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

The COVID-19 Genomics UK (COG-UK) Consortium; Sanger Covid Team

doi:10.1016/j.cell.2021.08.014

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

The COVID-19 Genomics UK (COG-UK) Consortium
, Sanger Covid Team

Department of Medicine
EaStCHEM School of Chemistry, University of Edinburgh
Pennsylvania State University
Public Health Wales
University of Liverpool
University of Birmingham
Cardiff University
MRC-University of Glasgow Centre for Virus Research
University of Oxford
Royal Veterinary College University of London

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

171 Citas (Scopus)

Resumen

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.

Idioma original	Inglés
Páginas (desde-hasta)	5179-5188.e8
Publicación	Cell
Volumen	184
N.º	20
DOI	https://doi.org/10.1016/j.cell.2021.08.014
Estado	Publicada - 30 sep. 2021
Publicado de forma externa	Sí

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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, SARS-CoV-2, evolution, genomic epidemiology, genomics, recombination, variants",

author = "\{The COVID-19 Genomics UK (COG-UK) Consortium\} and \{Sanger Covid Team\} and 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 Loman, \{Nicholas J.\} and Connor, \{Thomas R.\} and Robertson, \{David L.\} and Pybus, \{Oliver G.\} and Andrew Rambaut and Robson, \{Samuel C.\} and Tanya Golubchi and \{Martinez Nunez\}, \{Rocio T.\} and Catherine Ludden and Sally Corden and Ian Johnston and David Bonsall and Smith, \{Colin P.\} and Awan, \{Ali R.\} and Giselda Bucca and \{Estee Torok\}, M. and Kordo Saeed and Prieto, \{Jacqui A.\} and Jackson, \{David K.\} and Hamilton, \{William L.\} and Snell, \{Luke B.\} and Catherine Moore and Harrison, \{Ewan M.\} and Sonia Goncalves and Jackson, \{Leigh M.\} and Goodfellow, \{Ian G.\} and Fairley, \{Derek J.\} and Loose, \{Matthew W.\} and Joanne Watkins and Rich Livett and Samuel Moses",

note = "Publisher Copyright: {\textcopyright} 2021 The Authors",

year = "2021",

month = sep,

day = "30",

doi = "10.1016/j.cell.2021.08.014",

language = "Ingl{\'e}s",

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AU - Jackson, Ben

AU - Boni, Maciej F.

AU - Bull, Matthew J.

AU - Colleran, Amy

AU - Colquhoun, Rachel M.

AU - Darby, Alistair C.

AU - Haldenby, Sam

AU - Hill, Verity

AU - Lucaci, Anita

AU - McCrone, John T.

AU - Nicholls, Samuel M.

AU - O’Toole, Áine

AU - Pacchiarini, Nicole

AU - Poplawski, Radoslaw

AU - Scher, Emily

AU - Todd, Flora

AU - Webster, Hermione J.

AU - Whitehead, Mark

AU - Wierzbicki, Claudia

AU - Loman, Nicholas J.

AU - Connor, Thomas R.

AU - Robertson, David L.

AU - Pybus, Oliver G.

AU - Rambaut, Andrew

AU - Robson, Samuel C.

AU - Golubchi, Tanya

AU - Martinez Nunez, Rocio T.

AU - Ludden, Catherine

AU - Corden, Sally

AU - Johnston, Ian

AU - Bonsall, David

AU - Smith, Colin P.

AU - Awan, Ali R.

AU - Bucca, Giselda

AU - Estee Torok, M.

AU - Saeed, Kordo

AU - Prieto, Jacqui A.

AU - Jackson, David K.

AU - Hamilton, William L.

AU - Snell, Luke B.

AU - Moore, Catherine

AU - Harrison, Ewan M.

AU - Goncalves, Sonia

AU - Jackson, Leigh M.

AU - Goodfellow, Ian G.

AU - Fairley, Derek J.

AU - Loose, Matthew W.

AU - Watkins, Joanne

AU - Livett, Rich

AU - Moses, Samuel

PY - 2021/9/30

Y1 - 2021/9/30

N2 - 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.

AB - 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.

KW - B.1.1.7

KW - SARS-CoV-2

KW - evolution

KW - genomic epidemiology

KW - genomics

KW - recombination

KW - variants

UR - https://www.scopus.com/pages/publications/85114700839

U2 - 10.1016/j.cell.2021.08.014

DO - 10.1016/j.cell.2021.08.014

M3 - Artículo

AN - SCOPUS:85114700839

SN - 0092-8674

VL - 184

SP - 5179-5188.e8

JO - Cell

JF - Cell

IS - 20

ER -

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

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