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

Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., Rambaut, Andrew, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic. Cell. ISSN 0092-8674 (In Press)

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Official URL: https://doi.org/10.1016/j.cell.2021.08.014

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.

Item Type: Article
Additional Information: Funding information: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. Also MRC (MC UU 1201412), UKRI/Wellcome (COG-UK), Wellcome Trust Collaborator Award (206298/Z/17/Z – ARTIC Network; TCW Wellcome Trust Award 204802/Z/16/Z. Matthew Bashton, Andrew Nelson, Darren Smith, Greg Young are members of the COVID-19 Genomics UK (COG-UK) consortium.
Uncontrolled Keywords: SARS-CoV-2, evolution, recombination, genomic epidemiology, B.1.1.7, variants
Subjects: B900 Others in Subjects allied to Medicine
C100 Biology
C500 Microbiology
C900 Others in Biological Sciences
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Rachel Branson
Date Deposited: 08 Sep 2021 13:14
Last Modified: 08 Sep 2021 13:15
URI: http://nrl.northumbria.ac.uk/id/eprint/47105

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