{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T06:40:47Z","timestamp":1791614447089,"version":"4.3.4"},"reference-count":21,"publisher":"American Medical Association (AMA)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JAMA Netw Open"],"abstract":"<jats:sec id=\"ab-zoi230727-4\"><jats:title>Importance<\/jats:title><jats:p>Nirmatrelvir-ritonavir is an oral antiviral medication that improves outcomes in SARS-CoV-2 infections. However, there is concern that antiviral resistance will develop and that these viruses could be selected for after treatment.<\/jats:p><\/jats:sec><jats:sec id=\"ab-zoi230727-5\"><jats:title>Objective<\/jats:title><jats:p>To determine the prevalence of low-frequency SARS-CoV-2 variants in patient samples that could be selected for by nirmatrelvir-ritonavir.<\/jats:p><\/jats:sec><jats:sec id=\"ab-zoi230727-6\"><jats:title>Design, Setting, and Participants<\/jats:title><jats:p>This retrospective cohort study was conducted at 4 laboratories that serve community hospitals, academic tertiary care centers, and COVID-19 assessment centers in Ontario, Canada. Participants included symptomatic or asymptomatic patients who tested positive for SARS-CoV-2 virus and submitted virus samples for diagnostic testing between March 2020 and January 2023.<\/jats:p><\/jats:sec><jats:sec id=\"ab-zoi230727-7\"><jats:title>Exposure<\/jats:title><jats:p>SARS-CoV-2 infection.<\/jats:p><\/jats:sec><jats:sec id=\"ab-zoi230727-8\"><jats:title>Main Outcomes and Measures<\/jats:title><jats:p>Samples with sufficient viral load underwent next-generation genome sequencing to identify low-frequency antiviral resistance variants that could not be identified through conventional sequencing.<\/jats:p><\/jats:sec><jats:sec id=\"ab-zoi230727-9\"><jats:title>Results<\/jats:title><jats:p>This study included 78\u202f866 clinical samples with next-generation whole-genome sequencing data for SARS-CoV-2. Low-frequency variants in the viral <jats:italic>nsp5<\/jats:italic> gene were identified in 128 isolates (0.16%), and no single variant associated with antiviral resistance was predominate.<\/jats:p><\/jats:sec><jats:sec id=\"ab-zoi230727-10\"><jats:title>Conclusions and Relevance<\/jats:title><jats:p>This cohort study of low-frequency variants resistant to nirmatrelvir-ritonavir found that these variants were very rare in samples from patients with SARS-CoV-2, suggesting that selection of these variants by nirmatrelvir-ritonavir following the initiation of treatment may also be rare. Surveillance efforts that involve sequencing of viral isolates should continue to monitor for novel resistance variants as nirmatrelvir-ritonavir is used more broadly.<\/jats:p><\/jats:sec>","DOI":"10.1001\/jamanetworkopen.2023.24963","type":"journal-article","created":{"date-parts":[[2023,7,21]],"date-time":"2023-07-21T15:31:51Z","timestamp":1689953511000},"page":"e2324963","source":"Crossref","is-referenced-by-count":18,"title":["Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023"],"prefix":"10.1001","volume":"6","author":[{"given":"Calvin P.","family":"Sjaarda","sequence":"first","affiliation":[{"name":"Division of Microbiology, Kingston Health Sciences Centre, Kingston, Ontario, Canada"},{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynette","family":"Lau","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared T.","family":"Simpson","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto General Hospital, Toronto, Ontario, Canada"},{"name":"Department of Molecular Genetics, Department of Computer Science, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramzi","family":"Fattouh","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada"},{"name":"Li Ka Shing Knowledge Institute, St Michael\u2019s Hospital, Unity Health Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mia J.","family":"Biondi","sequence":"additional","affiliation":[{"name":"School of Nursing, York University, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Finlay","family":"Maguire","sequence":"additional","affiliation":[{"name":"Shared Hospital Laboratory, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron","family":"Campigotto","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujia","family":"Feng","sequence":"additional","affiliation":[{"name":"Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyla","family":"Tozer","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henry","family":"Wong","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Kingston Health Sciences Centre, Kingston, Ontario, Canada"},{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilson W. L.","family":"Sung","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Kim","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian R.","family":"Marshall","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prameet M.","family":"Sheth","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Kingston Health Sciences Centre, Kingston, Ontario, Canada"},{"name":"Department of Pathology and Molecular Medicine, Queen\u2019s University, Kingston, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Kozak","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada"},{"name":"Shared Hospital Laboratory, Toronto, Ontario, Canada"},{"name":"Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"10","published-online":{"date-parts":[[2023,7,21]]},"reference":[{"issue":"15","key":"zoi230727r1","doi-asserted-by":"publisher","first-page":"1397","DOI":"10.1056\/NEJMoa2118542","article-title":"Oral nirmatrelvir for high-risk, nonhospitalized adults with COVID-19.","volume":"386","author":"Hammond","year":"2022","journal-title":"N Engl J Med"},{"issue":"3","key":"zoi230727r2","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1016\/S1473-3099(11)70318-8","article-title":"Antiviral resistance during the 2009 influenza A H1N1 pandemic: public health, laboratory, and clinical