{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T21:40:39Z","timestamp":1783546839743,"version":"3.55.0"},"reference-count":51,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2021,8,30]],"date-time":"2021-08-30T00:00:00Z","timestamp":1630281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000233","name":"Genome British Columbia","doi-asserted-by":"publisher","award":["UPP029"],"award-info":[{"award-number":["UPP029"]}],"id":[{"id":"10.13039\/501100000233","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Despite the effectiveness of direct-acting antiviral agents in treating hepatitis C virus (HCV), cases of treatment failure have been associated with the emergence of resistance-associated substitutions. To better guide clinical decision-making, we developed and validated a near-whole-genome HCV genotype-independent next-generation sequencing strategy. HCV genotype 1\u20136 samples from direct-acting antiviral agent treatment-na\u00efve and -treated HCV-infected individuals were included. Viral RNA was extracted using a NucliSens easyMAG and amplified using nested reverse transcription-polymerase chain reaction. Libraries were prepared using Nextera XT and sequenced on the Illumina MiSeq sequencing platform. Data were processed by an in-house pipeline (MiCall). Nucleotide consensus sequences were aligned to reference strain sequences for resistance-associated substitution identification and compared to NS3, NS5a, and NS5b sequence data obtained from a validated in-house assay optimized for HCV genotype 1. Sequencing success rates (defined as achieving &gt;100-fold read coverage) approaching 90% were observed for most genotypes in samples with a viral load &gt;5 log10 IU\/mL. This genotype-independent sequencing method resulted in &gt;99.8% nucleotide concordance with the genotype 1-optimized method, and 100% agreement in genotype assignment with paired line probe assay-based genotypes. The assay demonstrated high intra-run repeatability and inter-run reproducibility at detecting substitutions above 2% prevalence. This study highlights the performance of a freely available laboratory and bioinformatic approach for reliable HCV genotyping and resistance-associated substitution detection regardless of genotype.<\/jats:p>","DOI":"10.3390\/v13091721","type":"journal-article","created":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:13:17Z","timestamp":1630465997000},"page":"1721","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay"],"prefix":"10.3390","volume":"13","author":[{"given":"Hope R.","family":"Lapointe","sequence":"first","affiliation":[{"name":"Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"},{"name":"BC Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiyan","family":"Dong","sequence":"additional","affiliation":[{"name":"BC Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Winnie W. Y.","family":"Dong","sequence":"additional","affiliation":[{"name":"BC Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Don","family":"Kirkby","sequence":"additional","affiliation":[{"name":"BC Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Conan","family":"Woods","sequence":"additional","affiliation":[{"name":"BC Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Art F. Y.","family":"Poon","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9403-3190","authenticated-orcid":false,"given":"Anita Y. M.","family":"Howe","sequence":"additional","affiliation":[{"name":"British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. Richard","family":"Harrigan","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2722-5288","authenticated-orcid":false,"given":"Chanson J.","family":"Brumme","sequence":"additional","affiliation":[{"name":"BC Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"},{"name":"Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,8,30]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2017). Global Hepatitis Report 2017, World Health Organization."},{"key":"ref_2","unstructured":"World Health Organization (2014). 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