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

Jackson, Ben, Boni, Maciej F, Bull, Matthew J, Colleran, Amy, Colquhoun, Rachel M, Darby, Alistair C ORCID: 0000-0002-3786-6209, Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T
et al (show 14 more authors) (2021) Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184 (20). 5179-+.

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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.

Item Type: Article
Uncontrolled Keywords: COVID-19 Genomics UK (COG-UK) Consortium, Humans, Computational Biology, Phylogeny, Recombination, Genetic, Base Sequence, Gene Frequency, Genotype, Mutation, Polymorphism, Single Nucleotide, Genome, Viral, Pandemics, United Kingdom, Whole Genome Sequencing, COVID-19, SARS-CoV-2
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 04 Feb 2022 11:48
Last Modified: 03 Oct 2023 08:32
DOI: 10.1016/j.cell.2021.08.014
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