{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:48:37Z","timestamp":1782272917157,"version":"3.54.5"},"reference-count":28,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T00:00:00Z","timestamp":1781913600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Human immunodeficiency virus type 1 exhibits extensive genetic diversity, which has important implications for molecular epidemiology, recombinant-pattern assessment, and antiretroviral resistance surveillance. In Mexico, HIV-1 molecular surveillance has historically relied mainly on partial pol gene sequencing, limiting the ability to compare lineage assignments across gag, pol, and env regions. We analyzed plasma samples from 40 treatment-na\u00efve adults receiving care at a tertiary-care hospital in Mexico using a commercial amplicon-based multiregion HIV-1 genomic sequencing workflow. DeepChek\u00ae was used as the primary workflow for read processing, mutation calling, region-level subtype assignment, and antiretroviral resistance interpretation. Resistance interpretation was restricted to antiretroviral target regions with sufficient coverage, mainly reverse transcriptase, protease, integrase, and capsid, when available. Drug resistance mutations were identified in 6\/40 participants (15.0%) when mutation-level resistance findings in RT, PR, and IN were considered; one additional sample showed a capsid inhibitor-nonsusceptible NGS call. NNRTI-associated findings were identified in 2\/40 patients (5.0%), whereas NRTI- and PI-associated findings were identified in 1\/40 patients (2.5%). Accessory or secondary INSTI-associated substitutions were detected in 2\/40 patients (5.0%). Region-level subtype analysis revealed frequent discordant assignments across amplified segments, which is consistent with complex mosaic profiles; however, these findings are interpreted as region-level subtypes and recombinant-pattern assignments rather than continuous whole-genome recombination maps. One sample had insufficient RT\/PROT\/INT coverage for drug resistance interpretation in the complete DeepChek report and was retained only for regions meeting quality thresholds. These findings support the value of multiregion HIV-1 sequencing for local molecular surveillance while emphasizing the need for transparent region-level coverage reporting, cautious interpretation of recombinant-pattern calls, and transparent repository reporting.<\/jats:p>","DOI":"10.3390\/ijms27125571","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:09:17Z","timestamp":1782270557000},"page":"5571","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Amplicon-Based Multiregion Genomic Characterization of HIV-1 in a Tertiary-Care Hospital in Mexico: Antiretroviral Resistance Mutations and Subtype Diversity"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9817-6183","authenticated-orcid":false,"given":"Eduardo","family":"Garc\u00eda-Moncada","sequence":"first","affiliation":[{"name":"Medical School, National Polytechnic Institute, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6240-3468","authenticated-orcid":false,"given":"Enoc Mariano","family":"Cort\u00e9s-Malag\u00f3n","sequence":"additional","affiliation":[{"name":"Research Division, Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"},{"name":"Genetics Laboratory, Hospital Nacional Homeop\u00e1tico, Mexico City 06800, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6498-6684","authenticated-orcid":false,"given":"Jes\u00fas Alejandro","family":"Pineda-Migranas","sequence":"additional","affiliation":[{"name":"Medical School, National Polytechnic Institute, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Montserrat","family":"Ruiz Santana","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n en Salud, Hospital de Alta Especialidad de Ixtapaluca, Servicios de Salud del Instituto Mexicano del Seguro Social para el Bienestar (IMSS-BIENESTAR), Ixtapaluca 56530, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9409-5896","authenticated-orcid":false,"given":"Iliana Alejandra","family":"Cort\u00e9s-Ort\u00edz","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00e9tica y Diagn\u00f3stico Molecular, Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8954-3243","authenticated-orcid":false,"given":"Jos\u00e9 Francisco","family":"Escutia Dom\u00ednguez","sequence":"additional","affiliation":[{"name":"Facultad de Estudios Superiores Cuautitl\u00e1n, Campo 1, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Mexico City 54740, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4508-5370","authenticated-orcid":false,"given":"Daniel Agust\u00edn","family":"Bravata-Alc\u00e1ntara","sequence":"additional","affiliation":[{"name":"National School of Medicine and Homeopathy, National Polytechnic Institute, Av. Guillermo Massieu Helguera 239, Ticom\u00e1n, Mexico City 07320, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo","family":"Acosta-Altamirano","sequence":"additional","affiliation":[{"name":"Hospital General de M\u00e9xico, Mexico City 06726, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sa\u00fal David","family":"Razo-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Facultad de Estudios Superiores Zaragoza, Campus 2, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Iztapalapa, Mexico City 09230, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel Alberto","family":"Castillo Mendez","sequence":"additional","affiliation":[{"name":"Academia de Nutrici\u00f3n, Plantel Cuautepec, Colegio de Ciencias y Humanidades, Universidad Aut\u00f3noma de la Ciudad de M\u00e9xico, La Palma, Mexico City 07160, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1006-592X","authenticated-orcid":false,"given":"M\u00f3nica","family":"Sierra-Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n en Salud, Hospital de Alta Especialidad de Ixtapaluca, Servicios de Salud del Instituto Mexicano del Seguro Social para el Bienestar (IMSS-BIENESTAR), Ixtapaluca 56530, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Carlos","family":"Bravata-Alc\u00e1ntara","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n en Salud, Hospital de Alta Especialidad de Ixtapaluca, Servicios de Salud del Instituto Mexicano del Seguro Social para el Bienestar (IMSS-BIENESTAR), Ixtapaluca 56530, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/j.virusres.2012.06.015","article-title":"The origin of genetic diversity in HIV-1","volume":"169","author":"Smyth","year":"2012","journal-title":"Virus Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1056\/NEJMra0706737","article-title":"The challenge of HIV-1 subtype diversity","volume":"358","author":"Taylor","year":"2008","journal-title":"N. Engl. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1097\/00042560-200202010-00013","article-title":"Who-Unaids Network for HIV Isolation Characterization. Estimated global distribution and regional spread of HIV-1 genetic subtypes in the year 2000","volume":"29","author":"Osmanov","year":"2002","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Wan, Z., and Zhang, C. (2024). How to report and make sense of a new HIV-1 circulating recombinant form?. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1343143"},{"key":"ref_5","unstructured":"Los Alamos National Laboratory (2026). HIV Sequence Database: Circulating Recombinant Forms (CRFs)."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"101596","DOI":"10.1016\/j.bjid.2021.101596","article-title":"HIV-1 genetic diversity and drug resistance mutations in the northern Brazilian region","volume":"25","author":"Crispim","year":"2021","journal-title":"Braz. J. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1093\/infdis\/jiad327","article-title":"Geographic and Population Distributions of Human Immunodeficiency Virus (HIV)-1 and HIV-2 Circulating Subtypes: A Systematic Literature Review and Meta-analysis (2010\u20132021)","volume":"228","author":"Williams","year":"2023","journal-title":"J. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1089\/aid.2009.0195","article-title":"Molecular epidemiology of HIV type 1 in Mexico: Emergence of BG and BF intersubtype recombinants","volume":"26","year":"2010","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Smoquina, F., Berno, G., Forbici, F., Sberna, G., Rozera, G., Abbate, I., Lazzari, E., Amendola, A., Mazzotta, V., and Gagliardini, R. (2025). Improved HIV-1 Subtyping Accuracy Using near Full-Length Sequencing: A Comparison of Common Tools. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms262311666"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"105491","DOI":"10.1016\/j.jcv.2023.105491","article-title":"Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing","volume":"164","author":"Faraci","year":"2023","journal-title":"J. Clin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1097\/QAI.0000000000003195","article-title":"Brief Report: Comparative Analysis of Pre-existing HIV Drug Resistance Mutations in Proviral DNA Using Next-Generation Sequencing and Routine HIV RNA Genotyping","volume":"93","author":"Gaitan","year":"2023","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_12","unstructured":"ABL Diagnostics (2026, June 09). DeepChek\u00ae-HIV Software (CE-IVD). Available online: https:\/\/www.ablsa.com\/laboratory-applications\/deepchek-hiv-software-ce-ivd\/."