{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T07:37:03Z","timestamp":1765438623768,"version":"build-2065373602"},"reference-count":64,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2020,5,16]],"date-time":"2020-05-16T00:00:00Z","timestamp":1589587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Over the past decade, there has been an increase in the adoption of next generation sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs conventional Sanger sequencing as it has much higher throughput, lower cost when samples are batched and, most importantly, significantly higher sensitivities for variants present at low frequencies, which may have significant clinical implications. Despite the advantages of NGS, Sanger sequencing remains the gold standard for HIVDR testing, largely due to the lack of standardization of NGS-based HIVDR testing. One important aspect of standardization includes external quality assessment (EQA) strategies and programs. Current EQA for Sanger-based HIVDR testing includes proficiency testing where samples are sent to labs and the performance of the lab conducting such assays is evaluated. The current methods for Sanger-based EQA may not apply to NGS-based tests because of the fundamental differences in their technologies and outputs. Sanger-based genotyping reports drug resistance mutations (DRMs) data as dichotomous, whereas NGS-based HIVDR genotyping also reports DRMs as numerical data (percent abundance). Here we present an overview of the need to develop EQA for NGS-based HIVDR testing and some unique challenges that may be encountered.<\/jats:p>","DOI":"10.3390\/v12050550","type":"journal-article","created":{"date-parts":[[2020,5,18]],"date-time":"2020-05-18T02:43:42Z","timestamp":1589769822000},"page":"550","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges"],"prefix":"10.3390","volume":"12","author":[{"given":"Emma R.","family":"Lee","sequence":"first","affiliation":[{"name":"National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8903-0203","authenticated-orcid":false,"given":"Feng","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Sandstrom","sequence":"additional","affiliation":[{"name":"National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5451-6294","authenticated-orcid":false,"given":"Hezhao","family":"Ji","sequence":"additional","affiliation":[{"name":"National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,5,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1373\/clinchem.2008.112789","article-title":"Next-generation sequencing:from basic research to diagnostics","volume":"55","author":"Voelkerding","year":"2009","journal-title":"Clin. Chem."},{"key":"ref_2","first-page":"S292","article-title":"Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity","volume":"221","author":"Melendrez","year":"2020","journal-title":"J. Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.virusres.2016.12.008","article-title":"Promises and pitfalls of Illumina sequencing for HIV resistance genotyping","volume":"239","author":"Brumme","year":"2017","journal-title":"Virus Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.virusres.2016.10.019","article-title":"Deep sequencing for HIV-1 clinical management","volume":"239","author":"Paredes","year":"2017","journal-title":"Virus Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S1473-3099(11)70255-9","article-title":"Effect of pretreatment HIV-1 drug resistance on immunological, virological, and drug-resistance outcomes of first-line antiretroviral treatment in sub-Saharan Africa: A multicentre cohort study","volume":"12","author":"Hamers","year":"2012","journal-title":"Lancet Infect. Dis."},{"key":"ref_6","first-page":"1749","article-title":"Pretreatment HIV drug resistance increases regimen switches in sub-saharan Africa","volume":"61","author":"Boender","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e579","DOI":"10.1016\/S2352-3018(16)30119-9","article-title":"Pretreatment HIV-drug resistance in Mexico and its impact on the effectiveness of first-line antiretroviral therapy: A nationally representative 2015 WHO survey","volume":"3","author":"Ji","year":"2016","journal-title":"Lancet HIV"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Vandenhende, M.A., Bellecave, P., Recordon-Pinson, P., Reigadas, S., Bidet, Y., Bruyand, M., Bonnet, F., Lazaro, E., Neau, D., and Fleury, H. (2014). Prevalence and evolution of low frequency HIV drug resistance mutations detected by ultra deep sequencing in patients experiencing first line antiretroviral therapy failure. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0086771"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1093\/cid\/civ102","article-title":"Pretreatment HIV Drug Resistance and HIV-1 Subtype C Are Independently Associated with Virologic Failure: Results from the Multinational PEARLS (ACTG A5175) Clinical Trial","volume":"60","author":"Kantor","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1093\/jac\/dku426","article-title":"Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: A multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing","volume":"70","author":"Schuurman","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e638","DOI":"10.1016\/S2352-3018(18)30177-2","article-title":"Clinically relevant thresholds for ultrasensitive HIV drug resistance testing: A multi-country nested case-control study","volume":"5","author":"Inzaule","year":"2018","journal-title":"Lancet HIV"},{"key":"ref_12","first-page":"2","article-title":"Standardization and quality management in next-generation sequencing","volume":"10","author":"Endrullat","year":"2016","journal-title":"Appl. Transl. Genom."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1128\/JCM.00949-16","article-title":"Assuring the quality of next-generation sequencing in clinical microbiology and public health laboratories","volume":"54","author":"Gargis","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nbt.2403","article-title":"Assuring the quality of next-generation sequencing in clinical laboratory practice","volume":"30","author":"Gargis","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e00261-19","DOI":"10.1128\/JCM.00261-19","article-title":"Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)","volume":"5","author":"Hutchins","year":"2019","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","unstructured":"(2020, February 10). WHO: Content Sheet 10-1: Overview of External Quality Assessment (EQA). Available online: https:\/\/www.who.int\/ihr\/training\/laboratory_quality\/10_b_eqa_contents.pdf."