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.

我们提供了 2020 年底和 2021 年初在英国采样的重组 SARS-CoV-2 病毒的多个独立起源的证据。它们的基因组携带单核苷酸多态性和缺失，这是所关注的 B.1.1.7 变体的特征，但缺乏谱系定义突变的完整补充。相反，它们的基因组的其余部分与与重组体同时在同一地理区域传播的非 B.1.1.7 病毒共享连续的遗传变异。在四个案例中，有证据表明重组源病毒继续传播，其中包括 2 个月内 45 个已测序病例组成的一个传播集群。重组断点的推断基因组位置表明，每个社区传播的重组病毒都从 B.1.1.7 亲本病毒继承了其刺突区域，这与 B.1.1.7 突变组的传播优势一致。