{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T02:13:40Z","timestamp":1793240020782,"version":"4.5.0"},"reference-count":58,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"51","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sci. Adv."],"published-print":{"date-parts":[[2022,12,23]]},"abstract":"<jats:p>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\u00a0+\u00a0E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F\u00a0+\u00a0E166V decreased replication and Mpro activity, L50F and L50F\u00a0+\u00a0E166V 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\u00a0+\u00a0E166V 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.<\/jats:p>","DOI":"10.1126\/sciadv.add7197","type":"journal-article","created":{"date-parts":[[2022,12,21]],"date-time":"2022-12-21T13:58:26Z","timestamp":1671631106000},"source":"Crossref","is-referenced-by-count":204,"title":["Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system"],"prefix":"10.1126","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6330-3170","authenticated-orcid":true,"given":"Yuyong","family":"Zhou","sequence":"first","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0469-767X","authenticated-orcid":true,"given":"Karen Anbro","family":"Gammeltoft","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5301-0232","authenticated-orcid":true,"given":"Line Abildgaard","family":"Ryberg","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Long V.","family":"Pham","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8648-3266","authenticated-orcid":true,"given":"Helena Damtoft","family":"Tj\u00f8rnelund","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7344-433X","authenticated-orcid":true,"given":"Alekxander","family":"Binderup","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos Rene","family":"Duarte Hernandez","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlota","family":"Fernandez-Antunez","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7748-2840","authenticated-orcid":true,"given":"Anna","family":"Offersgaard","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2527-5751","authenticated-orcid":true,"given":"Ulrik","family":"Fahn\u00f8e","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9754-2663","authenticated-orcid":true,"given":"G\u00fcnther Herbert Johannes","family":"Peters","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3699-1814","authenticated-orcid":true,"given":"Santseharay","family":"Ramirez","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7815-4806","authenticated-orcid":true,"given":"Jens","family":"Bukh","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2805-0256","authenticated-orcid":true,"given":"Judith Margarete","family":"Gottwein","sequence":"additional","affiliation":[{"name":"Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital\u2013Hvidovre, 2650 Hvidovre, Denmark."},{"name":"CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_3_2_2","unstructured":"COVID-19: EMA recommends conditional marketing authorisation for Paxlovid | European Medicines Agency;www.ema.europa.eu\/en\/news\/covid-19-ema-recommends-conditional-marketing-authorisation-paxlovid."},{"key":"e_1_3_3_3_2","unstructured":"Fact sheet for healthcare providers: Emergency use authorization for Paxlovid TM highlights of emergency use authorization;www.fda.gov\/media\/155050\/download."},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2118542"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2116044"},{"key":"e_1_3_3_6_2","unstructured":"Fact sheet for patients and caregivers emergency use authorization (EUA) of Lagevrio\u2122 (molnupiravir) capsules for coronavirus disease 2019 (COVID-19);www.fda.gov\/media\/155055\/download."},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2116846"},{"key":"e_1_3_3_8_2","unstructured":"Veklury | European Medicines Agency;www.ema.europa.eu\/en\/medicines\/human\/EPAR\/veklury."},{"key":"e_1_3_3_9_2","unstructured":"Fact sheet for health care providers emergency use authorization (EUA) of Veklury\u00ae (remdesivir);www.samc.com\/assets\/documents\/covid19\/nursing\/remdesivir_eua-hcp-fact-sheet-8-2020.pdf."},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2007764"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04594-4"},{"key":"e_1_3_3_12_2","unstructured":"Fact sheet for healthcare providers: Emergency use authorization for bebtelovimab highlights of emergency use authorization (EUA). These highlights of the EUA do not include all the information needed to use BEBTELOVIMAB under the EUA;www.fda.gov\/media\/156152\/download."},{"key":"e_1_3_3_13_2","first-page":"95","article-title":"Effect of oral nirmatrelvir on long COVID Symptoms: 4 cases and rationale for systematic studies","volume":"7","author":"Peluso M. J.","year":"2022","unstructured":"M. J.\u00a0Peluso, K.\u00a0Anglin, M. S.\u00a0Durstenfeld, J. N.\u00a0Martin, J. D.\u00a0Kelly, P. Y.\u00a0Hsue, T. J.\u00a0Henrich, S. G.\u00a0Deeks,Effect of oral nirmatrelvir on long COVID Symptoms: 4 cases and rationale for systematic studies. Pathog. Immun.7,95\u2013103 (2022).","journal-title":"Pathog. Immun."},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2018.07.020"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00097-21"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02680-20"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl4784"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.3390\/v14020172"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2005.09.012"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.77433"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscombsci.0c00058"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep20918"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2009.12.4272"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abq7360"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMc2206449"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMc2205944"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-93361-y"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.3390\/v13102082"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines10010075"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines9070706"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-020-0356-z"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1007\/s13238-021-00883-2"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1021\/acsinfecdis.1c00237"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks375"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/0005-2728(92)90081-C"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1021\/ct300400x"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4067"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21367"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23067"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20291"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.softx.2015.06.001"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.328693"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1080\/00268978300102851"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04464-z"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb3405"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23073507"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19662-4"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1039\/D0SC02823A"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1039\/D1RA08752E"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M310875200"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M502556200"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1093\/jb\/mvm246"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1039\/D1CC01449H"}],"container-title":["Science Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.science.org\/doi\/pdf\/10.1126\/sciadv.add7197","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T17:36:09Z","timestamp":1704821769000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.science.org\/doi\/10.1126\/sciadv.add7197"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,23]]},"references-count":58,"journal-issue":{"issue":"51","published-print":{"date-parts":[[2022,12,23]]}},"alternative-id":["10.1126\/sciadv.add7197"],"URL":"https:\/\/doi.org\/10.1126\/sciadv.add7197","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.06.06.494921","asserted-by":"object"}]},"ISSN":["2375-2548"],"issn-type":[{"value":"2375-2548","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,23]]},"article-number":"eadd7197"}}