},{"key":"ref_17","unstructured":"Wayne, P., and CSLI (2015). Quality System Regulation for Laboratory-Developed Tests: A Practical Guide for the Laboratory, Clinical Laboratory Standards Institute."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1093\/ajcp\/aqz096","article-title":"Regulation of Laboratory-Developed Tests","volume":"152","author":"Genzen","year":"2019","journal-title":"Am. J. Clin. Pathol."},{"key":"ref_19","unstructured":"U.S. Department of Health and Human Services, Rockville, M., and CMS (1988). Clinical Laboratory Improvement Ammendments of 1988 (part 493), Centers for Medicare and Medicaid Services."},{"key":"ref_20","unstructured":"(2014). (CLSI 2014) Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine, CLSI. Approved Guideline; MM09-A2 2014."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"983","DOI":"10.5858\/arpa.2012-0311-RA","article-title":"Current Landscape and New Paradigms of Proficiency Testing and External Quality Assessment for Molecular Genetics","volume":"137","author":"Kalman","year":"2013","journal-title":"Arch. Pathol. Lab. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"S266","DOI":"10.1093\/cid\/cir992","article-title":"Genotyping external quality assurance in the world health organization HIV drug resistance laboratory network during 2007\u20132010","volume":"54","author":"Parkin","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.jcv.2008.08.021","article-title":"HIV-1 drug resistance genotyping quality assessment: Results of the ENVA7 Genotyping Proficiency Programme","volume":"43","author":"Pandit","year":"2008","journal-title":"J. Clin. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.jviromet.2009.03.016","article-title":"TREAT Asia Quality Assessment Scheme (TAQAS) to standardize the outcome of HIV genotypic resistance testing in a group of Asian laboratories","volume":"159","author":"Land","year":"2009","journal-title":"J. Virol. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1089\/aid.2014.0059","article-title":"Japanese external quality assessment program to standardize HIV-1 drug-resistance testing (JEQS2010 program) using in vitro transcribed RNA as reference material","volume":"31","author":"Yoshida","year":"2015","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.1128\/JCM.06689-11","article-title":"Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool","volume":"50","author":"Harrigan","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1086\/503914","article-title":"Web Resources for HIV Type 1 Genotypic-Resistance Test Interpretation","volume":"42","author":"Liu","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"ref_28","first-page":"111","article-title":"2019 update of the drug resistance mutations in HIV-1","volume":"27","author":"Wensing","year":"2019","journal-title":"Top. Antivir. Med."},{"key":"ref_29","unstructured":"WHO (2017). Who\/Hivresnet HIV Drug Resistance, WHO."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1101\/gr.6468307","article-title":"Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance","volume":"17","author":"Wang","year":"2007","journal-title":"Genome Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e91","DOI":"10.1093\/nar\/gkm435","article-title":"DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations","volume":"35","author":"Hoffmann","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-45328-3","article-title":"A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance","volume":"9","author":"Taylor","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"S829","DOI":"10.1093\/infdis\/jix397","article-title":"Next-Generation Human Immunodeficiency Virus Sequencing for Patient Management and Drug Resistance Surveillance","volume":"216","author":"Edgil","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2942","DOI":"10.1128\/JCM.00650-15","article-title":"Development and validation of two screening assays for the hepatitis C virus NS3 Q80K polymorphism associated with reduced response to combination treatment regimens containing simeprevir","volume":"53","author":"Chui","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1093\/bioinformatics\/bty919","article-title":"Measurement error and variant-calling in deep Illumina sequencing of HIV","volume":"35","author":"Howison","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"481","DOI":"10.5858\/arpa.2014-0250-CP","article-title":"College of American pathologists\u2019 laboratory standards for next-generation sequencing clinical tests","volume":"139","author":"Aziz","year":"2015","journal-title":"Arch. Pathol. Lab. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/j.jmoldx.2015.07.004","article-title":"Next-Generation Sequencing for Infectious Disease Diagnosis and Management: A Report of the Association for Molecular Pathology","volume":"17","author":"Lefterova","year":"2015","journal-title":"J. Mol. Diagn."},{"key":"ref_38","unstructured":"Parkin, N., Zaccaro, D., Avila-Rios, S., Brumme, C., Hunt, G., Ji, H., Kantor, R., Mbisa, J., Paredes, R., and Rivera-Amill, V. (2018, January 22\u201323). Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping. Proceedings of the XXVII International HIV Drug Resistance and Treatment Strategies Workshop, Johannesburg, South Africa."},{"key":"ref_39","unstructured":"WHO (2020, February 10). World Health Organization Global Strategy For The Surveillance And Monitoring Of HIV Drug Resistance. HIV\/AIDS Programme. Available online: http:\/www.who.int\/hiv\/pub\/drugresistance\/drug_resistance_strategy\/en\/."