served as a powerful impetus in the study of biology of coronaviruses: new routes of virus penetration into the human cells were identified, features of the replication cycle were studied, and new functions of coronavirus proteins were elucidated. It should be recognized that the pandemic was accompanied by the need to obtain and publish results within a short time, which led to the emergence of an array of conflicting data and low reproducibility of research results. We systematized and analyzed scientific literature, filtered the results according to reliability of the methods of analysis used, and prepared a review describing molecular mechanisms of functioning of the SARS-CoV-2 coronavirus. This review considers organization of the genome of the SARS-CoV-2 virus, mechanisms of its gene expression and entry of the virus into the cell, provides information on key mutations that characterize different variants of the virus, and their contribution to pathogenesis of the disease.
Collapse
Affiliation(s)
- Rimma N. Mingaleeva
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| | - Nigina A. Nigmatulina
- State Autonomous Public Health Institution “Republican Clinical Hospital”, Ministry of Health of the Republic of Tatarstan, 420064 Kazan, Russia
| | - Liliya M. Sharafetdinova
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| | - Albina M. Romozanova
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| | - Aida G. Gabdoulkhakova
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| | - Yuliya V. Filina
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| | - Rafael F. Shavaliyev
- State Autonomous Public Health Institution “Republican Clinical Hospital”, Ministry of Health of the Republic of Tatarstan, 420064 Kazan, Russia
| | - Albert A. Rizvanov
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| | - Regina R. Miftakhova
- Federal State Autonomous Educational Institution of Higher Education “Kazan (Volga Region) Federal University”, 420008 Kazan, Russia
| |
Collapse
|
31
|
Abstract
The field of molecular epidemiology responded to the SARS-CoV-2 pandemic with an unrivaled amount of whole viral genome sequencing. By the time this sentence is published we will have well surpassed 1.5 million whole genomes, more than 4 times the number of all microbial whole genomes deposited in GenBank and 35 times the total number of viral genomes. This extraordinary dataset that accrued in near real time has also given us an opportunity to chart the global and local evolution of a virus as it moves through the world population. The data itself presents challenges that have never been dealt with in molecular epidemiology, and tracking a virus that is changing so rapidly means that we are often running to catch up. Here we review what is known about the evolution of the virus, and the critical impact that whole genomes have had on our ability to trace back and track forward the spread of lineages of SARS-CoV-2. We then review what whole genomes have told us about basic biological properties of the virus such as transmissibility, virulence, and immune escape with a special emphasis on pediatric disease. We couch this discussion within the framework of systematic biology and phylogenetics, disciplines that have proven their worth again and again for identifying and deciphering the spread of epidemics, though they were largely developed in areas far removed from infectious disease and medicine.
Collapse
Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| |
Collapse
|
32
|
Gomes MS, Pereira L. Special Issue: From Host-Pathogen Interaction to Host-Directed Therapies. Microorganisms 2021; 9:microorganisms9122606. [PMID: 34946207 PMCID: PMC8707891 DOI: 10.3390/microorganisms9122606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Maria Salomé Gomes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- Correspondence: (M.S.G.); (L.P.)
| | - Luisa Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: (M.S.G.); (L.P.)
| |
Collapse
|
33
|
Letizia AG, Arnold CE, Adhikari BN, Voegtly LJ, Glang L, Rice GK, Goforth CW, Schilling MA, Weir DL, Malagon F, Ramos I, Vangeti S, Gonzalez-Reiche AS, Cer RZ, Sealfon SC, van Bakel H, Bishop-Lilly KA. Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit. Pathogens 2021; 10:pathogens10121589. [PMID: 34959544 PMCID: PMC8709254 DOI: 10.3390/pathogens10121589] [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: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
We used epidemiologic and viral genetic information to identify a case of likely reinfection in an otherwise healthy, young Marine recruit enrolled in the prospective, longitudinal COVID-19 Health Action Response for Marines (CHARM) study, and we paired these findings with serological studies. This participant had a positive RT-PCR to SARS-CoV-2 upon routine sampling on study day 7, although he was asymptomatic at that time. He cleared the infection within seven days. On study day 46, he had developed symptoms consistent with COVID-19 and tested positive by RT-PCR for SARS-CoV-2 again. Viral whole genome sequencing was conducted from nares swabs at multiple time points. The day 7 sample was determined to be lineage B.1.340, whereas both the day 46 and day 49 samples were B.1.1. The first positive result for anti-SARS-CoV-2 IgM serology was collected on day 49 and for IgG on day 91. This case appears most consistent with a reinfection event. Our investigation into this case is unique in that we compared sequence data from more than just paired specimens, and we also assayed for immune response after both the initial infection and the later reinfection. These data demonstrate that individuals who have experienced an infection with SARS-CoV-2 may fail to generate effective or long-lasting immunity, similar to endemic human beta coronaviruses.
