{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T04:09:42Z","timestamp":1784779782665,"version":"3.55.0"},"reference-count":61,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T00:00:00Z","timestamp":1590537600000},"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>HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21\u201322 February, 2018), a second \u201cWinnipeg Consensus\u201d symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium\u2019s goals and highlights.<\/jats:p>","DOI":"10.3390\/v12060586","type":"journal-article","created":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T05:35:52Z","timestamp":1590557752000},"page":"586","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Are We Ready for NGS HIV Drug Resistance Testing? The Second \u201cWinnipeg Consensus\u201d Symposium"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5451-6294","authenticated-orcid":false,"given":"Hezhao","family":"Ji","sequence":"first","affiliation":[{"name":"National HIV and Retrovirology Laboratories 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":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Sandstrom","sequence":"additional","affiliation":[{"name":"National HIV and Retrovirology Laboratories 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":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6553-691X","authenticated-orcid":false,"given":"Roger","family":"Paredes","sequence":"additional","affiliation":[{"name":"IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s\/n, 08916 Badalona, Catalonia, Spain"},{"name":"Infectious Diseases Department, Hospital Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. Richard","family":"Harrigan","sequence":"additional","affiliation":[{"name":"Division of AIDS, Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, 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":"British Columbia Centre for Excellence in HIV\/AIDS, Vancouver, BC V6Z 1Y6, Canada"},{"name":"Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago","family":"Avila Rios","sequence":"additional","affiliation":[{"name":"Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6194-1395","authenticated-orcid":false,"given":"Marc","family":"Noguera-Julian","sequence":"additional","affiliation":[{"name":"IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s\/n, 08916 Badalona, Catalonia, Spain"},{"name":"Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic\u2013Central University of Catalonia (UVic\u2013UCC), Can Baumann, Ctra. de Roda, 70, 08500 Vic, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5824-3388","authenticated-orcid":false,"given":"Neil","family":"Parkin","sequence":"additional","affiliation":[{"name":"Data First Consulting Inc., Sebastopol, CA 95472, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3659-1108","authenticated-orcid":false,"given":"Rami","family":"Kantor","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,5,27]]},"reference":[{"key":"ref_1","unstructured":"(2020, January 30). AIDSinfo. FDA-Approved HIV Medicines, Available online: https:\/\/aidsinfo.nih.gov\/understanding-hiv-aids\/fact-sheets\/21\/58\/fda-approved-hiv-medicines."},{"key":"ref_2","unstructured":"National Institute of Allergy and Infectious Diseases (2018). Drugs That Fight HIV-1: A Reference Guide for Prescription HIV-1 Medications."},{"key":"ref_3","first-page":"131","article-title":"Treatment as prevention for HIV infection: Current data, challenges, and global perspectives","volume":"20","author":"Yombi","year":"2018","journal-title":"AIDS Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/S0165-6147(02)02054-0","article-title":"Targeting HIV: Antiretroviral therapy and development of drug resistance","volume":"23","year":"2002","journal-title":"Trends Pharm. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1126\/science.7824947","article-title":"HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy","volume":"267","author":"Coffin","year":"1995","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2565","DOI":"10.1172\/JCI119443","article-title":"Perspectives series: Host\/pathogen interactions. Dynamics of HIV-1 replication in vivo","volume":"99","author":"Ho","year":"1997","journal-title":"J. Clin. Investig."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1128\/MMBR.05023-11","article-title":"Viral quasispecies evolution","volume":"76","author":"Domingo","year":"2012","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.meegid.2016.08.031","article-title":"HIV-1 drug resistance and resistance testing","volume":"46","author":"Clutter","year":"2016","journal-title":"Infect. Genet. Evol."},{"key":"ref_9","unstructured":"WHO (2017). Global Action Plan on HIV Drug Resistance 2017\u20132021, WHO."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1093\/cid\/ciz372","article-title":"Clinical impact and cost-effectiveness of genotype testing at human immunodeficiency virus diagnosis in the United States","volume":"70","author":"Hyle","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Phillips, A.N., Cambiano, V., Nakagawa, F., Magubu, T., Miners, A., Ford, D., Pillay, D., De Luca, A., Lundgren, J., and Revill, P. (2014). Cost-Effectiveness of HIV Drug Resistance Testing to Inform Switching to Second Line Antiretroviral Therapy in Low Income Settings. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0109148"},{"key":"ref_12","unstructured":"Department of Health and Human Services (DHHS) (2020, May 26). Guidelines for the Use of Antiretroviral Agents in Adults and Adolescents Living with HIV 2017, Available online: https:\/\/aidsinfo.nih.gov\/contentfiles\/AdultandAdolescentGL003510.pdf."