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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HighlightsThe region spanning surface antigen and polymerase genes was sequenced in 51 out of 118 HBsAg positive patients in the Central African Republic.Three potentials HBV Immune Escape Mutants sY100C, sA128V, sM133T as well as several polymerase mutants were detected.HBV genotypes E were dominant (96%) compared to subgenotype A1 (4%).Serotype ayw4 accounted for genotype E and ayw1 accounted for subgenotype A1.