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

The COVID-19 Genomics UK (COG-UK) Consortium, Sanger Covid Team (2021) Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184 (20). 5179-5188.e8. ISSN 0092-8674

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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 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
Additional Information:	Data and code availability: All the code used to perform the analyses here is available at: https://github.com/COG-UK/UK-recombination-analysis
Uncontrolled Keywords:	b.1.1.7,evolution,genomic epidemiology,genomics,recombination,sars-cov-2,variants,general biochemistry,genetics and molecular biology ,/dk/atira/pure/subjectarea/asjc/1300/1300
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Science Faculty of Science > School of Biological Sciences Faculty of Medicine and Health Sciences > School of Health Sciences Faculty of Arts and Humanities > School of History Faculty of Science > School of Computing Sciences Faculty of Science > School of Pharmacy (former - to 2024)
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health Faculty of Medicine and Health Sciences > Research Centres > Norwich Institute for Healthy Aging Faculty of Medicine and Health Sciences > Research Groups > Musculoskeletal Medicine Faculty of Medicine and Health Sciences > Research Groups > Nutrition and Preventive Medicine
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	30 Apr 2026 14:30
Last Modified:	02 May 2026 12:57
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102849
DOI:	10.1016/j.cell.2021.08.014

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