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HIV Drug Resistance in Adults Initiating or Reinitiating Antiretroviral Therapy in Uruguay-Results of a Nationally Representative Survey, 2018-2019. Viruses 2023; 15:v15020490. [PMID: 36851704 PMCID: PMC9961578 DOI: 10.3390/v15020490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
The first nationally representative cross-sectional HIV drug resistance (HIVDR) survey was conducted in Uruguay in 2018-2019 among adults diagnosed with HIV and initiating or reinitiating antiretroviral therapy (ART). Protease, reverse transcriptase, and integrase genes of HIV-1 were sequenced. A total of 206 participants were enrolled in the survey; 63.2% were men, 85.7% were >25 years of age, and 35.6% reported previous exposure to antiretroviral (ARV) drugs. The prevalence of HIVDR to efavirenz or nevirapine was significantly higher (OR: 1.82, p < 0.001) in adults with previous ARV drug exposure (20.3%, 95% CI: 18.7-22.0%) compared to adults without previous ARV drug exposure (12.3%, 11.0-13.8%). HIVDR to any nucleoside reverse transcriptase inhibitors was 10.3% (9.4-11.2%). HIVDR to ritonavir-boosted protease inhibitors was 1.5% (1.1-2.1%); resistance to ritonavir-boosted darunavir was 0.9% (0.4-2.1%) among adults without previous ARV drug exposure and it was not observed among adults with previous ARV drug exposure. Resistance to integrase inhibitors was 12.7% (11.7-13.8%), yet HIVDR to dolutegravir, bictegravir, and cabotegravir was not observed. The high level (>10%) of HIVDR to efavirenz highlights the need to accelerate the transition to the WHO-recommended dolutegravir-based ART. Access to dolutegravir-based ART should be prioritised for people reporting previous ARV drug exposure.
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Springfield O, Brouwer KC, Avila-Rios S, Morales-Miranda S, Mehta SR. Molecular epidemiology of HIV-1 among adult female sex workers at the Guatemala-Mexico border. Glob Public Health 2023; 18:2278873. [PMID: 37944916 PMCID: PMC10808948 DOI: 10.1080/17441692.2023.2278873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
ABSTRACTSex workers have been demonstrated to have increased vulnerabilities to HIV and a high population prevalence of the disease. Despite their increased risk, sex workers have been underrepresented in molecular epidemiology studies assessing HIV in Mesoamerica. This study aims to describe the sociodemographic characteristics and phylogenetic profile of HIV-1 within a cohort of HIV-positive female sex workers (FSW) situated at the Guatemala-Mexico border. HIV viral sequences were collected from a cohort of FSW ≥18 years of age from San Marcos, Guatemala (n = 6) and compared to viral sequences collected as part of the Mesoamerican Drug Resistance Monitoring Programme to assess HIV viral diversity in Mexico and Guatemala (n = 3956). All of the FSW sampled were determined to have genetically unrelated HIV infections, suggesting multiple introductions of the virus and/or the potential existence of populations not captured by current surveillance efforts. Many reported numerous vulnerabilities that may have heightened their risk of acquiring and transmitting HIV through sex work activities. Our phylogenetic analysis indicated that national surveillance programmes may not fully capture the viral diversity among FSW and their clients within this region. Additional research is needed to fully capture HIV diversity and transmission in Mesoamerica, especially in the Guatemala-Mexico border region.
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Affiliation(s)
- Olivia Springfield
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - Kimberly C. Brouwer
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Sonia Morales-Miranda
- Consorcio de Investigación sobre VIH SIDA TB Consorcio de Investigación en Salud, Cuernavaca, Morelos, México
| | - Sanjay R. Mehta
- University of California San Diego School of Medicine, La Jolla, California, USA
- San Diego Veterans Affairs Medical Center, San Diego, California, USA
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Avila-Rios S, García-Morales C, Reyes-Terán G, González-Rodríguez A, Matías-Florentino M, Mehta SR, Chaillon A. Phylodynamics of HIV in the Mexico City Metropolitan Region. J Virol 2022; 96:e0070822. [PMID: 35762759 PMCID: PMC9327710 DOI: 10.1128/jvi.00708-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.
