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dos Santos MC, Fintelman-Rodrigues N, da Silva ADPD, Silva RLN, Seixas VC, Batista-da-Silva AA, Ferreira MA, Bozza PT, Bozza FA, Souza TML. Does viral circulation in slums have a global impact? The lesson learned from SARS-CoV-2 circulation in Complexo de favelas da Maré, Rio de Janeiro, Brazil. Front Microbiol 2025; 16:1483895. [PMID: 40012790 PMCID: PMC11861056 DOI: 10.3389/fmicb.2025.1483895] [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: 08/20/2024] [Accepted: 01/13/2025] [Indexed: 02/28/2025] Open
Abstract
Because of growing inequalities, more than one-third of the worldwide population is expected to live in slums by 2050. Although slum dwellers are at increased risk of infectious diseases, this population may have been overlooked with respect to the sustainability of virus evolution. In this study, we aimed to analyze the genetic diversity and evolution of SARS-CoV-2 in the Complexo de Favelas da Maré slum, Rio de Janeiro, Brazil, and assess its impact on the global spread of the virus. We found that this slum harbored multiple strains of SARS-CoV-2, and its amplification and genetic diversity connected with the global circulation from 2020 to 2022. Thus, enhancing surveillance in slums could be important for future epidemic/pandemic preparedness by connecting virus genetic diversity in this region with its circulation at divergent locations.
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Affiliation(s)
- Monique Cristina dos Santos
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, Brazil
| | - Aline de Paula Dias da Silva
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, Brazil
| | | | - Victor Corrêa Seixas
- Instituto de Biologia, Universidade Federal Fluminense (UFF), Rio de Janeiro, Brazil
| | - Amanda A. Batista-da-Silva
- Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
- Department of Industrial Engineering, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Alves Ferreira
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, Brazil
| | - Patrícia T. Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Fernando A. Bozza
- Instituto de Biologia, Universidade Federal Fluminense (UFF), Rio de Janeiro, Brazil
- D’Or Institute for Research and Education, Rio de Janeiro, Brazil
- Tecgraf Institute, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago Moreno L. Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, Brazil
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2
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Alemán GV, Cerpas C, Juarez JG, Moreira H, Arguello S, Coloma J, Harris E, Gordon A, Bennett SN, Balmaseda Á. Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 pandemic. Sci Rep 2025; 15:4817. [PMID: 39924561 PMCID: PMC11808107 DOI: 10.1038/s41598-024-84113-9] [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: 05/29/2024] [Accepted: 12/19/2024] [Indexed: 02/11/2025] Open
Abstract
The global circulation of SARS-CoV-2 has been extensively documented; however, the dynamics within Central America, particularly Nicaragua, remain underexplored. This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtained via next-generation sequencing. These sequences were selected nationwide and analyzed for variant classification, lineage predominance, and phylogenetic diversity. We employed both Illumina and Oxford Nanopore Technologies for all sequencing procedures. Results indicated a temporal and spatial shift in dominant lineages, initially from B.1 and A.2 in early 2020 to various Omicron subvariants toward the study's end. Significant lineage shifts correlated with changes in COVID-19 positivity rates, underscoring the epidemiological impact of variant dissemination. Comparative analysis with regional data underscored the low diversity of circulating lineages in Nicaragua and their delayed introduction compared to other countries in the Central American region. The study also linked specific viral mutations with hospitalization rates, emphasizing the clinical relevance of genomic surveillance. This research advances the understanding of SARS-CoV-2 evolution in Nicaragua and provides valuable information regarding its genetic diversity for public health officials in Central America. We highlight the critical role of ongoing genomic surveillance in identifying emergent lineages and informing public health strategies.
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Affiliation(s)
| | - Cristhiam Cerpas
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | | | | | | | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Ángel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua.
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua.
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3
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Rustagi V, Gupta SRR, Talwar C, Singh A, Xiao ZZ, Jamwal R, Bala K, Bhaskar AK, Nagar S, Singh IK. SARS-CoV-2 pathophysiology and post-vaccination severity: a systematic review. Immunol Res 2024; 73:17. [PMID: 39692912 DOI: 10.1007/s12026-024-09553-x] [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: 10/17/2024] [Accepted: 12/02/2024] [Indexed: 12/19/2024]
Abstract
Currently, COVID-19 is still striking after 4 years of prevalence, with millions of cases and thousands of fatalities being recorded every month. The virus can impact other major organ systems, including the gastrointestinal tract (GIT), cardiovascular, central nervous system, renal, and hepatobiliary systems. The resulting organ dysfunction from SARS-CoV-2 may be attributed to one or a combination of mechanisms, such as direct viral toxicity, disruptions in the renin-angiotensin-aldosterone system (RAAS), thrombosis, immune dysregulation, and ischemic injury due to vasculitis. SARS-CoV-2 vaccines effectively reduce the severity of the disease, hospitalizations, and mortality. As of October 2024, 13.58 billion vaccine doses have been administered, with an average of 6959 daily doses. Also, the boosters are given after the primary immunization in a homologous and heterologous manner. The vaccines imposed severe potential health side effects such as clotting or obstruction of blood vessels termed arterial or venous thrombosis, autoimmune damage of nerve cells (Guillain-Barré syndrome; GBS), intense activation of coagulation system (vaccine-induced thrombotic thrombocytopenia), acute ischemic stroke (AIS) and cerebral venous sinus thrombosis (CVST), myocarditis, pericarditis, and glomerular disease. Overall, it is essential to highlight that the significant benefits of COVID-19 vaccination far outweigh the low risk of conditions. mRNA-based vaccine technology has emerged as a rapidly deployable vaccine candidate and a viable alternative to existing vaccines. It has a very low probability of adverse health effects, confirmed by data represented by Preferred Reporting Items for Systematic Reviews and Meta-Analyses, Vaccine Adverse Event Reporting System (VAERS), Yellow card approved under CDC, WHO.
