{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:59:42Z","timestamp":1789088382569,"version":"build-2803163510"},"posted":{"date-parts":[[2025,5,13]]},"group-title":"Microbiology","reference-count":43,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T00:00:00Z","timestamp":1747094400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,13]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>The emergence of SARS-CoV-2 variants has necessitated continuous updating of vaccines. In contrast, antivirals remained effective as they target conserved viral proteins that are essential for the viral life cycle. However, several mutations in SARS-CoV-2 that may affect the efficacy of United States (US) Food and Drug Administration (FDA)-approved antivirals have been recently identified. Detecting drug-resistant SARS-CoV-2 mutants and investigating their escape mechanism(s) are critical to guide the selection of effective antiviral therapies. In this study, we constructed an attenuated recombinant (r)SARS-CoV-2 lacking the open reading frame (ORF) proteins 3a and 7b but expressing nanoluciferase (Nluc), rSARS-CoV-2 \u03943a7b-Nluc, to facilitate tracking viral infection. Using this virus, we selected drug-resistant mutants to the main viral protease (Mpro) inhibitor nirmatrelvir. After passaging \u03943a7b-Nluc 10 times in the presence of increasing concentrations of nirmatrelvir, a virus population with enhanced resistance was selected. We identified two non-synonymous mutations (L50F and R188G) in Mpro, encoded by the non-structural protein 5 (NSP5) gene. Using reverse genetics, we generated rSARS-CoV-2 \u03943a7b-Nluc containing the identified L50F and R188G mutations, individually or in combination, and assessed their contribution to nirmatrelvir resistance. Our results indicate that both mutations are involved in escaping from nirmatrelvir. Altogether, our results demonstrate the feasibility of using rSARS-CoV-2 \u03943a7b-Nluc variant to identify and validate mutations that confer resistance to FDA-approved antiviral drugs without the concern of conducting gain of function (GoF) experiments with wild-type (WT) forms of SARS-CoV-2.<\/jats:p>\n                <jats:sec>\n                  <jats:title>IMPORTANCE<\/jats:title>\n                  <jats:p>Small-molecule antiviral drugs have been used for the treatment of SARS-CoV-2 infections. However, drug-resistant SARS-CoV-2 mutants to currently US FDA-approved Mpro targeting antivirals have been identified. Information on SARS-CoV-2 escape mutants and mutations affecting the antiviral activity of licensed antivirals remain limited. In this study, we developed a nanoluciferase (Nluc)-expressing attenuated recombinant (r)SARS-CoV-2 lacking the ORF 3a and 7b proteins (\u03943a7b-Nluc) to identify nirmatrelvir resistant mutants without the biosafety concerns associated with gain-of-function (GoF) research using wild-type (WT) SARS-CoV-2. Using \u03943a7b-Nluc, we have selected variants with reduced sensitivity to nirmatrelvir that were validated by the generation of rSARS-CoV-2 \u03943a7b-Nluc containing the candidate L50F and R188G mutations in Mpro. These results demonstrate the feasibility of using rSARS-CoV-2 \u03943a7b-Nluc to safely identify and validate drug-resistant mutants overcoming concerns originating from adaptation studies using WT SARS-CoV-2.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.05.09.653029","type":"posted-content","created":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T23:45:12Z","timestamp":1747179912000},"source":"Crossref","is-referenced-by-count":3,"title":["A luminescent attenuated SARS-CoV-2 for the identification and validation of drug-resistant mutants"],"prefix":"10.64898","author":[{"given":"Yao","family":"Ma","sequence":"first","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1934-9494","authenticated-orcid":false,"given":"Chengjin","family":"Ye","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed Magdy","family":"Khalil","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"},{"name":"Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara H.","family":"Mahmoud","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"},{"name":"Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth B.","family":"Sobolik","sequence":"additional","affiliation":[{"name":"Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7443-0527","authenticated-orcid":false,"given":"Alexander L","family":"Greninger","sequence":"additional","affiliation":[{"name":"Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esteban","family":"Castro","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel","family":"Jackson","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahmoud","family":"Bayoumi","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"},{"name":"Virology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2034-2107","authenticated-orcid":false,"given":"Richard K","family":"Plemper","sequence":"additional","affiliation":[{"name":"Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7084-0804","authenticated-orcid":false,"given":"Luis","family":"Martinez-Sobrido","sequence":"additional","affiliation":[{"name":"Texas Biomedical Research Institute, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041121373882000_2025.05.09.653029v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2024.03.008"},{"key":"2026041121373882000_2025.05.09.653029v1.2","doi-asserted-by":"crossref","unstructured":"Davies NG , Abbott S , Barnard RC , Jarvis CI , Kucharski AJ , Munday JD , Pearson CAB , Russell TW , Tully DC , Washburne AD , Wenseleers T , Gimma A , Waites W , Wong KLM , van Zandvoort K , Silverman JD , Group CC-W , Consortium C-GU , Diaz-Ordaz K , Keogh R , Eggo RM , Funk S , Jit M , Atkins KE , Edmunds WJ . 2021. 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