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Affiliation(s)
- Santiago Avila-Rios
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Ministry of Health, Mexico City, Mexico
| | | | | | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
- Veterans Affairs Health System, San Diego, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
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García-Morales C, Tapia-Trejo D, Matías-Florentino M, Quiroz-Morales VS, Dávila-Conn V, Beristain-Barreda Á, Cárdenas-Sandoval M, Becerril-Rodríguez M, Iracheta-Hernández P, Macías-González I, García-Mendiola R, Guzmán-Carmona A, Zarza-Sánchez E, Cruz RA, González-Rodríguez A, Reyes-Terán G, Ávila-Ríos S. HIV Pretreatment Drug Resistance Trends in Mexico City, 2017-2020. Pathogens 2021; 10:1587. [PMID: 34959542 PMCID: PMC8708254 DOI: 10.3390/pathogens10121587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
In response to increasing pretreatment drug resistance (PDR), Mexico changed its national antiretroviral treatment (ART) policy, recommending and procuring second-generation integrase strand-transfer inhibitor (INSTI)-based regimens as preferred first-line options since 2019. We present a four-year observational study describing PDR trends across 2017-2020 at the largest HIV diagnosis and primary care center in Mexico City. A total of 6688 baseline protease-reverse transcriptase and 6709 integrase sequences were included. PDR to any drug class was 14.4% (95% CI, 13.6-15.3%). A significant increasing trend for efavirenz/nevirapine PDR was observed (10.3 to 13.6%, p = 0.02). No increase in PDR to second-generation INSTI was observed, remaining under 0.3% across the study period. PDR was strongly associated with prior exposure to ART (aOR: 2.9, 95% CI: 1.9-4.6, p < 0.0001). MSM had higher odds of PDR to efavirenz/nevirapine (aOR: 2.0, 95% CI: 1.0-3.7, p = 0.04), reflecting ongoing transmission of mutations such as K103NS and E138A. ART restarters showed higher representation of cisgender women and injectable drug users, higher age, and lower education level. PDR to dolutegravir/bictegravir remained low in Mexico City, although further surveillance is warranted given the short time of ART optimization. Our study identifies demographic characteristics of groups with higher risk of PDR and lost to follow-up, which may be useful to design differentiated interventions locally.
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Affiliation(s)
- Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Verónica Sonia Quiroz-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Vanessa Dávila-Conn
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Ángeles Beristain-Barreda
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Miroslava Cárdenas-Sandoval
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Manuel Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Patricia Iracheta-Hernández
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Israel Macías-González
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Rebecca García-Mendiola
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Alejandro Guzmán-Carmona
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Eduardo Zarza-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Raúl Adrián Cruz
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Andrea González-Rodríguez
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Periférico Sur 4809, Colonia Arenal de Tepepan, Mexico City 14610, Mexico;
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
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Caro-Vega Y, Alarid-Escudero F, Enns EA, Sosa-Rubí S, Chivardi C, Piñeirúa-Menendez A, García-Morales C, Reyes-Terán G, Sierra-Madero JG, Ávila-Ríos S. Retention in Care, Mortality, Loss-to-Follow-Up, and Viral Suppression among Antiretroviral Treatment-Naïve and Experienced Persons Participating in a Nationally Representative HIV Pre-Treatment Drug Resistance Survey in Mexico. Pathogens 2021; 10:pathogens10121569. [PMID: 34959524 PMCID: PMC8706073 DOI: 10.3390/pathogens10121569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/20/2022] Open
Abstract
We describe associations of pretreatment drug resistance (PDR) with clinical outcomes such as remaining in care, loss to follow-up (LTFU), viral suppression, and death in Mexico, in real-life clinical settings. We analyzed clinical outcomes after a two-year follow up period in participants of a large 2017–2018 nationally representative PDR survey cross-referenced with information of the national ministry of health HIV database. Participants were stratified according to prior ART exposure and presence of efavirenz/nevirapine PDR. Using a Fine-Gray model, we evaluated virological suppression among resistant patients, in a context of competing risk with lost to follow-up and death. A total of 1823 participants were followed-up by a median of 1.88 years (Interquartile Range (IQR): 1.59–2.02): 20 (1%) were classified as experienced + resistant; 165 (9%) naïve + resistant; 211 (11%) experienced + non-resistant; and 1427 (78%) as naïve + non-resistant. Being ART-experienced was associated with a lower probability of remaining in care (adjusted Hazard Ratio(aHR) = 0.68, 0.53–0.86, for the non-resistant group and aHR = 0.37, 0.17–0.84, for the resistant group, compared to the naïve + non-resistant group). Heterosexual cisgender women compared to men who have sex with men [MSM], had a lower viral suppression (aHR = 0.84, 0.70–1.01, p = 0.06) ART-experienced persons with NNRTI-PDR showed the worst clinical outcomes. This group was enriched with women and persons with lower education and unemployed, which suggests higher levels of social vulnerability.