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Affiliation(s)
- Vanshika Rustagi
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India
| | - Shradheya R R Gupta
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India
| | - Chandni Talwar
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi (South Campus), New Delhi, 110021, India
| | - Zhen-Zhu Xiao
- Department of Biological Sciences, The George Washington University, Washington, D.C, 20052, USA
| | - Rahul Jamwal
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India
| | - Kiran Bala
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India
| | - Akash Kumar Bhaskar
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Shekhar Nagar
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India.
| | - Indrakant K Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India.
- Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi, 110007, India.
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4
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Simoes MP, Hodcroft EB, Simmonds P, Albert J, Alidjinou EK, Ambert-Balay K, Andrés C, Antón A, Auvray C, Bailly JL, Baldanti F, Bastings C, Beard S, Berengua C, Berginc N, Bloemen M, Blomqvist S, Bosma F, Böttcher S, Bubba L, Buderus S, Cabrerizo M, Calvo C, Celma C, Ceriotti F, Clark G, Costa I, Coste-Burel M, Couderé K, Cremer J, del Cuerpo Casas M, Daehne T, de Beer J, de Ceano-Vivas M, De Gascun C, de Rougemont A, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dillner L, Dorenberg DH, Ducancelle A, Dudman S, Dyrdak R, Eis-Huebinger AM, Falces-Romero I, Farkas A, Feeney S, Fernandez-Garcia MD, Flipse J, Franck KT, Galli C, Garrigue I, Geeraedts F, Georgieva I, Giardina F, Guiomar R, Hauzenberger E, Heikens E, Henquell C, Hober D, Hönemann M, Howson-Wells H, Hruškar Ž, Ikonen N, Imbert B, Jansz AR, Jeannoël M, Jiřincová H, Josset L, Keeren K, Kramer-Lindhout N, Krokstad S, Lazrek M, Le Guillou-Guillemette H, Lefeuvre C, Lind A, Lunar MM, Maier M, Marque-Juillet S, McClure CP, McKenna J, Meijer A, Menasalvas Ruiz A, Mengual-Chuliá B, Midgley S, Mirand A, Molenkamp R, Montes M, Moreno-Docón A, Morley U, Murk JL, Navascués-Ortega A, Nijhuis R, Nikolaeva-Glomb L, Nordbø SA, Numanovic S, Oggioni M, Oñate Vergara E, et alSimoes MP, Hodcroft EB, Simmonds P, Albert J, Alidjinou EK, Ambert-Balay K, Andrés C, Antón A, Auvray C, Bailly JL, Baldanti F, Bastings C, Beard S, Berengua C, Berginc N, Bloemen M, Blomqvist S, Bosma F, Böttcher S, Bubba L, Buderus S, Cabrerizo M, Calvo C, Celma C, Ceriotti F, Clark G, Costa I, Coste-Burel M, Couderé K, Cremer J, del Cuerpo Casas M, Daehne T, de Beer J, de Ceano-Vivas M, De Gascun C, de Rougemont A, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dillner L, Dorenberg DH, Ducancelle A, Dudman S, Dyrdak R, Eis-Huebinger AM, Falces-Romero I, Farkas A, Feeney S, Fernandez-Garcia MD, Flipse J, Franck KT, Galli C, Garrigue I, Geeraedts F, Georgieva I, Giardina F, Guiomar R, Hauzenberger E, Heikens E, Henquell C, Hober D, Hönemann M, Howson-Wells H, Hruškar Ž, Ikonen N, Imbert B, Jansz AR, Jeannoël M, Jiřincová H, Josset L, Keeren K, Kramer-Lindhout N, Krokstad S, Lazrek M, Le Guillou-Guillemette H, Lefeuvre C, Lind A, Lunar MM, Maier M, Marque-Juillet S, McClure CP, McKenna J, Meijer A, Menasalvas Ruiz A, Mengual-Chuliá B, Midgley S, Mirand A, Molenkamp R, Montes M, Moreno-Docón A, Morley U, Murk JL, Navascués-Ortega A, Nijhuis R, Nikolaeva-Glomb L, Nordbø SA, Numanovic S, Oggioni M, Oñate Vergara E, Pacaud J, Pacreau ML, Panning M, Pariani E, Pekova L, Pellegrinelli L, Petrovec M, Pietsch C, Pilorge L, Piñeiro L, Piralla A, Poljak M, Prochazka B, Rabella N, Rahamat-Langendoen JC, Rainetova P, Reynders M, Riezebos-Brilman A, Roorda L, Savolainen-Kopra C, Schuffenecker I, Smeets LC, Stoyanova A, Stefic K, Swanink C, Tabain I, Tjhie J, Thouault L, Tumiotto C, Uceda Renteria S, Uršič T, Vallet S, Van Ranst M, Van Wunnik P, Verweij JJ, Vila J, Wintermans B, Wollants E, Wolthers KC, Xavier López-Labrador F, Fischer TK, Harvala H, Benschop KSM. Epidemiological and Clinical Insights into the Enterovirus D68 Upsurge in Europe 2021-2022 and Emergence of Novel B3-Derived Lineages, ENPEN Multicentre Study. J Infect Dis 2024; 230:e917-e928. [PMID: 38547499 PMCID: PMC11481312 DOI: 10.1093/infdis/jiae154] [Show More Authors] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 03/27/2024] [Indexed: 10/17/2024] Open
Abstract
Enterovirus D68 (EV-D68) infections are associated with severe respiratory disease and acute flaccid myelitis (AFM). The European Non-Polio Enterovirus Network (ENPEN) aimed to investigate the epidemiological and genetic characteristics of EV-D68 infections and its clinical impact during the fall-winter season of 2021-2022. From 19 European countries, 58 institutes reported 10 481 (6.8%) EV-positive samples of which 1004 (9.6%) were identified as EV-D68 (including 852 respiratory samples). Clinical data were reported for 969 cases; 78.9% of infections were reported in children (0-5 years); and 37.9% of cases were hospitalized. Acute respiratory distress was commonly noted (93.1%) followed by fever (49.4%). Neurological problems were observed in 6.4% of cases including 6 diagnosed with AFM. Phylodynamic/Nextstrain and phylogenetic analyses based on 694 sequences showed the emergence of 2 novel B3-derived lineages, with no regional clustering. In conclusion, we describe a large-scale European EV-D68 upsurge with severe clinical impact and the emergence of B3-derived lineages.
