Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe
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 mutationsand deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K,S477N and deletions HV69∆, Y144∆, and LLA241/243∆. 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 state-of-the-art phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.
Gytis Dudas (1,2); Samuel L. Hong (3); Barney I. Potter (3); Sébastien Calvignac-Spencer (4,5); Frédéric S. Niatou-Singa (6); Thais B. Tombolomako (6); Terence Fuh-Neba (6); Ulrich Vickos (7,8); Markus Ulrich (4); Fabian H. Leendertz (4); Kamran Khan (9,10,11); Carmen Huber (9); Alexander Watts (9); Ingrida Olendraitė (2,12); Joost Snijder (13); Kim N. Wijnant (13); Alexandre M.J.J. Bonvin (14); Pascale Martres (15); Sylvie Behillil (16,17); Ahidjo Ayouba (18); Martin Foudi Maidadi (19); Dowbiss Meta Djomsi (19); Celestin Godwe (19); Christelle Butel (18); Aistis Šimaitis (20); Miglė Gabrielaitė (21); Monika Katėnaitė (2); Rimvydas Norvilas (2,22); Ligita Raugaitė (2); Giscard Wilfried Koyaweda (23); Jephté Kaleb Kandou (23); Rimvydas Jonikas (24); Inga Nasvytienė (24); Živilė Žemeckienė (24); Dovydas Gečys (25); Kamilė Tamušauskaitė (25); Milda Norkienė (26); Emilija Vasiliūnaitė (26); Danguolė Žiogienė (26); Albertas Timinskas (26); Marius Šukys (24,27); Mantas Šarauskas (24); Gediminas Alzbutas (28); Adrienne Amuri Aziza (29,30); Eddy Kinganda Lusamaki (29,30); Jean-Claude Makangara Cigolo (29,30); Francisca Muyembe Mawete (29,30); Emmanuel Lokilo Lofiko (29); Placide Mbala Kingebeni (29,30); Jean-Jacques Muyembe Tamfum (29,30); Marie Roseline Darnycka Belizaire (31); René Ghislain Essomba (32,33); Marie Claire Okomo Assoumou (32,33); Akenji Blaise Mboringong (32); Alle Baba Dieng (34); Dovilė Juozapaitė (2); Salome Hosch (35); Justino Obama (36); Mitoha Ondo'o Ayekaba (36); Daniel Naumovas (2); Arnoldas Pautienius (37); Clotaire Donatien Rafaï (23); Astra Vitkauskienė (38); Rasa Ugenskienė (24,27); Alma Gedvilaitė (26); Darius Čereškevičius (24,25); Vaiva Lesauskaitė (25); Lukas Žemaitis (25,39); Laimonas Griškevičius (2); Guy Baele (3);
1 Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
2 Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
3 Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
4 Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353 Berlin, Germany
5 Viral Evolution, Robert Koch Institute, 13353 Berlin, Germany
6 WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
7 Infectious and Tropical Diseases Unit, Department of medicine, Amitie Hospital, Bangui, Central African Republic
8 Academic Department of Pediatrics, Clinical immunology and vaccinology, Children’s Hospital Bambino Gesù, IRCCS, Rome, Italy
9 BlueDot, Toronto, ON M5J 1A7, Canada
10 Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1A6, Canada
11 Section of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
12 Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital Lab, CB2 2QQ, United Kingdom
13 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
14 Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
15 Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France
16 Molecular Genetics of RNA viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
17 National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
18 TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis 34394 Montpellier cedex, France
19 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
20 The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania
21 Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
22 Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
23 Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
24 Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
25 Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
26 Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
27 Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
28 Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
29 National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
30 University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
31 World Health Organization, Central African Republic Office, Central African Republic
32 National Public Health Laboratory, Ministry of Public Health, Cameroon
33 Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
34 World Health Organization, Cameroon Office, Cameroon
35 Swiss Tropical and Public Health Institute, Basel, Switzerland
36 Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
37 Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
38 Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
39 National Public Health Surveillance Laboratory, Vilnius, Lithuania