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Affiliation(s)
- Yanink Caro-Vega
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14000, Mexico; (Y.C.-V.); (J.G.S.-M.)
| | | | - Eva A. Enns
- Division of Health Policy and Management, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Sandra Sosa-Rubí
- Center for Health Systems Research, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (S.S.-R.); (C.C.)
| | - Carlos Chivardi
- Center for Health Systems Research, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (S.S.-R.); (C.C.)
| | | | - Claudia García-Morales
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico; (C.G.-M.); (G.R.-T.)
| | - Gustavo Reyes-Terán
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico; (C.G.-M.); (G.R.-T.)
| | - Juan G. Sierra-Madero
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14000, Mexico; (Y.C.-V.); (J.G.S.-M.)
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico; (C.G.-M.); (G.R.-T.)
- Correspondence: ; Tel.: +52-(55)-5666-7985 (ext. 133)
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Ma N, Chen XH, Zhao Y, Kang X, Pan S, Yao WQ. HIV-1 molecular transmission network among sexually transmitted populations in Liaoning Province, China. Medicine (Baltimore) 2021; 100:e26640. [PMID: 34260561 PMCID: PMC8284760 DOI: 10.1097/md.0000000000026640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/24/2021] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION In recent years, with the development of molecular epidemiology, molecular transmission networks based on evolutionary theory and sequence analysis have been widely used in research on human immunodeficiency virus (HIV)-1 transmission dynamics and precise intervention for high-risk populations. The HIV-1 molecular transmission network is a new method to study the population's access to the network, the characteristics of clustering, and the characteristics of interconnection in the network. Here, we analyzed the characteristics of the HIV-1 molecular transmission network of sexually transmitted people in Liaoning Province. METHODS A study of HIV-infected persons who were sexually transmitted in Liaoning Province from 2003 to 2019. HIV-1 RNA was extracted, amplified and sequenced, and a phylogenetic tree was constructed to determine the subtype using the well matched pol gene region sequence. The gene distance between sequences was calculated, the threshold was determined, and the molecular transmission network was constructed. RESULTS 109 samples of pol gene region were obtained. The main subtype of HIV-1 was CRF01_AE, followed by B, CRF07_BC, etc. 12.8% of them were resistant to HIV. At the threshold of 0.55 gene distance, 60.6% of them entered the HIV-1 molecular transmission network. Workers, sample source voluntary counseling and testing, other testing, subtype B and drug resistance are the factors influencing the access to HIV-1 molecular transmission network. The subtype of CRF01_AE formed 6 clusters in the molecular transmission network. In the network, the difference of connection degree between different subtypes was statistically significant. DISCUSSION The three subtypes CRF01_AE, CRF07_BC and B that enter the molecular transmission network do not have interconnections, and they form clusters with each other. It shows that the risk of transmission among the three subtypes is less than the risk of transmission within each subtype. The factors affecting HIV-1 entry into the molecular transmission network were occupation, sample source, genotype and drug resistance. The L33F mutation at the HIV-1 resistance mutation site constitutes the interconnection in the largest transmission cluster in the network. The epidemiological characteristics of HIV-infected persons in each molecular transmission cluster show that 97% of the study subjects come from the same area and have a certain spatial aggregation. CONCLUSION Constructing a molecular transmission network and conducting long-term monitoring, while taking targeted measures to block the spread of HIV can achieve precise prevention and control.