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Affiliation(s)
- Margarida Pires Simoes
- Centre for Infectious Disease Control, Dutch National Public Health Institute, Bilthoven, The Netherlands
- European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Emma B Hodcroft
- Geneva Center of Emerging Viral Diseases, Geneva University Hospital and University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Peter Simmonds
- Nuffield Department for Medicine, University of Oxford, Oxford, United Kingdom
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Enagnon K Alidjinou
- Laboratoire de Virologie ULR, Univ Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Katia Ambert-Balay
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology-Serology, University Hospital of Dijon Bourgogne, Dijon, France
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut of Research, Vall d‘Hebron Barcelona Hospital Campus, Barcelona, Spain
- Microbiology Department, Hospital Unviersitario La Paz, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut of Research, Vall d‘Hebron Barcelona Hospital Campus, Barcelona, Spain
- Microbiology Department, Hospital Unviersitario La Paz, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Christelle Auvray
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology-Serology, University Hospital of Dijon Bourgogne, Dijon, France
| | - Jean-Luc Bailly
- Labaratoire Microorganismes: Génome Environnement-Epidemiology and Physiopathology of Enterovirus Diseases LMGE-EPIE Team, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Università Degli Studi di Pavia, Pavia, Italy
| | - Capser Bastings
- Laboratory for Medical Microbiology, Eurofins-PAMM, Veldhoven, The Netherlands
| | - Stuart Beard
- Enteric Virus Unit, UK Health Security Agency, London, United Kingdom
| | - Carla Berengua
- Microbiology Department, Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natasa Berginc
- National Laboratory of Health, Environment, and Food, Laboratory for Public Health Virology, Ljubljana, Slovenia
| | - Mandy Bloemen
- Clinical and Epidemiological Virology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Soile Blomqvist
- Department of Health Security, Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Froukje Bosma
- Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands
| | - Sindy Böttcher
- National Reference Laboratory for Poliomyelitis and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | | | - Stafan Buderus
- GFO Kliniken Bonn, Betriebsstätte St Marien, Bonn, Germany
| | - Maria Cabrerizo
- Enterovirus and Viral Gastroenteritis Lab, National Centre for Microbiology, Instituto de Salud Carlos III and the Spanish Research Networks Consortium of Epidemiology and Public Health, Madrid, Spain
| | - Cristina Calvo
- Pediatric and Infectious Diseases Department, Hospital Universtiario La Paz, Fundación IdiPaz, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Celma
- Enteric Virus Unit, UK Health Security Agency, London, United Kingdom
| | - Ferruccio Ceriotti
- Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gemma Clark
- Clinical Microbiology, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
| | - Inës Costa
- National Reference Laboratory for Influenza and Other Respiratory Viruses, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Marianne Coste-Burel
- Virology Department, Centre Hospitalier Universitaire Hôtel Dieu, University Hospital, Nantes, France
| | - Karen Couderé
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth Tweesteden Hospital, Tilburg, The Netherlands
| | - Jeroen Cremer
- Centre for Infectious Disease Control, Dutch National Public Health Institute, Bilthoven, The Netherlands
| | - Margarita del Cuerpo Casas
- Microbiology Department, Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Theo Daehne
- Institute of Virology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jessica de Beer
- Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands
| | - Maria de Ceano-Vivas
- Pediatric and Infectious Diseases Department, Hospital Universtiario La Paz, Fundación IdiPaz, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Cillian De Gascun
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Alexis de Rougemont
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology-Serology, University Hospital of Dijon Bourgogne, Dijon, France
| | - Jonathan Dean
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | | | - Sabine Diedrich
- National Reference Laboratory for Poliomyelitis and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | - Javier Diez-Domingo
- Center for Public Health Research (Foundation for the Promotion of Health and Biomedical Research in the Valencian Community), Generalitat Valenciana, Valencia, Spain, and the Spanish Research Networks Consortium of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid Spain
| | - Lena Dillner
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Dagny H Dorenberg
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexandra Ducancelle
- Laboratoire de Virologie, Département de Biologie des Agents Infectieux, Centre Hospitalier Universitaire Angers, Angers, France
| | - Susanne Dudman
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Insititute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Robert Dyrdak
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Iker Falces-Romero
- Microbiology Department, Hospital Unviersitario La Paz, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Agnes Farkas
- National Public Health Center, Budapest, Hungary
| | - Susan Feeney
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, United Kingdom
| | - Maria D Fernandez-Garcia
- Enterovirus and Viral Gastroenteritis Lab, National Centre for Microbiology, Instituto de Salud Carlos III and the Spanish Research Networks Consortium of Epidemiology and Public Health, Madrid, Spain
| | - Jacky Flipse
- Laboratory for Medical Microbiology and Immunology, Rijnstate, Velp, The Netherlands
| | - Kristina T Franck
- Danish World Health Organization National Reference Laboratory for Poliovirus, Statens Serum Institut, Copenhagen, Denmark
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Isabelle Garrigue
- Virology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Felix Geeraedts
- Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands
| | - Irina Georgieva
- National Reference Laboratory for Enteroviruses, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federica Giardina
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Università Degli Studi di Pavia, Pavia, Italy
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and Other Respiratory Viruses, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | | | - Esther Heikens
- Department of Medical Microbiology, St Jansdal Hospital, Harderwijk, The Netherlands
| | - Cécille Henquell