},{"key":"ref_13","first-page":"177","article-title":"Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society\u2013USA Panel","volume":"68","author":"Calvez","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5463","DOI":"10.1073\/pnas.74.12.5463","article-title":"DNA sequencing with chain-terminating inhibitors","volume":"74","author":"Sanger","year":"1977","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","first-page":"77","article-title":"European recommendations for the clinical use of HIV drug resistance testing: 2011 update","volume":"13","author":"Vandamme","year":"2011","journal-title":"Aids Rev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1086\/596736","article-title":"Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment\u2013Naive Patients Significantly Impact Treatment Outcomes","volume":"199","author":"Simen","year":"2009","journal-title":"J. Infect. Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1128\/JCM.41.8.3559-3565.2003","article-title":"Quality Control Trial for Human Immunodeficiency Virus Type 1 Drug Resistance Testing Using Clinical Samples Reveals Problems with Detecting Minority Species and Interpretation of Test Results","volume":"41","author":"Korn","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Johnson, J.A., Li, J.-F., Wei, X., Lipscomb, J., Irlbeck, D., Craig, C., Smith, A., E Bennett, D., Monsour, M., and Sandstrom, P. (2008). Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment\u2013Na\u00efve Populations and Associate with Reduced Treatment Efficacy. PLoS Med., 5.","DOI":"10.1371\/journal.pmed.0050158"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"871","DOI":"10.3851\/IMP1839","article-title":"Next-generation sequencing of dried blood spot specimens: A novel approach to HIV drug-resistance surveillance","volume":"16","author":"Ji","year":"2011","journal-title":"Antivir. Ther."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"8970","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_21","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors","volume":"437","author":"Margulies","year":"2005","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/128_2012_329","article-title":"Next Generation Sequencing: Chemistry, Technology and Applications","volume":"336","author":"Hui","year":"2012","journal-title":"Chem. Diagn."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1411","DOI":"10.1097\/QAD.0b013e3282fc972e","article-title":"Massively parallel pyrosequencing in HIV research","volume":"22","author":"Bushman","year":"2008","journal-title":"AIDS"},{"key":"ref_24","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_25","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_26","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1093\/jac\/dky428","article-title":"Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART","volume":"74","author":"Derache","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.1093\/jac\/dku278","article-title":"Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: Implications for use in low- and middle-income countries","volume":"69","author":"Ekici","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_28","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_29","doi-asserted-by":"crossref","unstructured":"Ji, H., Mass\u00e9, N., Tyler, S., Liang, B., Li, Y., Merks, H., Graham, M., Sandstrom, P., and Brooks, J. (2010). HIV Drug Resistance Surveillance Using Pooled Pyrosequencing. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009263"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Ji, H., Li, Y., Liang, B., Pilon, R., MacPherson, P., Bergeron, M., Kim, J., Graham, M., Van Domselaar, G., and Sandstrom, P. (2013). Pyrosequencing Dried Blood Spots Reveals Differences in HIV Drug Resistance between Treatment Na\u00efve and Experienced Patients. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0056170"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1089\/aid.2014.0031","article-title":"Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain","volume":"31","author":"Keys","year":"2015","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"6824","DOI":"10.1128\/AAC.01490-15","article-title":"HIV Drug Resistance Testing by High-Multiplex \u201cWide\u201d Sequencing on the MiSeq Instrument","volume":"59","author":"Lapointe","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"21846","DOI":"10.7448\/IAS.20.1.21846","article-title":"Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000\u20132014","volume":"20","author":"Moscona","year":"2017","journal-title":"J. Int. AIDS Soc."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1093\/jac\/dky003","article-title":"HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform","volume":"73","author":"Raymond","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e00105","DOI":"10.1128\/JCM.00105-18","article-title":"Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing","volume":"56","author":"Tzou","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1001\/jama.2011.375","article-title":"Low-Frequency HIV-1 Drug Resistance Mutations and Risk of NNRTI-Based Antiretroviral Treatment Failure","volume":"305","author":"Li","year":"2011","journal-title":"JAMA"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e267","DOI":"10.1016\/S1473-3099(16)30118-9","article-title":"Affordable HIV drug-resistance testing for monitoring of antiretroviral therapy in sub-Saharan Africa","volume":"16","author":"Inzaule","year":"2016","journal-title":"Lancet Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"7556","DOI":"10.1038\/s41598-018-25888-6","article-title":"Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: A comparison of Sanger and high-throughput sequencing","volume":"8","author":"Telele","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"749","DOI":"10.3389\/fmicb.2019.00749","article-title":"Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing","volume":"10","author":"Alves","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_40","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_41","unstructured":"FDA (2019). FDA Authorizes Marketing of First Next-Generation Sequencing Test for Detecting HIV-1 Drug Resistance Mutations."