Collapse
Affiliation(s)
- Andrew G. Letizia
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Catherine E. Arnold
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; (C.E.A.); (B.N.A.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Bishwo N. Adhikari
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; (C.E.A.); (B.N.A.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Carl W. Goforth
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Megan A. Schilling
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Dawn L. Weir
- Infectious Disease Directorate, Naval Medical Research Center, Silver Spring, MD 20910, USA; (A.G.L.); (C.W.G.); (M.A.S.); (D.L.W.)
| | - Francisco Malagon
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Leidos, Inc., Reston, VA 20190, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology at Mount Sinai, New York, NY 10029, USA; (A.S.G.-R.); (H.v.B.)
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.R.); (S.V.); (S.C.S.)
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology at Mount Sinai, New York, NY 10029, USA; (A.S.G.-R.); (H.v.B.)
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702, USA; (L.J.V.); (L.G.); (G.K.R.); (F.M.); (R.Z.C.)
- Correspondence:
| |
Collapse
|
34
|
Al-Beltagi S, Goulding LV, Chang DK, Mellits KH, Hayes CJ, Gershkovich P, Coleman CM, Chang KC. Emergent SARS-CoV-2 variants: comparative replication dynamics and high sensitivity to thapsigargin. Virulence 2021; 12:2946-2956. [PMID: 34793280 PMCID: PMC8667886 DOI: 10.1080/21505594.2021.2006960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/31/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022] Open
Abstract
The struggle to control the COVID-19 pandemic is made challenging by the emergence of virulent SARS-CoV-2 variants. To gain insight into their replication dynamics, emergent Alpha (A), Beta (B) and Delta (D) SARS-CoV-2 variants were assessed for their infection performance in single variant- and co-infections. The effectiveness of thapsigargin (TG), a recently discovered broad-spectrum antiviral, against these variants was also examined. Of the 3 viruses, the D variant exhibited the highest replication rate and was most able to spread to in-contact cells; its replication rate at 24 h post-infection (hpi) based on progeny viral RNA production was over 4 times that of variant A and 9 times more than the B variant. In co-infections, the D variant boosted the replication of its co-infected partners at the expense of its own initial performance. Furthermore, co-infection with AD or AB combination conferred replication synergy where total progeny (RNA) output was greater than the sum of corresponding single-variant infections. All variants were highly sensitive to TG inhibition. A single pre-infection priming dose of TG effectively blocked all single-variant infections and every combination (AB, AD, BD variants) of co-infection at greater than 95% (relative to controls) at 72 hpi. Likewise, TG was effective in inhibiting each variant in active preexisting infection. In conclusion, against the current backdrop of the dominant D variant that could be further complicated by co-infection synergy with new variants, the growing list of viruses susceptible to TG, a promising host-centric antiviral, now includes a spectrum of contemporary SARS-CoV-2 viruses.
Collapse
Affiliation(s)
- Sarah Al-Beltagi
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | | | - Daniel K.E. Chang
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | | | - Pavel Gershkovich
- School of Pharmacy, University of Nottingham, University Park, Nottingham, UK
| | | | - Kin-Chow Chang
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| |
Collapse
|
35
|
Evolution of the SARS-CoV-2 genome and emergence of variants of concern. Arch Virol 2021; 167:293-305. [PMID: 34846601 PMCID: PMC8629736 DOI: 10.1007/s00705-021-05295-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/22/2021] [Indexed: 01/08/2023]
Abstract
The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and the emergence of novel strains, each described by co-segregation of a particular set of sequence variations. Variants designated G, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) are important lineages that emerged sequentially and are considered variants of concern. A notable feature of the last four, each of which ultimately evolved from clade G, is the large number (≥ 20) of co-segregating sequence variations associated with them. Several variations are in the spike gene, and some variations are shared among or between strains. Meanwhile, observation of recurrent infections with the same or different SARS-CoV-2 lineages has raised concerns about the duration of the immune responses induced by the initial infection or the vaccine that was administered. While the alpha strain is sensitive to immune responses induced by earlier strains, the beta, gamma, and delta strains can escape antibody neutralization. Apart from random replication errors, intra-host RNA editing, chronic infections, and recombination are processes that may promote the accumulation of sequence changes in the SARS-CoV-2 genome. The known contribution of recombination to coronavirus evolution and recent data pertaining to SARS-CoV-2 suggest that recombination may be particularly important. Continued surveillance of the SARS-CoV-2 genome is imperative.
