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

Ben Jackson; Maciej F. Boni; Matthew J. Bull; Amy Colleran; Rachel M. Colquhoun; Alistair C. Darby; Sam Haldenby; Verity Hill; Anita Lucaci; John T. McCrone; Samuel M. Nicholls; Áine O’Toole; Nicole Pacchiarini; Radoslaw Poplawski; Emily Scher; Flora Todd; Hermione J. Webster; Mark Whitehead; Claudia Wierzbicki; Nicholas J. Loman; Thomas R. Connor; David L. Robertson; Oliver G. Pybus; Andrew Rambaut; Samuel C. Robson; Tanya Golubchi; Rocio T. Martinez Nunez; Catherine Ludden; Sally Corden; Ian Johnston; David Bonsall; Colin P. Smith; Ali R. Awan; Giselda Bucca; M. Estee Torok; Kordo Saeed; Jacqui A. Prieto; David K. Jackson; William L. Hamilton; Luke B. Snell; Catherine Moore; Ewan M. Harrison; Sonia Goncalves; Leigh M. Jackson; Ian G. Goodfellow; Derek J. Fairley; Matthew W. Loose; Sally Forrest; Adam Westhorpe; Jonathan Ball

doi:10.1016/j.cell.2021.08.014

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

Ben Jackson, Maciej F. Boni, Matthew J. Bull, Amy Colleran, Rachel M. Colquhoun, Alistair C. Darby, Sam Haldenby, Verity Hill, Anita Lucaci, John T. McCrone, Samuel M. Nicholls, Áine O’Toole, Nicole Pacchiarini, Radoslaw Poplawski, Emily Scher, Flora Todd, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Nicholas J. LomanThomas R. Connor, David L. Robertson, Oliver G. Pybus, Andrew Rambaut, Samuel C. Robson, Tanya Golubchi, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Leigh M. Jackson, Ian G. Goodfellow, Derek J. Fairley, Matthew W. Loose, Sally Forrest, Adam Westhorpe, Jonathan Ball

Liverpool School of Tropical Medicine

Research output: Contribution to journal › Article › peer-review

164 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 Sept 2021

Keywords

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

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Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R. M., Darby, A. C., Haldenby, S., Hill, V., Lucaci, A., McCrone, J. T., Nicholls, S. M., O’Toole, Á., Pacchiarini, N., Poplawski, R., Scher, E., Todd, F., Webster, H. J., Whitehead, M., Wierzbicki, C., ... Ball, J. (2021). Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179-5188.e8. https://doi.org/10.1016/j.cell.2021.08.014

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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 = "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 Sally Forrest and Adam Westhorpe and Jonathan Ball",

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",

}

Jackson, B, Boni, MF, Bull, MJ, Colleran, A, Colquhoun, RM, Darby, AC, Haldenby, S, Hill, V, Lucaci, A, McCrone, JT, Nicholls, SM, O’Toole, Á, Pacchiarini, N, Poplawski, R, Scher, E, Todd, F, Webster, HJ, Whitehead, M, Wierzbicki, C, Loman, NJ, Connor, TR, Robertson, DL, Pybus, OG, Rambaut, A, Robson, SC, Golubchi, T, Martinez Nunez, RT, Ludden, C, Corden, S, Johnston, I, Bonsall, D, Smith, CP, Awan, AR, Bucca, G, Estee Torok, M, Saeed, K, Prieto, JA, Jackson, DK, Hamilton, WL, Snell, LB, Moore, C, Harrison, EM, Goncalves, S, Jackson, LM, Goodfellow, IG, Fairley, DJ, Loose, MW, Forrest, S, Westhorpe, A & Ball, J 2021, 'Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic', Cell, vol. 184, no. 20, pp. 5179-5188.e8. https://doi.org/10.1016/j.cell.2021.08.014

TY - JOUR

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

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 - Forrest, Sally

AU - Westhorpe, Adam

AU - Ball, Jonathan

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

U2 - 10.1016/j.cell.2021.08.014

DO - 10.1016/j.cell.2021.08.014

M3 - Article

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

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