- Labaratoire Microorganismes: Génome Environnement-Epidemiology and Physiopathology of Enterovirus Diseases LMGE-EPIE Team, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
- National Reference Centre for Enteroviruses and Parechoviruses-Associated Laboratory, Centre Hospitalier Universitaire Clermont-Ferrand, Clermont-Ferrand, France
| | - Didier Hober
- Laboratoire de Virologie ULR, Univ Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Mario Hönemann
- Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
| | - Hannah Howson-Wells
- Clinical Microbiology, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
| | - Željka Hruškar
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Niina Ikonen
- Department of Health Security, Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Berthemarie Imbert
- Virology Department, Centre Hospitalier Universitaire Hôtel Dieu, University Hospital, Nantes, France
| | - Arjan R Jansz
- Laboratory for Medical Microbiology, Eurofins-PAMM, Veldhoven, The Netherlands
| | - Marion Jeannoël
- National Reference Center for Enteroviruses and Parechoviruses, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Helena Jiřincová
- National Reference Laboratory for Enteroviruses, National Institute of Public Health, Prague, Czech Republic
| | - Laurence Josset
- National Reference Center for Enteroviruses and Parechoviruses, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Kathrin Keeren
- Commission for Polio Eradication in Germany, Robert Koch Institute, Berlin, Germany
| | - Naomie Kramer-Lindhout
- Laboratory Medical Microbiology and Immunology, Admiraal de Ruijter Hospital, Goes, The Netherlands
| | - Sidsel Krokstad
- Department of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Mouna Lazrek
- Laboratoire de Virologie ULR, Univ Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Hélène Le Guillou-Guillemette
- Laboratoire de Virologie, Département de Biologie des Agents Infectieux, Centre Hospitalier Universitaire Angers, Angers, France
| | - Caroline Lefeuvre
- Laboratoire de Virologie, Département de Biologie des Agents Infectieux, Centre Hospitalier Universitaire Angers, Angers, France
| | - Andreas Lind
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Maja M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Melanie Maier
- Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
| | | | - C Patrick McClure
- Wolfson Centre for Global Virus Research, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - James McKenna
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, United Kingdom
| | - Adam Meijer
- Centre for Infectious Disease Control, Dutch National Public Health Institute, Bilthoven, The Netherlands
| | - Ana Menasalvas Ruiz
- Pediatric Infectious Diseases Unit, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Beatriz Mengual-Chuliá
- Center for Public Health Research (Foundation for the Promotion of Health and Biomedical Research in the Valencian Community), Generalitat Valenciana, Valencia, Spain, and the Spanish Research Networks Consortium of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid Spain
| | - Sofie Midgley
- Danish World Health Organization National Reference Laboratory for Poliovirus, Statens Serum Institut, Copenhagen, Denmark
| | - Audrey Mirand
- Labaratoire Microorganismes: Génome Environnement-Epidemiology and Physiopathology of Enterovirus Diseases LMGE-EPIE Team, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
- National Reference Centre for Enteroviruses and Parechoviruses-Associated Laboratory, Centre Hospitalier Universitaire Clermont-Ferrand, Clermont-Ferrand, France
| | - Richard Molenkamp
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Milagrosa Montes
- Microbiology Department, Donostia University Hospital and Biogipuzkoa Health Research Institute, San Sebastián, Spain
| | - Antonio Moreno-Docón
- Microbiology Department, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano De Investigación Biosanitaria Arrixaca, Murcia University, Murcia, Spain
| | - Ursula Morley
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Jean-Luc Murk
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth Tweesteden Hospital, Tilburg, The Netherlands
| | | | - Roel Nijhuis
- Department of Medical Microbiology and Immunology, Meander Medical Center, Amersfoort, The Netherlands
| | - Lubomira Nikolaeva-Glomb
- National Reference Laboratory for Enteroviruses, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Svein A Nordbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sanela Numanovic
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Massimo Oggioni
- Microbiology and Virology Unit, Department of Diagnostic Services, Azienda Socio Sanitaria Territoriale della Brianza, Vimercate, Italy
| | - Eider Oñate Vergara
- Microbiology Department, Donostia University Hospital and Biogipuzkoa Health Research Institute, San Sebastián, Spain
| | - Jordi Pacaud
- Virology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Marie L Pacreau
- Service de Biologie, Centre Hospitalier de VersaillesLe Chesnay, France
| | - Marcus Panning
- Institute of Virology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Lili Pekova
- Clinic of Infectious Diseases, University Hospital Prof Dr Stoyan Kirkovich AD, Stara Zagora, Bulgaria
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Laboratory for the Diagnosis of Viral Infections, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Corinna Pietsch
- Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
| | - Léa Pilorge
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Brest Cedex, France
| | - Luis Piñeiro
- Microbiology Department, Donostia University Hospital and Biogipuzkoa Health Research Institute, San Sebastián, Spain
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Birgit Prochazka
- Austrian Agency for Health and Food Safety, National Reference Laboratory for Poliomyelitis, Vienna, Austria
| | - Nuria Rabella
- Microbiology Department, Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Petra Rainetova
- National Reference Laboratory for Enteroviruses, National Institute of Public Health, Prague, Czech Republic
| | - Marijke Reynders
- Laboratory Medicine, Molecular Microbiology, AZ St Jan Brugge-Oostende AV, Bruges, Belgium
| | | | - Lieuwe Roorda
- Department of Medical Microbiology, Maasstad Hospital, Rotterdam, The Netherlands
| | - Carita Savolainen-Kopra
- Department of Health Security, Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Isabelle Schuffenecker
- National Reference Center for Enteroviruses and Parechoviruses, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Leo C Smeets
- Department of Medical Microbiology, Reinier Haga Medical Diagnostic Center, Delft, The Netherlands
| | - Asya Stoyanova
- National Reference Laboratory for Enteroviruses, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Karl Stefic
- Laboratoire de Virologie INSERM U1259, Centre Hospitalier Régional, Universitaire de Tours, Tours, France
| | - Caroline Swanink