},{"key":"ref_13","unstructured":"ABL Diagnostics (2026, June 09). DeepChek\u00ae Assay Whole Genome HIV-1 Genotyping. Available online: https:\/\/www.abldiagnostics.com\/products\/deepchek-assay-whole-genome-hiv-1-genotyping\/."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Mohamed, S., Boulme, R., and Sayada, C. (2023). From Capillary Electrophoresis to Deep Sequencing: An Improved HIV-1 Drug Resistance Assessment Solution Using In Vitro Diagnostic (IVD) Assays and Software. Viruses, 15.","DOI":"10.3390\/v15020571"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1093\/jac\/dkz502","article-title":"Pretreatment HIV drug resistance spread within transmission clusters in Mexico City","volume":"75","author":"Chaillon","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100645","DOI":"10.1016\/j.ijregi.2025.100645","article-title":"Experience of a Nationwide implementation of single-tablet second-generation integrase inhibitors-based treatment in Mexico","volume":"15","author":"Rios","year":"2025","journal-title":"IJID Reg."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1093\/jac\/dkt316","article-title":"Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: Implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing","volume":"69","author":"Melikian","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1159\/000331998","article-title":"The HIVdb system for HIV-1 genotypic resistance interpretation","volume":"55","author":"Tang","year":"2012","journal-title":"Intervirology"},{"key":"ref_19","first-page":"457","article-title":"2025 update of the drug resistance mutations in HIV-1","volume":"33","author":"Wensing","year":"2025","journal-title":"Top. Antivir. Med."},{"key":"ref_20","unstructured":"Standford University HIV Drug Resistance Database (S.U.H.D.R) (2026). NNRTI Resistance Notes, HIV Drug Resistance Database."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1093\/jac\/dkr157","article-title":"Evolutionary pathways of transmitted drug-resistant HIV-1","volume":"66","author":"Pingen","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_22","unstructured":"ANRS-MIE Virology Network Resistance Group (2026, June 09). HIV-1 Genotypic Drug Resistance Interpretation Algorithm. Available online: https:\/\/hivfrenchresistance.org\/."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1159\/000332009","article-title":"The evolution of drug resistance interpretation algorithms: ANRS, REGA and extension of resistance analysis to HIV-1 group O and HIV-2","volume":"55","author":"Eberle","year":"2012","journal-title":"Intervirology"},{"key":"ref_24","unstructured":"HIV-GRADE (2026, June 09). HIV-GRADE Viral Genotypic Resistance Algorithms. Available online: https:\/\/www.hiv-grade.de\/cms\/grade\/."},{"key":"ref_25","unstructured":"National Center for Biotechnology Information (2026, June 09). Sequence Read Archive (SRA), Available online: https:\/\/www.ncbi.nlm.nih.gov\/sra."},{"key":"ref_26","unstructured":"National Center for Biotechnology Information (2026, June 09). Submit Your Project and Biological Samples: BioProject and BioSample Submissions, Available online: https:\/\/www.ncbi.nlm.nih.gov\/sra\/docs\/submitbio\/."},{"key":"ref_27","unstructured":"National Center for Biotechnology Information (2026, June 09). Submission Portal, Available online: https:\/\/submit.ncbi.nlm.nih.gov\/."},{"key":"ref_28","unstructured":"National Center for Biotechnology Information (2026, June 09). SRA Submission Quick Start, Available online: https:\/\/www.ncbi.nlm.nih.gov\/sra\/docs\/submit\/."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/12\/5571\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:19:27Z","timestamp":1782271167000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/12\/5571"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,20]]},"references-count":28,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["ijms27125571"],"URL":"https:\/\/doi.org\/10.3390\/ijms27125571","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,20]]}}}