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

Ben Jackson*, Maciej F. Boni, Matthew J. Bull, Amy Colleran, Rachel M. Colquhoun, Alistair C. Darby, Sam Haldenby, Verity Hill, Anita Lucaci, John T. McCrone, Samuel M. Nicholls, Áine O’toole, Nicole Pacchiarini, Radoslaw Poplawski, Emily Scher, Flora Todd, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, The COVID-19 Genomics UK (COG-UK) ConsortiumNicholas J. Loman, Thomas R. Connor, David L. Robertson, Oliver G. Pybus, Andrew Rambaut*, Matthew Bashton, Darren Smith, Andrew Nelson, Greg Young, Clare McCann

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
JournalCell
Early online date17 Aug 2021
DOIs
Publication statusE-pub ahead of print - 17 Aug 2021

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