- Laboratory for Medical Microbiology and Immunology, Rijnstate, Velp, The Netherlands
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Jeroen Tjhie
- Laboratory for Medical Microbiology, Eurofins-PAMM, Veldhoven, The Netherlands
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth Tweesteden Hospital, Tilburg, The Netherlands
| | - Luc Thouault
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Brest Cedex, France
| | - Camille Tumiotto
- Virology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Sara Uceda Renteria
- Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Tina Uršič
- Institute of Microbiology and Immunology, Laboratory for the Diagnosis of Viral Infections, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Sophie Vallet
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Brest Cedex, France
| | - Marc Van Ranst
- Clinical and Epidemiological Virology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Peter Van Wunnik
- Department of Medical Microbiology, Reinier Haga Medical Diagnostic Center, Delft, The Netherlands
| | - Jaco J Verweij
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth Tweesteden Hospital, Tilburg, The Netherlands
| | - Jorgina Vila
- Paediatric Hospital Medicine, Department of Paediatrics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Bas Wintermans
- Laboratory Medical Microbiology and Immunology, Admiraal de Ruijter Hospital, Goes, The Netherlands
| | - Elke Wollants
- Clinical and Epidemiological Virology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Katja C Wolthers
- Department of Medical Microbiology, OrganoVIR Labs, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - F Xavier López-Labrador
- Center for Public Health Research (Foundation for the Promotion of Health and Biomedical Research in the Valencian Community), Generalitat Valenciana, Valencia, Spain, and the Spanish Research Networks Consortium of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid Spain
| | - Thea Kolsen Fischer
- Department of Clinical Research, Nordsjællands Hospital, Hilleroed, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Heli Harvala
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford, United Kingdom
- National Health Service Blood and Transplant, Microbiology Services, Colindale, United Kingdom
| | - Kimberley S M Benschop
- Centre for Infectious Disease Control, Dutch National Public Health Institute, Bilthoven, The Netherlands
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5
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Alemán GV, Cerpas C, Juarez JG, Moreira H, Arguello S, Coloma J, Harris E, Gordon A, Bennett SN, Balmaseda Á. Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 Pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.596876. [PMID: 38895444 PMCID: PMC11185506 DOI: 10.1101/2024.06.03.596876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The global circulation of SARS-CoV-2 has been extensively documented, yet the dynamics within Central America, particularly Nicaragua, remain underexplored. This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtained via next-generation sequencing. These sequences were selected nationwide and analyzed for variant classification, lineage predominance, and phylogenetic diversity. We employed both Illumina and Oxford Nanopore Technologies for all sequencing procedures. Results indicated a temporal and spatial shift in dominant lineages, initially from B.1 and A.2 in early 2020 to various Omicron subvariants towards the study's end. Significant lineage shifts correlated with changes in COVID-19 positivity rates, underscoring the epidemiological impact of variant dissemination. The comparative analysis with regional data underscored the low diversity of circulating lineages in Nicaragua and their delayed introduction compared to other countries in the Central American region. The study also linked specific viral mutations with hospitalization rates, emphasizing the clinical relevance of genomic surveillance. This research advances the understanding of SARS-CoV-2 evolution in Nicaragua and provide valuable information regarding its genetic diversity for public health officials in Central America. We highlight the critical role of ongoing genomic surveillance in identifying emergent lineages and informing public health strategies.
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Affiliation(s)
| | - Cristhiam Cerpas
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia Ministerio de Salud, Managua, Nicaragua
| | | | | | | | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Ángel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia Ministerio de Salud, Managua, Nicaragua
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6
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Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024; 52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-y] [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: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
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Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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7
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Puenpa J, Chansaenroj J, Suwannakarn K, Poovorawan Y. Genomic epidemiology and evolutionary analysis during XBB.1.16-predominant periods of SARS-CoV-2 omicron variant in Bangkok, Thailand: December 2022-August 2023. Sci Rep 2024; 14:645. [PMID: 38182705 PMCID: PMC10770311 DOI: 10.1038/s41598-023-50856-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024] Open
Abstract
The growing occurrence of novel recombinants, such as XBB.1.16, has emerged and become predominant, raising concerns about the impact of genomic recombination on the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study investigated the molecular epidemiological trends and evolution of the Omicron XBB.1.16 epidemic in Bangkok between December 2022 and August 2023. Partial spike and complete genome sequencing of SARS-CoV-2 samples collected from collaborating hospitals were performed. The analysis of 491 partial spike sequences identified 15 distinct lineages, with XBB.1.16 dominating the lineages beginning in March 2023. Phylogenetic analysis revealed at least four distinct XBB.1.16 lineages, suggesting multiple independent introductions into Bangkok. The estimated emergence of XBB.1.16 occurred approximately in January 2022, with an evolutionary rate of 0.79 × 10-3 substitutions per site per year. Monitoring the genomic epidemiology and evolution of XBB.1.16 is vital for the early detection of new strains or emerging variants, which may guide vaccine design and the inclusion of new vaccine strains.
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Affiliation(s)
- Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kamol Suwannakarn
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok, Thailand.
