Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

Abstract

We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances, there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of 2 months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7's set of mutations.

Cited by papers we hold 5

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• Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination · 2022
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• SARS-CoV-2 Variants, Vaccines, and Host Immunity · 2022
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• Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape · 2022
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