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

Published version
Peer-reviewed

Type

Article

Change log

Authors

Potter, Barney I 
Calvignac-Spencer, Sébastien  ORCID logo  https://orcid.org/0000-0003-4834-0509
Niatou-Singa, Frédéric S 

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.

Description

Keywords

Africa, Central, Antibodies, Neutralizing, COVID-19, Europe, Humans, Immune Evasion, Mutation, Phylogeny, Phylogeography, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Travel

Journal Title

Nat Commun

Conference Name

Journal ISSN

2041-1723
2041-1723

Volume Title

12

Publisher

Springer Science and Business Media LLC