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1128\/JCM.43.1.406-413.2005","article-title":"Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis","volume":"43","author":"Palmer","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nmeth995","article-title":"Detection of minor drug-resistant populations by parallel allele-specific sequencing","volume":"4","author":"Cai","year":"2007","journal-title":"Nat. Methods"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4433","DOI":"10.1007\/s00018-016-2299-6","article-title":"Mechanisms of viral mutation","volume":"73","year":"2016","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1742-4690-9-89","article-title":"Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted\/founder genome","volume":"9","author":"Song","year":"2012","journal-title":"Retrovirology"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.jviromet.2018.08.001","article-title":"Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing","volume":"261","author":"Kireev","year":"2018","journal-title":"J. Virol. Methods"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Orton, R.J., Wright, C.F., Morelli, M.J., King, D.J., Paton, D.J., King, D.P., and Haydon, D.T. (2015). Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1456-x"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Kugelman, J.R., Wiley, M.R., Nagle, E.R., Reyes, D., Pfeffer, B.P., Kuhn, J.H., Sanchez-Lockhart, M., and Palacios, G.F. (2017). Error baseline rates of five sample preparation methods used to characterize RNA virus populations. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0171333"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Santiago, G.A., Vergne, E., Quiles, Y., Cosme, J., Vazquez, J., Medina, J.F., Medina, F., Col\u00f3n, C., Margolis, H., and Mu\u00f1oz-Jord\u00e1n, J.L. (2013). Analytical and Clinical Performance of the CDC Real Time RT-PCR Assay for Detection and Typing of Dengue Virus. PLoS Negl. Trop. Dis., 7.","DOI":"10.1371\/annotation\/ae27d48b-025f-47ce-8427-4af59f821ad7"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1016\/j.csbj.2019.05.001","article-title":"A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control","volume":"17","author":"Long","year":"2019","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"11571","DOI":"10.1021\/bi000579d","article-title":"Misincorporation by wild-type and mutant T7 RNA polymerases: Identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation","volume":"39","author":"Huang","year":"2000","journal-title":"Biochemistry"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2042-5783-4-1","article-title":"Deep sequencing of evolving pathogen populations : Applications, errors, and bioinformatic solutions","volume":"4","author":"Mcelroy","year":"2014","journal-title":"Microb. Inform. Exp."},{"key":"ref_51","first-page":"1173","article-title":"Viral Quasi Species","volume":"344","author":"Andino","year":"2015","journal-title":"Virology"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12977-016-0321-6","article-title":"Ultrasensitive single-genome sequencing: Accurate, targeted, next generation sequencing of hiv-1 rna","volume":"13","author":"Boltz","year":"2016","journal-title":"Retrovirology"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"8540","DOI":"10.1128\/JVI.00522-15","article-title":"Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations","volume":"89","author":"Zhou","year":"2015","journal-title":"J. Virol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Kou, R., Lam, H., Duan, H., Ye, L., Jongkam, N., Chen, W., Zhang, S., and Li, S. (2016). Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0146638"},{"key":"ref_55","unstructured":"Lee, E.R., Enns, E., Parkin, N., Brumme, C.J., Casadella, M., Howison, M., Avila Rios, S., Jennings, R., Capina, R., and Marinier, E. (2018, January 22\u201323). Characterization and data assessment of next generation sequencing-based genotyping using existing HIV-1 drug resistance proficiency panels. Proceedings of the XXVII International HIV Drug Resistance and Treatment Strategies Workshop, Johannesburg, South Africa."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Ji, H., Parkin, N., Gao, F., Denny, T., Jennings, C., Bremer, J., and Kantor, R. (2020). External quality assessment program for next generation sequencing-based HIV drug resistance testing: Logistical considerations. Viruses, (accepted on 14 May 2020).","DOI":"10.3390\/v12050556"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1128\/AAC.02710-13","article-title":"Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism","volume":"58","author":"Gibson","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: Ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Yang, X., Charlebois, P., Macalalad, A., Henn, M.R., and Zody, M.C. (2013). V-Phaser 2: Variant inference for viral populations. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-674"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Zagordi, O., Bhattacharya, A., Eriksson, N., and Beerenwinkel, N. (2011). ShoRAH: Estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-119"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1093\/bioinformatics\/btu587","article-title":"VirVarSeq: A low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering","volume":"31","author":"Verbist","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_62","unstructured":"Cassarino, T.G., Frampton, D., Sugar, R., Charles, E., and Zisis Kozlakidid, P.K. (2016). High-throughput pipeline for de-novo assembly and drug resistance mutations identifcation from next-generation sequencing viral data of residual diagnostic samples. bioRxiv."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.jviromet.2016.11.008","article-title":"MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing","volume":"240","author":"Huber","year":"2017","journal-title":"J. Virol. Methods"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.1038\/s41598-020-58544-z","article-title":"Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing","volume":"10","author":"Lee","year":"2020","journal-title":"Sci. Rep."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/5\/550\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:29:28Z","timestamp":1760174968000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/5\/550"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,16]]},"references-count":64,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5]]}},"alternative-id":["v12050550"],"URL":"https:\/\/doi.org\/10.3390\/v12050550","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2020,5,16]]}}}