{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T12:50:27Z","timestamp":1782305427117,"version":"3.54.5"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T00:00:00Z","timestamp":1575936000000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Mexican Government"},{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","doi-asserted-by":"publisher","award":["CONACyT SALUD-2017-01-289725"],"award-info":[{"award-number":["CONACyT SALUD-2017-01-289725"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of California San Diego Centre for AIDS Research (CFAR), an NIH-funded programme."}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Patients and methods<\/jats:title>\n                  <jats:p>HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (\u226520%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances &amp;lt;1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a\u2009\u2265\u20092% threshold to include low-frequency variants.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Pretreatment HIVDR reached 14.8% (95% CI 13.4%\u201316.2%) in the cohort overall and 9.6% (8.5%\u201310.8%) to NNRTIs. Putative links with at least one other sequence were found for 963\/2447 (39%) sequences, forming 326 clusters (2\u201320 individuals). The inferred network was assortative by age and municipality (P\u2009&amp;lt;\u20090.001). Clustering individuals were younger [adjusted OR (aOR) per year\u2009=\u20090.96, 95% CI 0.95\u20130.97, P\u2009&amp;lt;\u20090.001] and less likely to include women (aOR\u2009=\u20090.46, 95% CI 0.28\u20130.75, P\u2009=\u20090.002). Among clustering individuals, 175\/963 (18%) shared DRMs (involving 66 clusters), of which 66\/175 (38%) shared K103N\/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR\u2009=\u20090.93, 95% CI 0.88\u20130.98, P\u2009=\u20090.003).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkz502","type":"journal-article","created":{"date-parts":[[2019,11,8]],"date-time":"2019-11-08T15:12:53Z","timestamp":1573225973000},"page":"656-667","source":"Crossref","is-referenced-by-count":17,"title":["Pretreatment HIV drug resistance spread within transmission clusters in Mexico City"],"prefix":"10.1093","volume":"75","author":[{"given":"Margarita","family":"Mat\u00edas-Florentino","sequence":"first","affiliation":[{"name":"Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Secci\u00f3n XVI, CP 14080 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antoine","family":"Chaillon","sequence":"first","affiliation":[{"name":"University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago","family":"\u00c1vila-R\u00edos","sequence":"first","affiliation":[{"name":"Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Secci\u00f3n XVI, CP 14080 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjay R","family":"Mehta","sequence":"first","affiliation":[{"name":"University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9ctor E","family":"Paz-Ju\u00e1rez","sequence":"first","affiliation":[{"name":"Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Secci\u00f3n XVI, CP 14080 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel A","family":"Becerril-Rodr\u00edguez","sequence":"first","affiliation":[{"name":"Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Secci\u00f3n XVI, CP 14080 Mexico City, Mexico"},{"name":"Cl\u00ednica Especializada Condesa, Gral, Benjam\u00edn Hill 24, Hip\u00f3dromo Condesa, CP 06170 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia J","family":"del Arenal-S\u00e1nchez","sequence":"first","affiliation":[{"name":"Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Secci\u00f3n XVI, CP 14080 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia","family":"Pi\u00f1eir\u00faa-Men\u00e9ndez","sequence":"first","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Av. Combate de Celaya S\/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ver\u00f3nica","family":"Ruiz","sequence":"first","affiliation":[{"name":"Cl\u00ednica Especializada Condesa, Gral, Benjam\u00edn Hill 24, Hip\u00f3dromo Condesa, CP 06170 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Iracheta-Hern\u00e1ndez","sequence":"first","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Av. Combate de Celaya S\/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Israel","family":"Mac\u00edas-Gonz\u00e1lez","sequence":"first","affiliation":[{"name":"Cl\u00ednica Especializada Condesa, Gral, Benjam\u00edn Hill 24, Hip\u00f3dromo Condesa, CP 06170 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jehovani","family":"Tena-S\u00e1nchez","sequence":"first","affiliation":[{"name":"Cl\u00ednica Especializada Condesa, Gral, Benjam\u00edn Hill 24, Hip\u00f3dromo Condesa, CP 06170 Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florentino","family":"Badial-Hern\u00e1ndez","sequence":"first","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Av. 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