Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Publication date
2021-10-01
Authors
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.
Editors
Advisors
Supervisors
Document Type
Article
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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.
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
Citation
Dudas, G, Hong, S L, Potter, B I, Calvignac-Spencer, S, Niatou-Singa, F S, Tombolomako, T B, Fuh-Neba, T, Vickos, U, Ulrich, M, Leendertz, F H, Khan, K, Huber, C, Watts, A, Olendraitė, I, Snijder, J, Wijnant, K N, Bonvin, A M J J, Martres, P, Behillil, S, Ayouba, A, Maidadi, M F, Djomsi, D M, Godwe, C, Butel, C, Šimaitis, A, Gabrielaitė, M, Katėnaitė, M, Norvilas, R, Raugaitė, L, Koyaweda, G W, Kandou, J K, Jonikas, R, Nasvytienė, I, Žemeckienė, Ž, Gečys, D, Tamušauskaitė, K, Norkienė, M, Vasiliūnaitė, E, Žiogienė, D, Timinskas, A, Šukys, M, Šarauskas, M, Alzbutas, G, Aziza, A A, Lusamaki, E K, Cigolo, J C M, Mawete, F M, Lofiko, E L, Kingebeni, P M, Tamfum, J J M, Belizaire, M R D, Essomba, R G, Assoumou, M C O, Mboringong, A B, Dieng, A B, Juozapaitė, D, Hosch, S, Obama, J, Ayekaba, M O, Naumovas, D, Pautienius, A, Rafaï, C D, Vitkauskienė, A, Ugenskienė, R, Gedvilaitė, A, Čereškevičius, D, Lesauskaitė, V, Žemaitis, L, Griškevičius, L & Baele, G 2021, 'Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions', Nature Communications, vol. 12, no. 1, 5769, pp. 1-12. https://doi.org/10.1038/s41467-021-26055-8