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

COVID-19 Genomics UK COG-UK Consor; Jackson, B; Boni, MF; Bull, MJ; Colleran, A; Colquhoun, RM; Darby, AC; Haldenby, S; Hill, V; Lucaci, A; McCrone, JT; Nicholls, SM; O'Toole, A; Pacchiarini, N; Poplawski, R; Scher, E; Todd, F; Webster, HJ; Whitehead, M; Wierzbicki, C; Loman, NJ; Connor, TR; Robertson, DL; Pybus, OG; Rambaut, A

Authors

COVID-19 Genomics UK COG-UK Consor

B Jackson

MF Boni

MJ Bull

A Colleran

RM Colquhoun

AC Darby

S Haldenby

V Hill

A Lucaci

JT McCrone

SM Nicholls

A O'Toole

N Pacchiarini

R Poplawski

E Scher

F Todd

HJ Webster

M Whitehead

C Wierzbicki

NJ Loman

TR Connor

DL Robertson

OG Pybus

A Rambaut



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 lineagedefining 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.

Citation

COVID-19 Genomics UK COG-UK Consor, Jackson, B., Boni, M., Bull, M., Colleran, A., Colquhoun, R., …Rambaut, A. (2021). Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179-+. https://doi.org/10.1016/j.cell.2021.08.014

Journal Article Type Article
Acceptance Date Aug 11, 2021
Publication Date 2021
Deposit Date Jan 11, 2022
Publicly Available Date Jan 11, 2022
Print ISSN 0092-8674
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 184
Issue 20
Pages 5179-+
DOI https://doi.org/10.1016/j.cell.2021.08.014
Keywords RNA RECOMBINATION; MOLECULAR-BIOLOGY; CORONAVIRUS; ORIGIN; VIRUS
Public URL https://rvc-repository.worktribe.com/output/1555197

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