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"104229","DOI":"10.1016\/j.jcv.2019.104229","article-title":"Performance evaluation of the Vela Dx Sentosa next-generation sequencing system for HIV-1 DNA genotypic resistance","volume":"122","author":"Raymond","year":"2020","journal-title":"J. Clin. Virol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.jmoldx.2019.06.003","article-title":"Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing","volume":"21","author":"Weber","year":"2019","journal-title":"J. Mol. Diagn."},{"key":"ref_44","unstructured":"WHO (2018). The Use of Next-Generation Sequencing Technologies for the Detection of Mutations Associated with Drug Resistance in Mycobacterium Tuberculosis Complex: Technical Guide, World Health Organization."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e25193","DOI":"10.1002\/jia2.25193","article-title":"Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: The Winnipeg Consensus","volume":"21","author":"Ji","year":"2018","journal-title":"J. Int. AIDS Soc."},{"key":"ref_46","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_47","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":"2018","journal-title":"Bioinformatics"},{"key":"ref_48","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."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Bonsall, D., Golubchik, T., De Cesare, M., Limbada, M., Kosloff, B., MacIntyre-Cockett, G., Hall, M., Wymant, C., Ansari, M.A., and Abeler-Dorner, L. (2018). A comprehensive genomics solution for HIV surveillance and clinical monitoring in a global health setting. BioRxiv, 397083.","DOI":"10.1101\/397083"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"20166","DOI":"10.1073\/pnas.1110064108","article-title":"Accurate sampling and deep sequencing of the HIV-1 protease gene using a primer ID","volume":"108","author":"Jabara","year":"2011","journal-title":"Proc. Natl. Acad Sci. USA"},{"key":"ref_51","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_52","unstructured":"Parkin, N., Zaccaro, D., Avila-Rios, S., Brumme, C., Hunt, G., Ji, H., Kantor, R., Mbisa, J.L., Predes, 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_53","unstructured":"Lee, E.R., Parkin, N., Enns, E., 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_54","doi-asserted-by":"crossref","unstructured":"Ji, H., Parkin, N., Gao, F., Denny, T., Jennings, C., Sandstrom, P., and Kantor, R. (2020). External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations. Viruses, 12.","DOI":"10.3390\/v12050556"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Lee, E.R., Gao, F., Sandstrom, P., and Ji, H. (2020). External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges. Viruses, 12.","DOI":"10.3390\/v12050550"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"104277","DOI":"10.1016\/j.meegid.2020.104277","article-title":"Evaluation of haplotype callers for next-generation sequencing of viruses","volume":"82","author":"Eliseev","year":"2020","journal-title":"Infect Genet. Evol."},{"key":"ref_57","unstructured":"Jerzy, K. (2016). Analysis of Next-Generation Sequencing Data in Virology-Opportunities and Challenges. Next Generation Sequencing\u2014Advances, Applications and Challenges, IntechOpen. eBook (PDF)."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Marinier, E., Enns, E., Tran, C., Fogel, M., Peters, C., Kidwai, A., Ji, H., and Van Domselaar, G. (2019). quasitools: A Collection of Tools for Viral Quasispecies Analysis. BioRxiv.","DOI":"10.1101\/733238"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"925","DOI":"10.3851\/IMP1851","article-title":"Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels","volume":"16","author":"Kozal","year":"2011","journal-title":"Antivir. Ther."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1097\/QAD.0b013e3283427dcb","article-title":"Low level of the K103N HIV-1 above a threshold is associated with virological failure in treatment-naive individuals undergoing efavirenz-containing therapy","volume":"25","author":"Goodman","year":"2011","journal-title":"AIDS"},{"key":"ref_61","first-page":"1584","article-title":"Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact","volume":"221","author":"Bertagnolio","year":"2019","journal-title":"J. Infect. Dis."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/6\/586\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:33:01Z","timestamp":1760175181000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/6\/586"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,27]]},"references-count":61,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2020,6]]}},"alternative-id":["v12060586"],"URL":"https:\/\/doi.org\/10.3390\/v12060586","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,27]]}}}