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.
Highlights
Over a year into the pandemic and with an unprecedented reduction in human mobility worldwide, distinct SARSCoV-2 lineages have arisen in multiple geographic areas around the world[1,2,3]
In this study, we have presented evidence that a SARS-CoV-2 lineage designated B.1.620, first detected in Europe in late February, is associated with the central African region, where it appears to circulate at high prevalence, and has been introduced into Europe, North America, and Asia on multiple occasions
A fair number of known B.1.620 genomes that were sequenced in Europe stem from travel-related cases returning from Cameroon (Fig. 3), and recently sequenced genomes from Central African Republic (CAR) and Cameroon belong to lineage B.1.620, suggesting that the central African region is likely to be the immediate source of this lineage
Summary
Over a year into the pandemic and with an unprecedented reduction in human mobility worldwide, distinct SARSCoV-2 lineages have arisen in multiple geographic areas around the world[1,2,3]. We here describe a similar case in the form of a lineage designated B.1.620 that first caught our attention as a result of what was initially a small outbreak caused by a distinct and diverged lineage previously not detected in Lithuania, bearing multiple VOC-like mutations and deletions, many of which substantially alter the spike protein. Starting April 2nd 2021, targeted E484K PCR confirmed a growing cluster of cases with this mutation in Anykščiai municipality in Utena county with a total of 43 E484K+ cases out of 81 tested by April 28th (Supplementary Fig. S1) Up to this point, the Lithuanian genomic surveillance programme had sequenced over 10% of PCR-positive SARSCoV-2 cases in Lithuania and identified few lineages with E484K circulating in Lithuania. We provide a description of local transmission in Lithuania, France, Spain, Italy, and Germany through phylogenetic and phylogeographic analysis, and in Belgium through the collection of travel records
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