The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

ISARIC4C Investigators; Hannah Goldswain; Xiaofeng Dong; Rebekah Penrice-Randal; Muhannad Alruwaili; Ghada T. Shawli; Tessa Prince; Maia Kavanagh Williamson; Jayna Raghwani; Nadine Randle; Benjamin Jones; I’ah Donovan-Banfield; Francisco J. Salguero; Julia A. Tree; Yper Hall; Catherine Hartley; Maximilian Erdmann; James Bazire; Tuksin Jearanaiwitayakul; Malcolm G. Semple; Peter J. M. Openshaw; J. Kenneth  Baillie; Stevan R. Emmett; Paul Digard; David A. Matthews; Lance Turtle; Alistair C. Darby; Andrew D. Davidson; Miles W. Carroll; Julian A. Hiscox

doi:10.1186/s13059-023-02881-5

The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

ISARIC4C Investigators, Hannah Goldswain, Xiaofeng Dong, Rebekah Penrice-Randal, Muhannad Alruwaili, Ghada T. Shawli, Tessa Prince, Maia Kavanagh Williamson, Jayna Raghwani, Nadine Randle, Benjamin Jones, I’ah Donovan-Banfield, Francisco J. Salguero, Julia A. Tree, Yper Hall, Catherine Hartley, Maximilian Erdmann, James Bazire, Tuksin Jearanaiwitayakul, Malcolm G. SemplePeter J. M. Openshaw, J. Kenneth Baillie, Stevan R. Emmett, Paul Digard, David A. Matthews, Lance Turtle, Alistair C. Darby, Andrew D. Davidson, Miles W. Carroll, Julian A. Hiscox^*

^*Corresponding author for this work

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

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Abstract

Background: The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure.

Results: Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323.

Conclusions: These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.

Original language	English
Article number	47
Number of pages	23
Journal	Genome Biology
Volume	24
DOIs	https://doi.org/10.1186/s13059-023-02881-5
Publication status	Published - 13 Mar 2023

Bibliographical note

Funding:
This work was funded by U.S. Food and Drug Administration Medical Countermeasures Initiative contract (75F40120C00085) to JAH with Co-Is, MWC, ADD, AD, DAM, MGS, and LT. The article reflects the views of the authors and does not represent the views or policies of the FDA. The NHP work was funded by the Coalition of Epidemic Preparedness Innovations (CEPI) and the Medical Research Council Project CV220-060, “Development of an NHP model of infection and ADE with COVID-19 (SARS-CoV-2) both awarded to MWC. This work was also supported by the MRC (MR/W005611/1) G2P-UK: A national virology consortium to address phenotypic consequences of SARS-CoV-2 genomic variation (co-Is ADD and JAH). JAH is also funded by the Centre of Excellence in Infectious Diseases Research (CEIDR) and the Alder Hey Charity. The ISARIC4C sample collection and sequencing in this study was supported by grants from the Medical Research Council (grant MC_PC_19059), the National Institute for Health Research (NIHR; award CO-CIN-01), and the Medical Research Council (MRC; grant MC_PC_19059). JAH, MGS, MWC, and LT are supported by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with the UK Health Security Agency (UKHSA), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford (award 200907). LT is supported by a Wellcome Trust fellowship [205228/Z/16/Z]. PD and JKB acknowledge Institute Strategic Programme grant (no. BB/P013740/1) from the BBSRC.

Keywords

SARS-CoV-2
Evolution
Selection
Spike protein
Polymerase
NSP12
COVID-19
P323L

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ISARIC4C Investigators, Goldswain, H., Dong, X., Penrice-Randal, R., Alruwaili, M., Shawli, G. T., Prince, T., Williamson, M. K., Raghwani, J., Randle, N., Jones, B., Donovan-Banfield, I., Salguero, F. J., Tree, J. A., Hall, Y., Hartley, C., Erdmann, M., Bazire, J., Jearanaiwitayakul, T., ... Hiscox, J. A. (2023). The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection. Genome Biology, 24, Article 47. https://doi.org/10.1186/s13059-023-02881-5

@article{6a49bd826306478296833b9af5a58e32,

title = "The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection",

abstract = "Background: The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure.Results: Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323.Conclusions: These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.",

keywords = "SARS-CoV-2, Evolution, Selection, Spike protein, Polymerase, NSP12, COVID-19, P323L",

author = "{ISARIC4C Investigators} and Hannah Goldswain and Xiaofeng Dong and Rebekah Penrice-Randal and Muhannad Alruwaili and Shawli, {Ghada T.} and Tessa Prince and Williamson, {Maia Kavanagh} and Jayna Raghwani and Nadine Randle and Benjamin Jones and I{\textquoteright}ah Donovan-Banfield and Salguero, {Francisco J.} and Tree, {Julia A.} and Yper Hall and Catherine Hartley and Maximilian Erdmann and James Bazire and Tuksin Jearanaiwitayakul and Semple, {Malcolm G.} and Openshaw, {Peter J. M.} and Baillie, {J. Kenneth} and Emmett, {Stevan R.} and Paul Digard and Matthews, {David A.} and Lance Turtle and Darby, {Alistair C.} and Davidson, {Andrew D.} and Carroll, {Miles W.} and Hiscox, {Julian A.} and Christopher Green",