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8
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Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024; 26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
Abstract
The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Gabriela Betella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Dieine Estela Bernieri Schiavon
- Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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9
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Tay JH, Baele G, Duchene S. Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models. Mol Biol Evol 2023; 40:msad212. [PMID: 37738550 PMCID: PMC10560005 DOI: 10.1093/molbev/msad212] [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: 06/17/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023] Open
Abstract
Molecular evolutionary rate variation is a key aspect of the evolution of many organisms that can be modeled using molecular clock models. For example, fixed local clocks revealed the role of episodic evolution in the emergence of SARS-CoV-2 variants of concern. Like all statistical models, however, the reliability of such inferences is contingent on an assessment of statistical evidence. We present a novel Bayesian phylogenetic approach for detecting episodic evolution. It consists of computing Bayes factors, as the ratio of posterior and prior odds of evolutionary rate increases, effectively quantifying support for the effect size. We conducted an extensive simulation study to illustrate the power of this method and benchmarked it to formal model comparison of a range of molecular clock models using (log) marginal likelihood estimation, and to inference under a random local clock model. Quantifying support for the effect size has higher sensitivity than formal model testing and is straight-forward to compute, because it only needs samples from the posterior and prior distribution. However, formal model testing has the advantage of accommodating a wide range molecular clock models. We also assessed the ability of an automated approach, known as the random local clock, where branches under episodic evolution may be detected without their a priori definition. In an empirical analysis of a data set of SARS-CoV-2 genomes, we find "very strong" evidence for episodic evolution. Our results provide guidelines and practical methods for Bayesian detection of episodic evolution, as well as avenues for further research into this phenomenon.
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Affiliation(s)
- John H Tay
- Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sebastian Duchene
- Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
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10
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Scheuermann SE, Goff K, Rowe LA, Beddingfield BJ, Maness NJ. Real-Time Analysis of SARS-CoV-2-Induced Cytolysis Reveals Distinct Variant-Specific Replication Profiles. Viruses 2023; 15:1937. [PMID: 37766343 PMCID: PMC10537736 DOI: 10.3390/v15091937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The ability of each new SARS-CoV-2 variant to evade host humoral immunity is the focus of intense research. Each variant may also harbor unique replication capabilities relevant for disease and transmission. Here, we demonstrate a new approach to assessing viral replication kinetics using real-time cell analysis (RTCA). Virus-induced cell death is measured in real time as changes in electrical impedance through cell monolayers while images are acquired at defined intervals via an onboard microscope and camera. Using this system, we quantified replication kinetics of five clinically important viral variants: WA1/2020 (ancestral), Delta, and Omicron subvariants BA.1, BA.4, and BA.5. Multiple measures proved useful in variant replication comparisons, including the elapsed time to, and the slope at, the maximum rate of cell death. Important findings include significantly weaker replication kinetics of BA.1 by all measures, while BA.5 harbored replication kinetics at or near ancestral levels, suggesting evolution to regain replicative capacity, and both an altered profile of cell killing and enhanced fusogenicity of the Delta variant. Together, these data show that RTCA is a robust method to assess replicative capacity of any given SARS-CoV-2 variant rapidly and quantitatively, which may be useful in assessment of newly emerging variants.
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Affiliation(s)
- Sarah E. Scheuermann
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Lori A. Rowe
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Brandon J. Beddingfield
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Nicholas J. Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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11
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Justo Arevalo S, Uribe Calampa CS, Jimenez Silva C, Quiñones Aguilar M, Bouckaert R, Rebello Pinho JR. Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru. Nat Commun 2023; 14:3557. [PMID: 37322028 PMCID: PMC10272135 DOI: 10.1038/s41467-023-39216-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June-November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru.
- Laboratório Clínico do Hospital Israelita Albert Einstein, São Paulo, Brasil.
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil.
| | | | | | | | - Remco Bouckaert
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Joao Renato Rebello Pinho
- Laboratório Clínico do Hospital Israelita Albert Einstein, São Paulo, Brasil
- LIM03/07, Department of Gastroenterology and Pathology, University of São Paulo School of Medicine, São Paulo, Brazil
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12
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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13
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Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 551] [Impact Index Per Article: 275.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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14
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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15
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Neverov AD, Fedonin G, Popova A, Bykova D, Bazykin G. Coordinated evolution at amino acid sites of SARS-CoV-2 spike. eLife 2023; 12:e82516. [PMID: 36752391 PMCID: PMC9908078 DOI: 10.7554/elife.82516] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/15/2023] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 has adapted in a stepwise manner, with multiple beneficial mutations accumulating in a rapid succession at origins of VOCs, and the reasons for this are unclear. Here, we searched for coordinated evolution of amino acid sites in the spike protein of SARS-CoV-2. Specifically, we searched for concordantly evolving site pairs (CSPs) for which changes at one site were rapidly followed by changes at the other site in the same lineage. We detected 46 sites which formed 45 CSP. Sites in CSP were closer to each other in the protein structure than random pairs, indicating that concordant evolution has a functional basis. Notably, site pairs carrying lineage defining mutations of the four VOCs that circulated before May 2021 are enriched in CSPs. For the Alpha VOC, the enrichment is detected even if Alpha sequences are removed from analysis, indicating that VOC origin could have been facilitated by positive epistasis. Additionally, we detected nine discordantly evolving pairs of sites where mutations at one site unexpectedly rarely occurred on the background of a specific allele at another site, for example on the background of wild-type D at site 614 (four pairs) or derived Y at site 501 (three pairs). Our findings hint that positive epistasis between accumulating mutations could have delayed the assembly of advantageous combinations of mutations comprising at least some of the VOCs.
