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

The COVID-19 Genomics UK (COG-UK) Consortium, Sanger Covid Team

Research output: Contribution to journalArticlepeer-review

129 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)5179-5188.e8
Issue number20
Publication statusPublished - Sept 30 2021


  • B.1.1.7
  • evolution
  • genomic epidemiology
  • genomics
  • recombination
  • SARS-CoV-2
  • variants

ASJC Scopus subject areas

  • General Biochemistry,Genetics and Molecular Biology


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