Collapse
|
36
|
Mandala WL, Liu MKP. SARS-CoV-2 and HIV-1: Should HIV-1-Infected Individuals in Sub-Saharan Africa Be Considered a Priority Group for the COVID-19 Vaccines? Front Immunol 2021; 12:797117. [PMID: 34858440 PMCID: PMC8630634 DOI: 10.3389/fimmu.2021.797117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
Since its emergence in 2019 SARS-CoV-2 has proven to have a higher level of morbidity and mortality compared to the other prevailing coronaviruses. Although initially most African countries were spared from the devastating effect of SARS-CoV-2, at present almost every country has been affected. Although no association has been established between being HIV-1-infected and being more vulnerable to contracting COVID-19, HIV-1-infected individuals have a greater risk of developing severe COVID-19 and of COVID-19 related mortality. The rapid development of the various types of COVID-19 vaccines has gone a long way in mitigating the devastating effects of the virus and has controlled its spread. However, global vaccine deployment has been uneven particularly in Africa. The emergence of SARS-CoV-2 variants, such as Beta and Delta, which seem to show some subtle resistance to the existing vaccines, suggests COVID-19 will still be a high-risk infection for years. In this review we report on the current impact of COVID-19 on HIV-1-infected individuals from an immunological perspective and attempt to make a case for prioritising COVID-19 vaccination for those living with HIV-1 in Sub-Saharan Africa (SSA) countries like Malawi as one way of minimising the impact of COVID-19 in these countries.
Collapse
Affiliation(s)
- Wilson Lewis Mandala
- Academy of Medical Sciences, Malawi University of Science and Technology (MUST), Thyolo, Malawi
| | - Michael K. P. Liu
- Centre for Immunology and Vaccinology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| |
Collapse
|
37
|
Jacot D, Pillonel T, Greub G, Bertelli C. Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency Variants. J Clin Microbiol 2021; 59:e0094421. [PMID: 34319802 PMCID: PMC8451431 DOI: 10.1128/jcm.00944-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only a few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases. Hence, we aimed here to provide simple quality control criteria for SARS-CoV-2 sequencing to prevent erroneous interpretation of low-quality or contaminated data. We retrospectively investigated 647 SARS-CoV-2 genomes obtained over 10 tiled amplicons sequencing runs. We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis. Based on data distribution, critical values were established for 11 selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral RNA quantity. Low-frequency variants (<70% of supporting reads) can result from PCR amplification errors, sample cross contaminations, or presence of distinct SARS-CoV2 genomes in the sample sequenced. The number and the prevalence of low-frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations. Overall, we propose 11 metrics with fixed cutoff values as a simple tool to evaluate the quality of SARS-CoV-2 genomes, among which are cycle thresholds, mean depth, proportion of genome covered at least 10×, and the number of low-frequency variants combined with mutation prevalence data.
Collapse
Affiliation(s)
- Damien Jacot
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
38
|
Klempt P, Brzoň O, Kašný M, Kvapilová K, Hubáček P, Briksi A, Bezdíček M, Koudeláková V, Lengerová M, Hajdúch M, Dřevínek P, Pospíšilová Š, Kriegová E, Macek M, Kvapil P. Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic. Microorganisms 2021; 9:microorganisms9081671. [PMID: 34442750 PMCID: PMC8397935 DOI: 10.3390/microorganisms9081671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/03/2023] Open
Abstract
In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as well as vaccination strategy. To date, there is no comprehensive report on the distribution of SARS-CoV-2 genome variants in either the Czech Republic, including Central and Eastern Europe in general, during the first year of pandemic. In this study, we have analysed a representative cohort of SARS-CoV-2 genomes from 229 nasopharyngeal swabs of COVID-19 positive patients collected between March 2020 and February 2021 using validated reference-based sequencing workflow. We document the changing frequency of dominant variants of SARS-CoV-2 (from B.1 -> B.1.1.266 -> B.1.258 -> B.1.1.7) throughout the first year of the pandemic and list specific variants that could impact the diagnostic efficiency RT-qPCR assays. Moreover, our reference-based workflow provided evidence of superinfection in several samples, which may have contributed to one of the highest per capita numbers of COVID-19 cases and deaths during the first year of the pandemic in the Czech Republic.
