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

Mathematics

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

169 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 language	English
Pages (from-to)	5179-5188.e8
Journal	Cell
Volume	184
Issue number	20
DOIs	https://doi.org/10.1016/j.cell.2021.08.014
Publication status	Published - 30 Sep 2021

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.cell.2021.08.014

Cite this

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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, evolution, genomic epidemiology, genomics, recombination, SARS-CoV-2, 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 and Roberto Amato and Smith, \{Darren L.\} and Jeff Barrett and Aanensen, \{David M.\} and Curran, \{Martin D.\} and Surendra Parmar and Dinesh Aggarwal and Shepherd, \{James G.\} and Parker, \{Matthew D.\} and Sharon Glaysher and Matthew Bashton and Underwood, \{Anthony P.\} and Loveson, \{Katie F.\} and Carabelli, \{Alessandro M.\} and Templeton, \{Kate E.\} and Langford, \{Cordelia F.\} and John Sillitoe and Silva, \{Thushan I.de\} and Dennis Wang and Dominic Kwiatkowski and Justin O{\textquoteright}Grady and Simon Cottrell and Holden, \{Matthew T.G.\} and Thomson, \{Emma C.\} and Husam Osman and Monique Andersson and Chauhan, \{Anoop J.\} and Hassan-Ibrahim, \{Mohammed O.\} and Mara Lawniczak and Gupta, \{Ravi Kumar\} and Alex Alderton and Meera Chand and Chrystala Constantinidou and Meera Unnikrishnan and Hiscox, \{Julian A.\} and Steve Paterson and Inigo Martincorena and Volz, \{Erik M.\} and Page, \{Andrew J.\} and Bassett, \{Andrew R.\} and Ariani, \{Cristina V.\} and \{Spencer Chapman\}, \{Michael H.\} and Li, \{Kathy K.\} and Shah, \{Rajiv N.\} and Jesudason, \{Natasha G.\} and Yusri Taha and McHugh, \{Martin P.\} and Rebecca Dewar and Jahun, \{Aminu S.\} and Dorman, \{Matthew J.\}",

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

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 B.V.",

number = "20",

}

TY - JOUR

T1 - Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Sanger Covid Team

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

AU - Amato, Roberto

AU - Smith, Darren L.

AU - Barrett, Jeff

AU - Aanensen, David M.

AU - Curran, Martin D.

AU - Parmar, Surendra

AU - Aggarwal, Dinesh

AU - Shepherd, James G.

AU - Parker, Matthew D.

AU - Glaysher, Sharon

AU - Bashton, Matthew

AU - Underwood, Anthony P.

AU - Loveson, Katie F.

AU - Carabelli, Alessandro M.

AU - Templeton, Kate E.

AU - Langford, Cordelia F.

AU - Sillitoe, John

AU - Silva, Thushan I.de

AU - Wang, Dennis

AU - Kwiatkowski, Dominic

AU - O’Grady, Justin

AU - Cottrell, Simon

AU - Holden, Matthew T.G.

AU - Thomson, Emma C.

AU - Osman, Husam

AU - Andersson, Monique

AU - Chauhan, Anoop J.

AU - Hassan-Ibrahim, Mohammed O.

AU - Lawniczak, Mara

AU - Gupta, Ravi Kumar

AU - Alderton, Alex

AU - Chand, Meera

AU - Constantinidou, Chrystala

AU - Unnikrishnan, Meera

AU - Hiscox, Julian A.

AU - Paterson, Steve

AU - Martincorena, Inigo

AU - Volz, Erik M.

AU - Page, Andrew J.

AU - Bassett, Andrew R.

AU - Ariani, Cristina V.

AU - Spencer Chapman, Michael H.

AU - Li, Kathy K.

AU - Shah, Rajiv N.

AU - Jesudason, Natasha G.

AU - Taha, Yusri

AU - McHugh, Martin P.

AU - Dewar, Rebecca

AU - Jahun, Aminu S.

AU - Dorman, Matthew J.

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 - evolution

KW - genomic epidemiology

KW - genomics

KW - recombination

KW - SARS-CoV-2

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 - Article

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

Abstract

Keywords

UN SDGs

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