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Affiliation(s)
- Alexey Dmitrievich Neverov
- HSE UniversityMoscowRussian Federation
- Central Research Institute for EpidemiologyMoscowRussian Federation
| | - Gennady Fedonin
- Central Research Institute for EpidemiologyMoscowRussian Federation
- Moscow Institute of Physics and Technology (National Research University)MoscowRussian Federation
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of SciencesMoscowRussian Federation
| | - Anfisa Popova
- Central Research Institute for EpidemiologyMoscowRussian Federation
| | - Daria Bykova
- Central Research Institute for EpidemiologyMoscowRussian Federation
- Lomonosov Moscow State UniversityMoscowRussian Federation
| | - Georgii Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of SciencesMoscowRussian Federation
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
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16
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Wang Q, Ye S, Zhou Z, Song A, Zhu X, Peng J, Liang R, Yang C, Yu X, Huang X, Yu J, Qiu Y, Ge X. Key mutations in the spike protein of SARS-CoV-2 affecting neutralization resistance and viral internalization. J Med Virol 2023; 95:e28407. [PMID: 36519597 PMCID: PMC9877909 DOI: 10.1002/jmv.28407] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
To control the ongoing COVID-19 pandemic, a variety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have been developed. However, the rapid mutations of SARS-CoV-2 spike (S) protein may reduce the protective efficacy of the existing vaccines which is mainly determined by the level of neutralizing antibodies targeting S. In this study, we screened prevalent S mutations and constructed 124 pseudotyped lentiviral particles carrying these mutants. We challenged these pseudoviruses with sera vaccinated by Sinovac CoronaVac and ZF2001 vaccines, two popular vaccines designed for the initial strain of SARS-CoV-2, and then systematically assessed the susceptivity of these SARS-CoV-2 variants to the immune sera of vaccines. As a result, 14 S mutants (H146Y, V320I + S477N, V382L, K444R, L455F + S477N, L452M + F486L, F486L, Y508H, P521R, A626S, S477N + S698L, A701V, S477N + T778I, E1144Q) were found to be significantly resistant to neutralization, indicating reduced protective efficacy of the vaccines against these SARS-CoV-2 variants. In addition, F486L and Y508H significantly enhanced the utilization of human angiotensin-converting enzyme 2, suggesting a potentially elevated infectivity of these two mutants. In conclusion, our results show that some prevalent S mutations of SARS-CoV-2 reduced the protective efficacy of current vaccines and enhance the infectivity of the virus, indicating the necessity of vaccine renewal and providing direction for the development of new vaccines.
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Affiliation(s)
- Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Sheng‐Bao Ye
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Zhi‐Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - A‐Ling Song
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xi Zhu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Jia‐Mei Peng
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Rui‐Min Liang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Chen‐Hui Yang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xiao‐Wei Yu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina,Hunan Prevention and Treatment Institute for Occupational DiseasesChangshaHunanChina
| | - Xun Huang
- Department of Hospital Infection Control CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Jie Yu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xing‐Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina,Department of Hospital Infection Control CenterXiangya Hospital of Central South UniversityChangshaChina
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17
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Alves HJ, de Araújo JLF, Fonseca PLC, Moreira FRR, Bonfim DM, Queiroz DC, Miguita L, de Souza RM, Geddes VEV, Costa WC, de Oliveira JS, Medeiros ELA, de Souza CSA, Saliba JW, Menezes AL, de Oliveira ES, Adelino TER, Guimaraes NR, Ribeiro AA, Moreira RG, Zauli DAG, Silva JDP, Malta FSV, Ferreira ACDS, Silva AVFG, Alfenas-Zerbini P, de Souza FO, Sabino ADP, Xavier LDA, Carobin NV, de Carvalho AF, Lourenço KL, Teixeira SMR, Fernandes APSM, da Fonseca FG, Abrahão JS, Iani FCDM, Rodrigues RAL, de Souza RP, Aguiar RS. Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study. Viruses 2022; 14:v14122747. [PMID: 36560750 PMCID: PMC9781153 DOI: 10.3390/v14122747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Since its first identification in Brazil, the variant of concern (VOC) Gamma has been associated with increased infection and transmission rates, hospitalizations, and deaths. Minas Gerais (MG), the second-largest populated Brazilian state with more than 20 million inhabitants, observed a peak of cases and deaths in March-April 2021. We conducted a surveillance study in 1240 COVID-19-positive samples from 305 municipalities distributed across MG's 28 Regional Health Units (RHU) between 1 March to 27 April 2021. The most common variant was the VOC Gamma (71.2%), followed by the variant of interest (VOI) zeta (12.4%) and VOC alpha (9.6%). Although the predominance of Gamma was found in most of the RHUs, clusters of Zeta and Alpha variants were observed. One Alpha-clustered RHU has a history of high human mobility from countries with Alpha predominance. Other less frequent lineages, such as P.4, P.5, and P.7, were also identified. With our genomic characterization approach, we estimated the introduction of Gamma on 7 January 2021, at RHU Belo Horizonte. Differences in mortality between the Zeta, Gamma and Alpha variants were not observed. We reinforce the importance of vaccination programs to prevent severe cases and deaths during transmission peaks.
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Affiliation(s)
- Hugo José Alves
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - João Locke Ferreira de Araújo
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Diego Menezes Bonfim
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Lucyene Miguita
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rafael Marques de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Victor Emmanuel Viana Geddes
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Walyson Coelho Costa
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jaqueline Silva de Oliveira
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte 31585-200, Brazil
| | - Eva Lídia Arcoverde Medeiros
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte 31585-200, Brazil
| | | | | | - André Luiz Menezes
- Secretaria Municipal de Saúde, Prefeitura de Belo Horizonte, Belo Horizonte 30130-040, Brazil
| | | | | | | | | | - Rennan Garcias Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | | | | | - Alessandro Clayton de Souza Ferreira
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Poliane Alfenas-Zerbini
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Flavia Oliveira de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Adriano de Paula Sabino
- Laboratório de Institucional de Pesquisa em Biomarcadores, LINBIO, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Laura do Amaral Xavier
- Laboratório de Institucional de Pesquisa em Biomarcadores, LINBIO, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Natália Virtude Carobin
- Laboratório de Institucional de Pesquisa em Biomarcadores, LINBIO, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Alex Fiorini de Carvalho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil
| | - Karine Lima Lourenço
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil
| | | | | | | | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31279-901, Brazil
| | | | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31279-901, Brazil
| | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Correspondence: (R.P.d.S.); (R.S.A.)
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro 22281-100, Brazil
- Correspondence: (R.P.d.S.); (R.S.A.)
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18
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SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022; 14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [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: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil's genomic surveillance studies and contribute to future research execution.
