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 and Guy Baele ()
Additional contact information
Gytis Dudas: Gothenburg Global Biodiversity Centre
Samuel L. Hong: Immunology and Transplantation, Rega Institute, KU Leuven
Barney I. Potter: Immunology and Transplantation, Rega Institute, KU Leuven
Sébastien Calvignac-Spencer: Robert Koch Institute
Frédéric S. Niatou-Singa: WWF Central African Republic Programme Office
Thais B. Tombolomako: WWF Central African Republic Programme Office
Terence Fuh-Neba: WWF Central African Republic Programme Office
Ulrich Vickos: Amitié Hospital
Markus Ulrich: Robert Koch Institute
Fabian H. Leendertz: Robert Koch Institute
Kamran Khan: BlueDot
Carmen Huber: BlueDot
Alexander Watts: BlueDot
Ingrida Olendraitė: Vilnius University Hospital Santaros Klinikos
Joost Snijder: Utrecht University
Kim N. Wijnant: Utrecht University
Alexandre M.J.J. Bonvin: Utrecht University
Pascale Martres: Microbiology, Centre Hospitalier René Dubos
Sylvie Behillil: CNRS UMR 3569, Université de Paris, Institut Pasteur
Ahidjo Ayouba: TransVIHMI, Université de Montpellier, IRD, INSERM
Martin Foudi Maidadi: Institut de Recherches Médicales et D’études des Plantes Médicinales
Dowbiss Meta Djomsi: Institut de Recherches Médicales et D’études des Plantes Médicinales
Celestin Godwe: Institut de Recherches Médicales et D’études des Plantes Médicinales
Christelle Butel: TransVIHMI, Université de Montpellier, IRD, INSERM
Aistis Šimaitis: The Office of the Government of the Republic of Lithuania
Miglė Gabrielaitė: Center for Genomic Medicine, Rigshospitalet
Monika Katėnaitė: Vilnius University Hospital Santaros Klinikos
Rimvydas Norvilas: Vilnius University Hospital Santaros Klinikos
Ligita Raugaitė: Vilnius University Hospital Santaros Klinikos
Giscard Wilfried Koyaweda: Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP)
Jephté Kaleb Kandou: Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP)
Rimvydas Jonikas: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Inga Nasvytienė: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Živilė Žemeckienė: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Dovydas Gečys: Lithuanian University of Health Sciences
Kamilė Tamušauskaitė: Lithuanian University of Health Sciences
Milda Norkienė: Vilnius University
Emilija Vasiliūnaitė: Vilnius University
Danguolė Žiogienė: Vilnius University
Albertas Timinskas: Vilnius University
Marius Šukys: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Mantas Šarauskas: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Gediminas Alzbutas: Lithuanian University of Health Sciences
Adrienne Amuri Aziza: National Institute for Biomedical Research (INRB)
Eddy Kinganda Lusamaki: National Institute for Biomedical Research (INRB)
Jean-Claude Makangara Cigolo: National Institute for Biomedical Research (INRB)
Francisca Muyembe Mawete: National Institute for Biomedical Research (INRB)
Emmanuel Lokilo Lofiko: National Institute for Biomedical Research (INRB)
Placide Mbala Kingebeni: National Institute for Biomedical Research (INRB)
Jean-Jacques Muyembe Tamfum: National Institute for Biomedical Research (INRB)
Marie Roseline Darnycka Belizaire: World Health Organization, Central African Republic Office
René Ghislain Essomba: Ministry of Public Health
Marie Claire Okomo Assoumou: Ministry of Public Health
Akenji Blaise Mboringong: Ministry of Public Health
Alle Baba Dieng: Cameroon Office
Dovilė Juozapaitė: Vilnius University Hospital Santaros Klinikos
Salome Hosch: Swiss Tropical and Public Health Institute
Justino Obama: Ministry of Health and Social Welfare
Mitoha Ondo’o Ayekaba: Ministry of Health and Social Welfare
Daniel Naumovas: Vilnius University Hospital Santaros Klinikos
Arnoldas Pautienius: Lithuanian University of Health Sciences
Clotaire Donatien Rafaï: Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP)
Astra Vitkauskienė: Lithuanian University of Health Sciences
Rasa Ugenskienė: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Alma Gedvilaitė: Vilnius University
Darius Čereškevičius: Hospital of Lithuanian University of Health Sciences Kauno Klinikos
Vaiva Lesauskaitė: Lithuanian University of Health Sciences
Lukas Žemaitis: Lithuanian University of Health Sciences
Laimonas Griškevičius: Vilnius University Hospital Santaros Klinikos
Guy Baele: Immunology and Transplantation, Rega Institute, KU Leuven

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-021-26055-8

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