Summary 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. Graphical abstract Highlights • We find evidence for recombination in SARS-CoV-2 • We identify eight clear recombination events, four of which lead to onward transmission • Estimated breakpoints are consistent with coronavirus cellular replication dynamics • Transmitted recombinants inherited the more-transmissible B.1.1.7 spike gene Sampling from late 2020 to early 2021 provides evidence for SARS-CoV-2 recombination and onward community transmission of recombinant viruses that inherited the spike region from the B.1.1.7 (alpha) variant.
【저자키워드】 Evolution, SARS-CoV-2, Genomics, variants, B.1.1.7, Genomic epidemiology, Recombination, 【초록키워드】 viruses, coronavirus, Genome, mutations, variant, polymorphism, SARS-CoV-2 virus, Transmission, complement, virus, Replication, B.1.1.7 variant, spike gene, B.1.1.7, Genetic variation, Single-nucleotide polymorphisms, Recombination, Cluster, Deletion, Alpha, community transmission, sampling, characteristic, United Kingdom, cellular, Evidence, recombinant, lead, (alpha, Abstract, genomic location, circulating, onward transmission, deletions, instances, recombinants, SARS-CoV-2 recombination, independent, breakpoint, Course, identify, lack, sequenced, events, eight, provide, parental, Estimated, single-nucleotide, 【제목키워드】 pandemic, Transmission, recombinant, Generation, the SARS-CoV-2,