note = "Funding: This work was funded by U.S. Food and Drug Administration Medical Countermeasures Initiative contract (75F40120C00085) to JAH with Co-Is, MWC, ADD, AD, DAM, MGS, and LT. The article reflects the views of the authors and does not represent the views or policies of the FDA. The NHP work was funded by the Coalition of Epidemic Preparedness Innovations (CEPI) and the Medical Research Council Project CV220-060, “Development of an NHP model of infection and ADE with COVID-19 (SARS-CoV-2) both awarded to MWC. This work was also supported by the MRC (MR/W005611/1) G2P-UK: A national virology consortium to address phenotypic consequences of SARS-CoV-2 genomic variation (co-Is ADD and JAH). JAH is also funded by the Centre of Excellence in Infectious Diseases Research (CEIDR) and the Alder Hey Charity. The ISARIC4C sample collection and sequencing in this study was supported by grants from the Medical Research Council (grant MC_PC_19059), the National Institute for Health Research (NIHR; award CO-CIN-01), and the Medical Research Council (MRC; grant MC_PC_19059). JAH, MGS, MWC, and LT are supported by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with the UK Health Security Agency (UKHSA), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford (award 200907). LT is supported by a Wellcome Trust fellowship [205228/Z/16/Z]. PD and JKB acknowledge Institute Strategic Programme grant (no. BB/P013740/1) from the BBSRC.",

year = "2023",

month = mar,

day = "13",

doi = "10.1186/s13059-023-02881-5",

language = "English",

volume = "24",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central",

}

ISARIC4C Investigators, Goldswain, H, Dong, X, Penrice-Randal, R, Alruwaili, M, Shawli, GT, Prince, T, Williamson, MK, Raghwani, J, Randle, N, Jones, B, Donovan-Banfield, I, Salguero, FJ, Tree, JA, Hall, Y, Hartley, C, Erdmann, M, Bazire, J, Jearanaiwitayakul, T, Semple, MG, Openshaw, PJM, Baillie, JK, Emmett, SR, Digard, P, Matthews, DA, Turtle, L, Darby, AC, Davidson, AD, Carroll, MW & Hiscox, JA 2023, 'The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection', Genome Biology, vol. 24, 47. https://doi.org/10.1186/s13059-023-02881-5

TY - JOUR

T1 - The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

AU - ISARIC4C Investigators

AU - Goldswain, Hannah

AU - Dong, Xiaofeng

AU - Penrice-Randal, Rebekah

AU - Alruwaili, Muhannad

AU - Shawli, Ghada T.

AU - Prince, Tessa

AU - Williamson, Maia Kavanagh

AU - Raghwani, Jayna

AU - Randle, Nadine

AU - Jones, Benjamin

AU - Donovan-Banfield, I’ah

AU - Salguero, Francisco J.

AU - Tree, Julia A.

AU - Hall, Yper

AU - Hartley, Catherine

AU - Erdmann, Maximilian

AU - Bazire, James

AU - Jearanaiwitayakul, Tuksin

AU - Semple, Malcolm G.

AU - Openshaw, Peter J. M.

AU - Baillie, J. Kenneth

AU - Emmett, Stevan R.

AU - Digard, Paul

AU - Matthews, David A.

AU - Turtle, Lance

AU - Darby, Alistair C.

AU - Davidson, Andrew D.

AU - Carroll, Miles W.

AU - Hiscox, Julian A.

AU - Green, Christopher

N1 - Funding: This work was funded by U.S. Food and Drug Administration Medical Countermeasures Initiative contract (75F40120C00085) to JAH with Co-Is, MWC, ADD, AD, DAM, MGS, and LT. The article reflects the views of the authors and does not represent the views or policies of the FDA. The NHP work was funded by the Coalition of Epidemic Preparedness Innovations (CEPI) and the Medical Research Council Project CV220-060, “Development of an NHP model of infection and ADE with COVID-19 (SARS-CoV-2) both awarded to MWC. This work was also supported by the MRC (MR/W005611/1) G2P-UK: A national virology consortium to address phenotypic consequences of SARS-CoV-2 genomic variation (co-Is ADD and JAH). JAH is also funded by the Centre of Excellence in Infectious Diseases Research (CEIDR) and the Alder Hey Charity. The ISARIC4C sample collection and sequencing in this study was supported by grants from the Medical Research Council (grant MC_PC_19059), the National Institute for Health Research (NIHR; award CO-CIN-01), and the Medical Research Council (MRC; grant MC_PC_19059). JAH, MGS, MWC, and LT are supported by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with the UK Health Security Agency (UKHSA), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford (award 200907). LT is supported by a Wellcome Trust fellowship [205228/Z/16/Z]. PD and JKB acknowledge Institute Strategic Programme grant (no. BB/P013740/1) from the BBSRC.

PY - 2023/3/13

Y1 - 2023/3/13

N2 - Background: The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure.Results: Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323.Conclusions: These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.

AB - Background: The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure.Results: Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323.Conclusions: These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.

KW - SARS-CoV-2

KW - Evolution

KW - Selection

KW - Spike protein

KW - Polymerase

KW - NSP12

KW - COVID-19

KW - P323L

U2 - 10.1186/s13059-023-02881-5

DO - 10.1186/s13059-023-02881-5

M3 - Article

SN - 1474-7596

VL - 24

JO - Genome Biology

JF - Genome Biology

M1 - 47

ER -

The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

Abstract

Bibliographical note

Keywords

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