perspectives.","volume":"12","author":"Hurt","year":"2012","journal-title":"Lancet Infect Dis"},{"key":"zoi230727r3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.virol.2014.12.037","article-title":"Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations.","volume":"477","author":"Ji","year":"2015","journal-title":"Virology"},{"issue":"2","key":"zoi230727r4","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1001\/jama.286.2.196","article-title":"HIV-1 drug resistance profiles in children and adults with viral load of &lt;50 copies\/mL receiving combination therapy.","volume":"286","author":"Hermankova","year":"2001","journal-title":"JAMA"},{"issue":"6575","key":"zoi230727r5","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1126\/science.abl4784","article-title":"An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19.","volume":"374","author":"Owen","year":"2021","journal-title":"Science"},{"issue":"6","key":"zoi230727r6","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/S1473-3099(22)00873-8","article-title":"Viral burden rebound in hospitalised patients with COVID-19 receiving oral antivirals in Hong Kong: a population-wide retrospective cohort study.","volume":"23","author":"Wong","year":"2023","journal-title":"Lancet Infect Dis"},{"issue":"51","key":"zoi230727r7","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add7197","article-title":"Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system.","volume":"8","author":"Zhou","year":"2022","journal-title":"Sci Adv"},{"issue":"4","key":"zoi230727r9","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00869-22","article-title":"Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor paxlovid.","volume":"13","author":"Lee","year":"2022","journal-title":"mBio"},{"issue":"12","key":"zoi230727r10","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofac564","article-title":"Comparison of SARS-CoV-2 viral loads in the nasal mucosa of patients infected with BA.1, BA.2, or BA.5 Omicron lineages.","volume":"9","author":"Tozer","year":"2022","journal-title":"Open Forum Infect Dis"},{"issue":"6","key":"zoi230727r14","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2022.101972","article-title":"Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants.","volume":"298","author":"Greasley","year":"2022","journal-title":"J Biol Chem"},{"issue":"51","key":"zoi230727r16","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add7197","article-title":"Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system.","volume":"8","author":"Zhou","year":"2022","journal-title":"Sci Adv"},{"issue":"7944","key":"zoi230727r17","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1038\/s41586-022-05514-2","article-title":"Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir.","volume":"613","author":"Iketani","year":"2023","journal-title":"Nature"},{"issue":"656","key":"zoi230727r18","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abo0718","article-title":"Mutations in the SARS-CoV-2 RNA-dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms.","volume":"14","author":"Stevens","year":"2022","journal-title":"Sci Transl Med"},{"issue":"pt 3","key":"zoi230727r19","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1099\/0022-1317-83-3-581","article-title":"Mutational analysis of the active centre of coronavirus 3C-like proteases.","volume":"83","author":"Hegyi","year":"2002","journal-title":"J Gen Virol"},{"issue":"pt 3","key":"zoi230727r20","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1099\/0022-1317-83-3-595","article-title":"Conservation of substrate specificities among coronavirus main proteases.","volume":"83","author":"Hegyi","year":"2002","journal-title":"J Gen Virol"},{"issue":"6","key":"zoi230727r21","doi-asserted-by":"publisher","first-page":"E220","DOI":"10.1503\/cmaj.221608","article-title":"Population-based evaluation of the effectiveness of nirmatrelvir-ritonavir for reducing hospital admissions and mortality from COVID-19.","volume":"195","author":"Schwartz","year":"2023","journal-title":"CMAJ"},{"key":"zoi230727r8","doi-asserted-by":"crossref","unstructured":"Hu? Y, Lewandowski? EM, Tan? H, . Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.? bioRxiv. Preprint posted online September 6, 2022. doi:10.1101\/2022.06.28.497978","DOI":"10.1101\/2022.06.28.497978"},{"key":"zoi230727r11","unstructured":"Garrison? EM, Marth? G. Haplotype-based variant detection from short-read sequencing.? arXiv. Preprint posted online July 17, 2012. doi:10.48550\/arXiv.1207.3907"},{"key":"zoi230727r12","unstructured":"Loman? N, Rowe? W, Rambaut? A. nCoV-2019 novel coronavirus bioinformatics protocol. January 23, 2020. Accessed June 12, 2023. https:\/\/artic.network\/ncov-2019\/ncov2019-bioinformatics-sop.html"},{"key":"zoi230727r13","unstructured":"de Borja? R. ncov-tools version 1.9.1. September 1, 2022. Accessed June 12, 2023. https:\/\/github.com\/jts\/ncov-tools"},{"key":"zoi230727r15","doi-asserted-by":"crossref","unstructured":"Hu? Y, Lewandowski? EM, Tan? H, . Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.? bioRxiv. Preprint posted online June 28, 2022. doi:10.1101\/2022.06.28.497978","DOI":"10.1101\/2022.06.28.497978"}],"container-title":["JAMA Network Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/jamanetwork.com\/journals\/jamanetworkopen\/articlepdf\/2807483\/sjaarda_2023_oi_230727_1689263479.48117.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,21]],"date-time":"2023-07-21T15:31:55Z","timestamp":1689953515000},"score":1,"resource":{"primary":{"URL":"https:\/\/jamanetwork.com\/journals\/jamanetworkopen\/fullarticle\/2807483"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,21]]},"references-count":21,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2023,7,3]]}},"URL":"https:\/\/doi.org\/10.1001\/jamanetworkopen.2023.24963","relation":{},"ISSN":["2574-3805"],"issn-type":[{"value":"2574-3805","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,21]]}}}