Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Dudas, Gytis; Hong, Samuel L.; Potter, Barney I.; Calvignac-Spencer, Sébastien; Niatou-Singa, Frédéric S.; Tombolomako, Thais B.; Fuh-Neba, Terence; Vickos, Ulrich; Ulrich, Markus; Leendertz, Fabian H.; Khan, Kamran; Huber, Carmen; Watts, Alexander; Olendraitė, Ingrida; Snijder, Joost; Wijnant, Kim N.; Bonvin, Alexandre M.J.J.; Martres, Pascale; Behillil, Sylvie; Ayouba, Ahidjo; Maidadi, Martin Foudi; Djomsi, Dowbiss Meta; Godwe, Celestin; Butel, Christelle; Šimaitis, Aistis; Gabrielaitė, Miglė; Katėnaitė, Monika; Norvilas, Rimvydas; Raugaitė, Ligita; Koyaweda, Giscard Wilfried; Kandou, Jephté Kaleb; Jonikas, Rimvydas; Nasvytienė, Inga; Žemeckienė, Živilė; Gečys, Dovydas; Tamušauskaitė, Kamilė; Norkienė, Milda; Vasiliūnaitė, Emilija; Žiogienė, Danguolė; Timinskas, Albertas; Šukys, Marius; Šarauskas, Mantas; Alzbutas, Gediminas; Aziza, Adrienne Amuri; Lusamaki, Eddy Kinganda; Cigolo, Jean Claude Makangara; Mawete, Francisca Muyembe; Lofiko, Emmanuel Lokilo; Kingebeni, Placide Mbala; Tamfum, Jean Jacques Muyembe; Belizaire, Marie Roseline Darnycka; Essomba, René Ghislain; Assoumou, Marie Claire Okomo; Mboringong, Akenji Blaise; Dieng, Alle Baba; Juozapaitė, Dovilė; Hosch, Salome; Obama, Justino; Ayekaba, Mitoha Ondo’o; Naumovas, Daniel; Pautienius, Arnoldas; Rafaï, Clotaire Donatien; Vitkauskienė, Astra; Ugenskienė, Rasa; Gedvilaitė, Alma; Čereškevičius, Darius; Lesauskaitė, Vaiva; Žemaitis, Lukas; Griškevičius, Laimonas; Baele, Guy
(2021) Nature Communications, volume 12, issue 1, pp. 1 - 12
(Article)
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
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(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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Keywords: Africa, Central/epidemiology, Antibodies, Neutralizing/immunology, COVID-19/epidemiology, Europe/epidemiology, Humans, Immune Evasion/genetics, Mutation, Phylogeny, Phylogeography, SARS-CoV-2/classification, Spike Glycoprotein, Coronavirus/genetics, Travel/statistics & numerical data, General Physics and Astronomy, General Chemistry, General Biochemistry,Genetics and Molecular Biology
ISSN: 2041-1723
Publisher: Nature Publishing Group
Note: Funding Information: We gratefully acknowledge the authors from originating laboratories responsible for obtaining the specimens, as well as submitting laboratories where the genome data were generated and shared via GISAID, on which this research is based. An acknowledgement table with GISAID accession IDs of SARS-CoV-2 genomes used here is included. We thank all involved in the collection and processing of SARS-CoV-2 testing and genomic data, as well as associated metadata on individual travel histories. In particular, we would like to thank Marc Noguera Julian, Elisa Martro Catala, Samuel Cordey, Piet Maes, Keith Durkin, Bruno Verhasselt, Lize Cuypers, Lien Cattoir, Veerle Matheeussen, Vincent Enouf, Sylvie van der Werf, Etienne Simon-Lorière, Tobias Schindler, Vladimira Kou-delakova, Gabriel Gonzalez, Ariane Düx, Yanthe Nobel, Livia Patrono, Justas Dapkūnas and Andrew J. Tatem. We would like to thank Richard Neher and Kristian G. Andersen for thoughtful discussions. S.L.H. acknowledges support from the Research Foundation - Flanders (‘Fonds voor Wetenschappelijk Onderzoek - Vlaanderen,’ G0D5117N). B.P. and G.B. acknowledge support from the Internal Fondsen KU Leuven/Internal Funds KU Leuven (Grant No. C14/18/094). G.B. acknowledges support from the Research Foundation - Flanders (‘Fonds voor Wetenschappelijk Onderzoek - Vlaanderen,’ G0E1420N, G098321N). F.H.L. and T.F.N. were supported by WWF and German Research Council’s grant LE1813/14-1 (Great Ape Health in Tropical Africa), Research in CAR took place under permit #098/MRSIT/DIRCAB/CB.20, granted to T.T. by the Ministery of Scientific Research and Technological Innovation. J.S. acknowledges funding from the Dutch Research Council NWO Gravitation 2013 BOO, Institute for Chemical Immunology (ICI; 024.002.009). A.M.J.J.B. acknowledges the support of European Union Horizon 2020 projects BioExcel (823830) and EOSC-Hub (777536) projects. A.A. and C.B. acknowledge the support of the French National Research Institute for Sustainable Development (IRD). Publisher Copyright: © 2021, The Author(s).
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