article · Nature Communications
Genomic surveillance initiatives during the pandemic identified a distinct SARS-CoV-2 lineage designated B.1.620. Initially discovered in Lithuania, this lineage carries numerous mutations and deletions within its spike protein that are shared with recognised variants of concern, including E484K, S477N, and specific deletions like HV69Δ, Y144Δ, and LLA241/243Δ. These genetic characteristics suggest that the lineage has the potential to resist neutralising antibodies. Travel records and local monitoring demonstrate that B.1.620 established community transmission across Europe, with a notable focus on Lithuania. Additionally, genome sequencing efforts highlighted a significant prevalence of the lineage in Central Africa. Advanced phylogeographic inference methods combining genetic data with patient travel histories indicate that B.1.620 most likely originated in Central Africa prior to wider dissemination.
Tracking emerging viral lineages with mutations linked to antibody escape is vital for global public health. Understanding how variants spread across regions, including links between Central Africa and Europe, informs international disease surveillance and helps health authorities anticipate potential threats to immunity conferred by past infections or antibody therapies.
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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.
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DOI: 10.1038/s41467-021-26055-8
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