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

  1. Ben Jackson
  2. Maciej F Boni
  3. Matthew J Bull
  4. Amy Colleran
  5. Rachel M Colquhoun
  6. Alistair Darby
  7. Sam Haldenby
  8. Verity Hill
  9. Anita Lucaci
  10. John T McCrone
  11. Samuel Nicholls
  12. Áine O’Toole
  13. Nicole Pacchiarini
  14. Radoslaw Poplawski
  15. Emily Scher
  16. Flora Todd
  17. Hermione Webster
  18. Mark Whitehead
  19. Claudia Wierzbicki
  20. The COVID-19 Genomics UK (COG-UK) consortium
  21. Nicholas J Loman
  22. Thomas R Connor
  23. David L Robertson
  24. Oliver G Pybus
  25. Andrew Rambaut
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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 two 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.

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