Collapse
Affiliation(s)
- Petr Klempt
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
- Correspondence: ; Tel.: +420-739-394-373
| | - Ondřej Brzoň
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Kašný
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
| | - Kateřina Kvapilová
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Petr Hubáček
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Úvalu 84, 150 06 Prague, Czech Republic; (P.H.); (A.B.); (P.D.)
| | - Aleš Briksi
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Úvalu 84, 150 06 Prague, Czech Republic; (P.H.); (A.B.); (P.D.)
| | - Matěj Bezdíček
- Center of Molecular Biology and Genetics, Department of Internal Medicine-Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00 Brno, Czech Republic; (M.B.); (M.L.); (Š.P.)
| | - Vladimira Koudeláková
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 5, 77 515 Olomouc, Czech Republic; (V.K.); (M.H.)
| | - Martina Lengerová
- Center of Molecular Biology and Genetics, Department of Internal Medicine-Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00 Brno, Czech Republic; (M.B.); (M.L.); (Š.P.)
| | - Marian Hajdúch
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 5, 77 515 Olomouc, Czech Republic; (V.K.); (M.H.)
| | - Pavel Dřevínek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Úvalu 84, 150 06 Prague, Czech Republic; (P.H.); (A.B.); (P.D.)
| | - Šárka Pospíšilová
- Center of Molecular Biology and Genetics, Department of Internal Medicine-Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00 Brno, Czech Republic; (M.B.); (M.L.); (Š.P.)
| | - Eva Kriegová
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University Olomouc and University Hospital, Hněvotínská 3, 775 15 Olomouc, Czech Republic;
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine-Charles University and Motol University Hospital, V Úvalu 84, 150 05 Prague, Czech Republic;
| | - Petr Kvapil
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
| |
Collapse
|
39
|
Taghizadeh P, Salehi S, Heshmati A, Houshmand SM, InanlooRahatloo K, Mahjoubi F, Sanati MH, Yari H, Alavi A, Jamehdar SA, Dabiri S, Galehdari H, Haghshenas MR, Hashemian AM, Heidarzadeh A, Jahanzad I, Kheyrani E, Piroozmand A, Mojtahedi A, Nikoo HR, Rahimi Bidgoli MM, Rezvani N, Sepehrnejad M, Shakibzadeh A, Shariati G, Seyyedi N, MohammadSaleh Zahraei S, Safari I, Elahi E. Study on SARS-CoV-2 strains in Iran reveals potential contribution of co-infection with and recombination between different strains to the emergence of new strains. Virology 2021; 562:63-73. [PMID: 34265628 PMCID: PMC8214199 DOI: 10.1016/j.virol.2021.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
We aimed to describe SARS-CoV-2 strains in Iranians from nine distributed cities infected during two months expanding late 2020 and early 2021 by genotyping known informative single nucleotide in five PCR amplicons. Two variants associated with haplotype H1 (clade G) and nine additional variants associated with other haplotypes were genotyped, respectively, in RNA isolates of 244 and 85 individuals. The variants associated with the H1a (GR) and H1b (GH) haplotypes were most prevalent, indicating a significant change in infection pattern with passage of time. The most important findings were that recombinant genomes and co-infection, respectively, were surmised in 44.7% and 12.9% of the samples extensively genotyped. Partners of many of the recombinations were relatively common strains. Co-existing viruses were among those currently circulating in Iran. In addition to random mutations, co-infection with different existing strains and recombination between their genomes may significantly contribute to the emergence of new SARS-CoV-2 strains.
Collapse
Affiliation(s)
- Peyman Taghizadeh
- School of Biology, University College of Science, University of Tehran, Tehran, Iran
| | - Sadegh Salehi
- Cell and Molecular Biology Department, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ali Heshmati
- School of Biology, University College of Science, University of Tehran, Tehran, Iran
| | - Seyed Massoud Houshmand
- Department of Medical Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Forouzandeh Mahjoubi
- Department of Medical Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Medical Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hadi Yari
- Human Genetics Division, Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology, Tehran, Iran
| | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Saeid Amel Jamehdar
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Soroosh Dabiri
- Department of Laboratory Sciences, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hamid Galehdari
- Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Reza Haghshenas
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amir Masoud Hashemian
- Department of Emergency Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abtin Heidarzadeh
- Faculty of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | | | | | - Ahmad Piroozmand
- Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Ali Mojtahedi
- Microbiology Department, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Nayebali Rezvani
- Department of Clinical Biochemistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehdi Sepehrnejad
- COVID-19 Diagnosis Laboratory, Kashan University of Medical Sciences, Kashan, Iran
| | - Arash Shakibzadeh
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Shariati
- Department of Medical Genetics, Faculty of Medicine, Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Noorossadat Seyyedi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Iman Safari
- School of Biology, University College of Science, University of Tehran, Tehran, Iran.
