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 - Duarte Hernandez, Carlos Rene
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 - 2022/12/21
Y1 - 2022/12/21
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.
UR - http://www.scopus.com/inward/record.url?scp=85144598166&partnerID=8YFLogxK
U2 - 10.1126/sciadv.add7197
DO - 10.1126/sciadv.add7197
M3 - Journal article
C2 - 36542720
SN - 2375-2548
VL - 8
SP - eadd7197
JO - Science Advances
JF - Science Advances
IS - 51
M1 - eadd7197
ER -