Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

Yuyong Zhou; Karen Anbro Gammeltoft; Line Abildgaard Ryberg; Long V. Pham; Helena Damtoft Tjørnelund; Alekxander Binderup; Carlos Rene Duarte Hernandez; Carlota Fernandez-Antunez; Anna Offersgaard; Ulrik Fahnøe; Günther Herbert Johannes Peters; Santseharay Ramirez; Jens Bukh; Judith Margarete Gottwein

doi:10.1126/sciadv.add7197

Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

Yuyong Zhou
, Karen Anbro Gammeltoft
, Line Abildgaard Ryberg
, Long V. Pham
, Helena Damtoft Tjørnelund
, Alekxander Binderup
, Carlos Rene Duarte Hernandez
, Carlota Fernandez-Antunez
, Anna Offersgaard
, Ulrik Fahnøe
, Günther Herbert Johannes Peters
, Santseharay Ramirez
, Jens Bukh
, Judith Margarete Gottwein^*

^*Corresponding author for this work

Department of Chemistry

University of Copenhagen

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir in cell culture. Resistant variants harbored combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetics revealed that E166V and L50F + E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F + E166V decreased replication and Mpro activity, L50F and L50F + E166V variants had high fitness in the infectious system. Naturally occurring L50F compensated for fitness cost of E166V and promoted viral escape. Molecular dynamics simulations revealed that E166V and L50F + E166V weakened nirmatrelvir-Mpro binding. Polymerase inhibitor remdesivir and monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, and combination with nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatments with efficacy against SARS-CoV-2 and emerging sarbecoviruses.

Original language	English
Article number	eadd7197
Journal	Science Advances
Volume	8
Issue number	51
Number of pages	14
ISSN	2375-2548
DOIs	https://doi.org/10.1126/sciadv.add7197
Publication status	Published - 2022

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Zhou, Y., Gammeltoft, K. A., Ryberg, L. A., Pham, L. V., Tjørnelund, H. D., Binderup, A., Hernandez, C. R. D., Fernandez-Antunez, C., Offersgaard, A., Fahnøe, U., Peters, G. H. J., Ramirez, S., Bukh, J., & Gottwein, J. M. (2022). Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system. Science Advances, 8(51), Article eadd7197. https://doi.org/10.1126/sciadv.add7197

@article{3f6c81f693ab4100b45be62a8282a572,

title = "Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system",

abstract = "The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir in cell culture. Resistant variants harbored combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetics revealed that E166V and L50F + E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F + E166V decreased replication and Mpro activity, L50F and L50F + E166V variants had high fitness in the infectious system. Naturally occurring L50F compensated for fitness cost of E166V and promoted viral escape. Molecular dynamics simulations revealed that E166V and L50F + E166V weakened nirmatrelvir-Mpro binding. Polymerase inhibitor remdesivir and monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, and combination with nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatments with efficacy against SARS-CoV-2 and emerging sarbecoviruses.",

author = "Yuyong Zhou and Gammeltoft, \{Karen Anbro\} and Ryberg, \{Line Abildgaard\} and Pham, \{Long V.\} and Tj{\o}rnelund, \{Helena Damtoft\} and Alekxander Binderup and Hernandez, \{Carlos Rene Duarte\} and Carlota Fernandez-Antunez and Anna Offersgaard and Ulrik Fahn{\o}e and Peters, \{G{\"u}nther Herbert Johannes\} and Santseharay Ramirez and Jens Bukh and Gottwein, \{Judith Margarete\}",

note = "Publisher Copyright: Copyright {\textcopyright} 2022 The Authors, some rights reserved.",

year = "2022",

doi = "10.1126/sciadv.add7197",

language = "English",

volume = "8",

journal = "Science Advances",

issn = "2375-2548",

publisher = "American Association for the Advancement of Science",

number = "51",

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Zhou, Y, Gammeltoft, KA, Ryberg, LA, Pham, LV, Tjørnelund, HD, Binderup, A, Hernandez, CRD, Fernandez-Antunez, C, Offersgaard, A, Fahnøe, U, Peters, GHJ, Ramirez, S, Bukh, J & Gottwein, JM 2022, 'Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system', Science Advances, vol. 8, no. 51, eadd7197. https://doi.org/10.1126/sciadv.add7197

TY - JOUR

T1 - Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

AU - Zhou, Yuyong

AU - Gammeltoft, Karen Anbro

AU - Ryberg, Line Abildgaard

AU - Pham, Long V.

AU - Tjørnelund, Helena Damtoft

AU - Binderup, Alekxander

AU - Hernandez, Carlos Rene Duarte

AU - Fernandez-Antunez, Carlota

AU - Offersgaard, Anna

AU - Fahnøe, Ulrik

AU - Peters, Günther Herbert Johannes

AU - Ramirez, Santseharay

AU - Bukh, Jens

AU - Gottwein, Judith Margarete

PY - 2022

Y1 - 2022

N2 - The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir in cell culture. Resistant variants harbored combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetics revealed that E166V and L50F + E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F + E166V decreased replication and Mpro activity, L50F and L50F + E166V variants had high fitness in the infectious system. Naturally occurring L50F compensated for fitness cost of E166V and promoted viral escape. Molecular dynamics simulations revealed that E166V and L50F + E166V weakened nirmatrelvir-Mpro binding. Polymerase inhibitor remdesivir and monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, and combination with nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatments with efficacy against SARS-CoV-2 and emerging sarbecoviruses.

AB - The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir in cell culture. Resistant variants harbored combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetics revealed that E166V and L50F + E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F + E166V decreased replication and Mpro activity, L50F and L50F + E166V variants had high fitness in the infectious system. Naturally occurring L50F compensated for fitness cost of E166V and promoted viral escape. Molecular dynamics simulations revealed that E166V and L50F + E166V weakened nirmatrelvir-Mpro binding. Polymerase inhibitor remdesivir and monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, and combination with nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatments with efficacy against SARS-CoV-2 and emerging sarbecoviruses.

U2 - 10.1126/sciadv.add7197

DO - 10.1126/sciadv.add7197

M3 - Journal article

C2 - 36542720

AN - SCOPUS:85144598166

SN - 2375-2548

VL - 8

JO - Science Advances

JF - Science Advances

IS - 51

M1 - eadd7197

ER -

Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

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