| | - Elahe Elahi
- School of Biology, University College of Science, University of Tehran, Tehran, Iran.
| |
Collapse
|
40
|
Pedro N, Fernandes V, Cavadas B, Guimarães JT, Barros H, Tavares M, Pereira L. Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster. Viruses 2021; 13:1116. [PMID: 34200621 PMCID: PMC8226748 DOI: 10.3390/v13061116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/31/2022] Open
Abstract
Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission.
Collapse
Affiliation(s)
- Nicole Pedro
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Veronica Fernandes
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Bruno Cavadas
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - João Tiago Guimarães
- CHUSJ, Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal; (J.T.G.); (M.T.)
- FMUP, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Henrique Barros
- FMUP, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Margarida Tavares
- CHUSJ, Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal; (J.T.G.); (M.T.)
- FMUP, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Luisa Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| |
Collapse
|
41
|
SARS-CoV-2 Persistent Viral Shedding in the Context of Hydroxychloroquine-Azithromycin Treatment. Viruses 2021; 13:v13050890. [PMID: 34065871 PMCID: PMC8150993 DOI: 10.3390/v13050890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 nasopharyngeal shedding contributes to the spread of the COVID-19 epidemic. Among 3271 COVID-19 patients treated at the Hospital University Institute Méditerranée Infection, Marseille, France from 3 March to 27 April 2020, tested at least twice by qRT-PCR, the median SARS-CoV-2 nasopharyngeal shedding duration was 6 days (range 2–54 days). Compared with short shedders (qRT-PCR positivity < 10 days), 34 (1.04%) persistent shedders (qRT-PCR positivity ≥ 17 days; mean ± SD: 23.3 ± 3.8 days) were significantly older, with associated comorbidities, exhibiting lymphopenia, eosinopenia, increased D-dimer and increased troponin (p < 0.05), and were hospitalized in intensive care unit in 17.7% vs. 1.1% of cases (p < 0.0001). Viral culture was positive in six persistent shedders after day 10, including in one patient after day 17, and no viral co-pathogen was detected in 33 tested patients. Persistent shedders received azithromycin plus hydroxychloroquine ≥ 3 days in 26/34 (76.5%) patients, a figure significantly lower than in short shedders (86.6%) (p = 0.042). Accordingly, mortality was 14.7% vs. 0.5% (p < 0.0001). Persistent shedding was significantly associated with persistent dyspnea and anosmia/ageusia (p < 0.05). In the context of COVID-19 treatment, including treatment with azithromycin plus hydroxychloroquine, the persistence of SARS-CoV-2 nasopharyngeal shedding was a rare event, most frequently encountered in elderly patients with comorbidities and lacking azithromycin plus hydroxychloroquine treatment.
Collapse
|
42
|
In pursuit of the right tail for the COVID-19 incubation period. Public Health 2021; 194:149-155. [PMID: 33915459 PMCID: PMC7997403 DOI: 10.1016/j.puhe.2021.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 01/08/2023]
Abstract
Definition of the incubation period for COVID-19 is critical for implementing quarantine and thus infection control. Whereas the classical definition relies on the time from exposure to time of first symptoms, a more practical working definition is the time from exposure to time of first live virus excretion. For COVID-19, average incubation period times commonly span 5–7 days which are generally longer than for most typical other respiratory viruses. There is considerable variability reported however for the late right-hand statistical distribution. A small but yet epidemiologically important subset of patients may have the late end of the incubation period extend beyond the 14 days that is frequently assumed. Conservative assumptions of the right tail end distribution favor safety, but pragmatic working modifications may be required to accommodate high rates of infection and/or healthcare worker exposures. Despite the advent of effective vaccines, further attention and study in these regards are warranted. It is predictable that vaccine application will be associated with continued confusion over protection and its longevity. Measures for the application of infectivity will continue to be extremely relevant.
Collapse
|