@article{12152139c462488eb2489c3342e16ad3,
title = "Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic",
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{\textquoteright}s set of mutations.",
keywords = "SARS-CoV-2, evolution, recombination, genomic epidemiology, B.1.1.7, variants, genomics, Base Sequence/genetics, Genome, Viral, Pandemics, SARS-CoV-2/genetics, Gene Frequency, Humans, Genotype, Phylogeny, Computational Biology/methods, United Kingdom/epidemiology, COVID-19/epidemiology, Recombination, Genetic, Polymorphism, Single Nucleotide, Whole Genome Sequencing/methods, Mutation",
author = "Ben Jackson and Boni, {Maciej F.} and Bull, {Matthew J.} and Amy Colleran and Colquhoun, {Rachel M.} and Darby, {Alistair C.} and Sam Haldenby and Verity Hill and Anita Lucaci and McCrone, {John T.} and Nicholls, {Samuel M.} and {\'A}ine O{\textquoteright}toole and Nicole Pacchiarini and Radoslaw Poplawski and Emily Scher and Flora Todd and Webster, {Hermione J.} and Mark Whitehead and Claudia Wierzbicki and {The COVID-19 Genomics UK (COG-UK) Consortium} and Loman, {Nicholas J.} and Connor, {Thomas R.} and Robertson, {David L.} and Pybus, {Oliver G.} and Andrew Rambaut and Matthew Bashton and Darren Smith and Andrew Nelson and Greg Young and Clare McCann",
note = "Matthew Bashton, Andrew Nelson, Darren Smith, Greg Young are members of the COVID-19 Genomics UK (COG-UK) consortium. 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. ",
year = "2021",
month = sep,
day = "30",
doi = "10.1016/j.cell.2021.08.014",
language = "English",
volume = "184",
pages = "5179--5188.e8",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "20",
}