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

The COVID-19 Genomics UK (COG-UK) consortium

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)5179-5188.e8
JournalCell
Volume184
Issue number20
DOIs
Publication statusPublished - 30 Sep 2021
Externally publishedYes

Bibliographical note

Funding Information:
The authors thank two anonymous reviewers for comments on the manuscript. The COG-UK Consortium is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. O.G.P. was supported by the Oxford Martin School. J.T.M. R.M.C. N.J.L. and A.R. acknowledge the support of the Wellcome Trust (Collaborators Award 206298/Z/17/Z ? ARTIC network). D.L.R. acknowledges the support of the MRC (MC_UU_12014/12) and the Wellcome Trust (220977/Z/20/Z). E.S. and A.R. are supported by the European Research Council (grant agreement no. 725422 ? ReservoirDOCS). T.R.C. and N.J.L. acknowledge the support of the MRC, which provided the funding for the MRC CLIMB infrastructure used to analyze, store, and share the UK sequencing dataset (MR/L015080/1 and MR/T030062/1). The samples sequenced in Wales were sequenced partly using funding provided by the Welsh Government. Conceptualization, A.R. M.F.B. O.G.P. and B.J.; data curation, M.J.B. N.P. R.M.C. A.C. A.C.D. S.H. A.L. N.P. F.T. H.J.W. M.W. and C.W.; formal analysis, B.J.; interpretation, A.R. M.F.B. O.G.P. B.J. and J.T.M.; funding acquisition, A.R. T.R.C. N.J.L. O.G.P. and A.C.D.; resources, T.R.C. S.M.N. R.P. N.J.L. and R.M.C.; software, M.F.B. A.O.?T. E.S. B.J. and M.J.B.; visualization, B.J. A.O.?T. and V.H.; writing ? original draft, B.J. M.F.B. O.G.P. A.R. and D.L.R.; writing ? review and editing, all authors. The authors declare no competing interests. One or more of the authors of this paper self-identifies as living with a disability. The author list of this paper includes contributors from the location where the research was conducted who participated in the data collection, design, analysis, and/or interpretation of the work.

Funding Information:
The authors thank two anonymous reviewers for comments on the manuscript. The COG-UK Consortium is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (MC_PC_19027), and Genome Research Limited , operating as the Wellcome Sanger Institute . O.G.P. was supported by the Oxford Martin School . J.T.M., R.M.C., N.J.L., and A.R. acknowledge the support of the Wellcome Trust (Collaborators Award 206298/Z/17/Z – ARTIC network ). D.L.R. acknowledges the support of the MRC ( MC_UU_12014/12 ) and the Wellcome Trust ( 220977/Z/20/Z ). E.S. and A.R. are supported by the European Research Council (grant agreement no. 725422 – ReservoirDOCS ). T.R.C. and N.J.L. acknowledge the support of the MRC , which provided the funding for the MRC CLIMB infrastructure used to analyze, store, and share the UK sequencing dataset ( MR/L015080/1 and MR/T030062/1 ). The samples sequenced in Wales were sequenced partly using funding provided by the Welsh Government .

Publisher Copyright:
© 2021 The Authors

Keywords

  • B.1.1.7
  • SARS-CoV-2
  • evolution
  • genomic epidemiology
  • genomics
  • recombination
  • variants

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