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Almagro JC, Mellado-Sánchez G, Pedraza-Escalona M, Pérez-Tapia SM. Evolution of Anti-SARS-CoV-2 Therapeutic Antibodies. Int J Mol Sci 2022; 23:ijms23179763. [PMID: 36077159 PMCID: PMC9456190 DOI: 10.3390/ijms23179763] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 01/17/2023] Open
Abstract
Since the first COVID-19 reports back in December of 2019, this viral infection caused by SARS-CoV-2 has claimed millions of lives. To control the COVID-19 pandemic, the Food and Drug Administration (FDA) and/or European Agency of Medicines (EMA) have granted Emergency Use Authorization (EUA) to nine therapeutic antibodies. Nonetheless, the natural evolution of SARS-CoV-2 has generated numerous variants of concern (VOCs) that have challenged the efficacy of the EUA antibodies. Here, we review the most relevant characteristics of these therapeutic antibodies, including timeline of approval, neutralization profile against the VOCs, selection methods of their variable regions, somatic mutations, HCDR3 and LCDR3 features, isotype, Fc modifications used in the therapeutic format, and epitope recognized on the receptor-binding domain (RBD) of SARS-CoV-2. One of the conclusions of the review is that the EUA therapeutic antibodies that still retain efficacy against new VOCs bind an epitope formed by conserved residues that seem to be evolutionarily conserved as thus, critical for the RBD:hACE-2 interaction. The information reviewed here should help to design new and more efficacious antibodies to prevent and/or treat COVID-19, as well as other infectious diseases.
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Affiliation(s)
- Juan C. Almagro
- GlobalBio, Inc., 320 Concord Ave, Cambridge, MA 02138, USA
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I+D+i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Correspondence: (J.C.A.); (S.M.P.-T.)
| | - Gabriela Mellado-Sánchez
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I+D+i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Martha Pedraza-Escalona
- CONACyT-Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Sonia M. Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I+D+i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Correspondence: (J.C.A.); (S.M.P.-T.)
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Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B, McCrone JT, O’Toole Á, Price A, Sanderson T, Scher E, Southgate J, Volz E, Barclay WS, Barrett JC, Chand M, Connor T, Goodfellow I, Gupta RK, Harrison EM, Loman N, Myers R, Robertson DL, Pybus OG, Rambaut A. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evol 2022; 8:veac080. [PMID: 36533153 PMCID: PMC9752794 DOI: 10.1093/ve/veac080] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 01/06/2023] Open
Abstract
The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.
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Affiliation(s)
- Verity Hill
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Louis Du Plessis
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Dinesh Aggarwal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Rachel Colquhoun
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Nicholas Ellaby
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Eileen Gallagher
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Natalie Groves
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Ben Jackson
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J T McCrone
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Áine O’Toole
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Anna Price
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Emily Scher
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Joel Southgate
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
| | - Erik Volz
- MRC Unit for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meera Chand
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Guy’s and St Thomas’ Hospital NHS Trust, St Thomas’ Hospital, Westminster Bridge Rd, London SE1 7EH, UK
| | - Thomas Connor
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff CF14 4XW, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
| | - Ewan M Harrison
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard Myers
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Department of Pathobiology and Population Science, The Royal Veterinary College, London, UK
| | - Andrew Rambaut
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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Patel RS, Agrawal B. Heterologous immunity induced by 1 st generation COVID-19 vaccines and its role in developing a pan-coronavirus vaccine. Front Immunol 2022; 13:952229. [PMID: 36045689 PMCID: PMC9420909 DOI: 10.3389/fimmu.2022.952229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome virus-2 (SARS-CoV-2), the causative infectious agent of the COVID-19 pandemic, has led to multiple (4-6) waves of infections worldwide during the past two years. The development of vaccines against SARS-CoV-2 has led to successful mass immunizations worldwide, mitigating the worldwide mortality due the pandemic to a great extent. Yet the evolution of new variants highlights a need to develop a universal vaccine which can prevent infections from all virulent SARS-CoV-2. Most of the current first generation COVID-19 vaccines are based on the Spike protein from the original Wuhan-hu-1 virus strain. It is encouraging that they still protect from serious illnesses, hospitalizations and mortality against a number of mutated viral strains, to varying degrees. Understanding the mechanisms by which these vaccines provide heterologous protection against multiple highly mutated variants can reveal strategies to develop a universal vaccine. In addition, many unexposed individuals have been found to harbor T cells that are cross-reactive against SARS-CoV-2 antigens, with a possible protective role. In this review, we will discuss various aspects of natural or vaccine-induced heterologous (cross-reactive) adaptive immunity against SARS-CoV-2 and other coronaviruses, and their role in achieving the concept of a pan-coronavirus vaccine.
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Affiliation(s)
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Yale SARS-CoV-2 Genomic Surveillance Initiative, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Tay JH, Porter AF, Wirth W, Duchene S. The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate. Mol Biol Evol 2022; 39:msac013. [PMID: 35038741 PMCID: PMC8807201 DOI: 10.1093/molbev/msac013] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the substitution rate of SARS-CoV-2 suggest that its genome accrues around two mutations per month. However, VOCs can have 15 or more defining mutations and it is hypothesized that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analyzed genome sequence data from the GISAID database to assess whether the emergence of VOCs can be attributed to changes in the substitution rate of the virus and whether this pattern can be detected at a phylogenetic level using genome data. We fit a range of molecular clock models and assessed their statistical performance. Our analyses indicate that the emergence of VOCs is driven by an episodic increase in the substitution rate of around 4-fold the background phylogenetic rate estimate that may have lasted several weeks or months. These results underscore the importance of monitoring the molecular evolution of the virus as a means of understanding the circumstances under which VOCs may emerge.
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Affiliation(s)
- John H Tay
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Ashleigh F Porter
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Wytamma Wirth
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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