Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Gytis Dudas; Samuel L Hong; Barney I Potter; Sébastien Calvignac-Spencer; Frédéric S Niatou-Singa; Thais B Tombolomako; Terence Fuh-Neba; Ulrich Vickos; Markus Ulrich; Fabian H Leendertz; Kamran Khan; Carmen Huber; Alexander Watts; Ingrida Olendraitė; Joost Snijder; Kim N Wijnant; Alexandre M J J Bonvin; Pascale Martres; Sylvie Behillil; Ahidjo Ayouba; Martin Foudi Maidadi; Dowbiss Meta Djomsi; Celestin Godwe; Christelle Butel; Aistis Šimaitis; Miglė Gabrielaitė; Monika Katėnaitė; Rimvydas Norvilas; Ligita Raugaitė; Giscard Wilfried Koyaweda; Jephté Kaleb Kandou; Rimvydas Jonikas; Inga Nasvytienė; Živilė Žemeckienė; Dovydas Gečys; Kamilė Tamušauskaitė; Milda Norkienė; Emilija Vasiliūnaitė; Danguolė Žiogienė; Albertas Timinskas; Marius Šukys; Mantas Šarauskas; Gediminas Alzbutas; Adrienne Amuri Aziza; Eddy Kinganda Lusamaki; Jean-Claude Makangara Cigolo; Francisca Muyembe Mawete; Emmanuel Lokilo Lofiko; Placide Mbala Kingebeni; Jean-Jacques Muyembe Tamfum; Marie Roseline Darnycka Belizaire; René Ghislain Essomba; Marie Claire Okomo Assoumou; Akenji Blaise Mboringong; Alle Baba Dieng; Dovilė Juozapaitė; Salome Hosch; Justino Obama; Mitoha Ondo'o Ayekaba; Daniel Naumovas; Arnoldas Pautienius; Clotaire Donatien Rafaï; Astra Vitkauskienė; Rasa Ugenskienė; Alma Gedvilaitė; Darius Čereškevičius; Vaiva Lesauskaitė; Lukas Žemaitis; Laimonas Griškevičius; Guy Baele

doi:10.1038/s41467-021-26055-8

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Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

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Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Gytis Dudas, Samuel L Hong, Barney I Potter, Sébastien Calvignac-Spencer, Frédéric S Niatou-Singa, Thais B Tombolomako, Terence Fuh-Neba, Ulrich Vickos, Markus Ulrich, Fabian H Leendertz, …

Nature communications, Vol.12(1), pp.5769-12

01/10/2021

DOI: https://doi.org/10.1038/s41467-021-26055-8

PMID: 34599175

Résumé

Africa, Central - epidemiology

Antibodies, Neutralizing - immunology

COVID-19 - epidemiology

COVID-19 - transmission

COVID-19 - virology

Europe - epidemiology

Humans

Immune Evasion - genetics

Mutation

Phylogeny

Phylogeography

SARS-CoV-2 - classification

SARS-CoV-2 - genetics

SARS-CoV-2 - immunology

Spike Glycoprotein, Coronavirus - genetics

Travel - statistics & numerical data

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.

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Titre: Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Créateurs - sans rôle: Gytis Dudas - Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania. gytisdudas@gmail.com
Samuel L Hong - Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Barney I Potter - Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Sébastien Calvignac-Spencer - Robert Koch Institute
Frédéric S Niatou-Singa - WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
Thais B Tombolomako - WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
Terence Fuh-Neba - WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
Ulrich Vickos - Academic Department of Pediatrics, Clinical immunology and vaccinology, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
Markus Ulrich - Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
Fabian H Leendertz - Robert Koch Institute
Kamran Khan - University of Toronto
Carmen Huber - BlueDot, Toronto, ON, M5J 1A7, Canada
Alexander Watts - BlueDot, Toronto, ON, M5J 1A7, Canada
Ingrida Olendraitė - Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Lab, CB2 2QQ, Cambridge, UK
Joost Snijder - Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
Kim N Wijnant - Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
Alexandre M J J Bonvin - Utrecht University
Pascale Martres - Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France
Sylvie Behillil - National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
Ahidjo Ayouba - Université de Montpellier
Martin Foudi Maidadi - Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
Dowbiss Meta Djomsi - Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
Celestin Godwe - Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
Christelle Butel - TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
Aistis Šimaitis - The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania
Miglė Gabrielaitė - Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
Monika Katėnaitė - Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
Rimvydas Norvilas - Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
Ligita Raugaitė - Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
Giscard Wilfried Koyaweda - Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
Jephté Kaleb Kandou - Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
Rimvydas Jonikas - Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
Inga Nasvytienė - Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
Živilė Žemeckienė - Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
Dovydas Gečys - Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
Kamilė Tamušauskaitė - Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
Milda Norkienė - Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Emilija Vasiliūnaitė - Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Danguolė Žiogienė - Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Albertas Timinskas - Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Marius Šukys - Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
Mantas Šarauskas - Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
Gediminas Alzbutas - Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
Adrienne Amuri Aziza - University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
Eddy Kinganda Lusamaki - University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
Jean-Claude Makangara Cigolo - University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
Francisca Muyembe Mawete - University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
Emmanuel Lokilo Lofiko - National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
Placide Mbala Kingebeni - University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
Jean-Jacques Muyembe Tamfum - University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
Marie Roseline Darnycka Belizaire - World Health Organization, Central African Republic Office, Bangui, Central African Republic
René Ghislain Essomba - Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
Marie Claire Okomo Assoumou - Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
Akenji Blaise Mboringong - National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
Alle Baba Dieng - World Health Organization, Cameroon Office, Yaoundé, Cameroon
Dovilė Juozapaitė - Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
Salome Hosch - Swiss Tropical and Public Health Institute, Basel, Switzerland
Justino Obama - Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
Mitoha Ondo'o Ayekaba - Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
Daniel Naumovas - Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
Arnoldas Pautienius - Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
Clotaire Donatien Rafaï - Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
Astra Vitkauskienė - Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
Rasa Ugenskienė - Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
Alma Gedvilaitė - Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Darius Čereškevičius - Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
Vaiva Lesauskaitė - Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
Lukas Žemaitis - National Public Health Surveillance Laboratory, Vilnius, Lithuania
Laimonas Griškevičius - Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
Guy Baele - Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium. guy.baele@kuleuven.be
Détails de publication: Nature communications, Vol.12(1), pp.5769-12
Note de subvention: 001 / World Health Organization
Identifiants: 99148762009311
Unité académique: Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Langue: English
Type de ressource: Journal article