@article{fd2c01a85ed84cc7ad669768ba204b0e,
title = "Generation and transmission of interlineage 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 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.",
keywords = "B.1.1.7, evolution, genomic epidemiology, genomics, recombination, SARS-CoV-2, variants",
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 Catherine Moore and Page, \{Andrew J.\} and Helen Adams and David Buck and Kay, \{Gemma L.\} and Samir Dervisevic and Meader, \{Emma J.\} and Jones, \{Christopher R.\} and Katie Jones and Carl Jones and Robert Davies and Williams, \{Charlotte A.\} and Sophie Jones and Chris Jackson and Taylor, \{Ben E.W.\} and Mather, \{Alison E.\} and Giri Shankar and Rachel Jones and Rachael Stanley and Smith, \{Kim S.\} and Danielle Leek and Themoula Charalampous and Jonathan Moore and Davidson, \{Rose K.\} and Lindsay Coupland and Rebecca Williams and Studholme, \{David J.\} and Eileen Gallagher and David Lee and Baker, \{David J.\} and Steven Rudder and Alp Aydin and \{The COVID-19 Genomics UK (COG-UK) Consortium\} and \{Sanger Covid Team\}",
note = "Data and code availability: All the code used to perform the analyses here is available at: https://github.com/COG-UK/UK-recombination-analysis",
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 = "Elsevier",
number = "20",
}