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

• DOI: 10.1038/s41467-021-26055-8
• Publication Date: 2021-10-01T11:02:54Z
• Authors: Gytis Dudas; Samuel L. Hong; Barney I. Potter; Sébastien Calvign...; Frédéric S. Niato...; 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. ...; 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 ...; 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 Lus...; Jean-Claude Makan...; Francisca Muyembe...; Emmanuel Lokilo L...; Placide Mbala Kin...; Jean-Jacques Muye...; Marie Roseline Da...; René Ghislain Ess...; Marie Claire Okom...; Akenji Blaise Mbo...; Alle Baba Dieng; Dovilė Juozapaitė; Salome Hosch; Justino Obama; Mitoha Ondo’o Aye...; Daniel Naumovas; Arnoldas Pautienius; Clotaire Donatien...; Astra Vitkauskienė; Rasa Ugenskienė; Alma Gedvilaitė; Darius Čereškevičius; Vaiva Lesauskaitė; Lukas Žemaitis; Laimonas Griškevi...; Guy Baele
• Keywords: SARS-CoV-2/classification; 0301 basic medicine; Coronavirus/genetics; General Physics and Astronomy; /631/181/757; Phylogeny; COVID-19/epidemiology; ddc:610; Travel; 0303 health sciences; Travel/statistics & numerical data; Q; article; Africa, Central/epidemiology; Central/epidemiology; Antibodies, Neutralizing/immunology; Spike Glycoprotein; 3. Good health; phylogenetics; Multidisciplinary Sciences; Europe; Spike Glycoprotein, Coronavirus/genetics; Phylogeography; Spike Glycoprotein, Coronavirus; Science & Technology - Other Topics; 570; Science; General Biochemistry,Genetics and Molecular Biology; 610; Antibodies; Article; Europe/epidemiology; 03 medical and health sciences; /692/699/255/2514; Humans; Africa, Central; ddc:610; /631/181/735; Immune Evasion; Immune Evasion/genetics; Science & Technology; molecular evolution; SARS-CoV-2; /631/326/421; COVID-19; pathogens; General Chemistry; PERFORMANCE; Antibodies, Neutralizing; Neutralizing/immunology; SPIKE PROTEIN; MODEL; Africa; Mutation; INFERENCE; viral infection; 610 Medizin und Gesundheit

AbstractDistinct 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.