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Affiliation(s)
- Ning Ma
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Xing-hua Chen
- The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yan Zhao
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Xu Kang
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Shan Pan
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Wen-qing Yao
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
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Vrancken B, Mehta SR, Ávila-Ríos S, García-Morales C, Tapia-Trejo D, Reyes-Terán G, Navarro-Álvarez S, Little SJ, Hoenigl M, Pines HA, Patterson T, Strathdee SA, Smith DM, Dellicour S, Chaillon A. Dynamics and Dispersal of Local HIV Epidemics Within San Diego and Across The San Diego-Tijuana Border. Clin Infect Dis 2020; 73:e2018-e2025. [PMID: 33079188 DOI: 10.1093/cid/ciaa1588] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Evolutionary analyses of well-annotated HIV sequence data can provide insights into viral transmission patterns and associated factors. Here, we explored the transmission dynamics of the HIV-1 subtype B epidemic across the San Diego (US) - Tijuana (Mexico) border region to identify factors that could help guide public health policy. METHODS HIV pol sequences were collected from people with HIV in San Diego County and from Tijuana between 1996-2018. A multistep phylogenetic approach was used to characterize the dynamics of spread. The contribution of geospatial factors and HIV risk group to the local dynamics were evaluated. RESULTS Phylogeographic analyses of the 2,034 sequences revealed an important contribution of local transmission in sustaining the epidemic, as well as a complex viral migration network across the region. Geospatial viral dispersal between San Diego communities occurred predominantly among men-who-have-sex with-men with central San Diego being the main source (34.9%) and recipient (39.5%) of migration events. HIV migration was more frequent from San Diego county towards Tijuana than vice versa. Migrations were best explained by driving time between locations. CONCLUSION The US-Mexico border may not be a major barrier to the spread of HIV, which may stimulate coordinated transnational intervention approaches. Whereas a focus on central San Diego has the potential to avert most spread, the substantial viral migration independent of central San Diego shows that county-wide efforts will be more effective. Combined, this work shows that epidemiological information gleaned from pathogen genomes can uncover mechanisms that underlie sustained spread and, in turn, can be a building block of public health decision making.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Herestraat, Leuven, Belgium
| | - Sanjay R Mehta
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan, Colonia Sección XVI, CP, Mexico City, Mexico
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan, Colonia Sección XVI, CP, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan, Colonia Sección XVI, CP, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the Mexican National Institutes of Health, Periférico Sur, Arenal Tepepan, Mexico City, Mexico
| | | | - Susan J Little
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Martin Hoenigl
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Heather A Pines
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Thomas Patterson
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Herestraat, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, av. FD Roosevelt, Bruxelles, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
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Near point-of-care, point-mutation test to detect drug resistance in HIV-1: a validation study in a Mexican cohort. AIDS 2020; 34:1331-1338. [PMID: 32205723 DOI: 10.1097/qad.0000000000002524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Pretreatment HIV-drug resistance (PDR, HIVDR) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) is increasing globally. NNRTIs continue to be used as first-line antiretroviral therapy (ART) in some communities due to the cost of dolutegravir-based ART or dolutegravir-associated adverse events. A simplified version of the oligonucleotide ligation assay (OLA) - 'OLA-Simple' - is a low-cost, near point-of-care assay that provides ready-to-use lyophilized reagents and reports HIVDR mutations as colored lines on lateral flow strips. Our objective was to design and validate OLA-Simple for a Mexican cohort. DESIGN OLA-Simple probes to detect K65R, K103N/S, Y181C, M184V, and G190A were optimized for HIV Mexican sequences. Sixty clinical plasma specimens were analyzed by OLA-Simple by technicians blinded to Illumina-MiSeq sequences, and HIVDR results were compared. METHODS Plasma RNA was tested using OLA-Simple kits. OLA-Simple lateral flow strips were read by in-house software, and were classified as mutant or wild-type at each codon. The comparison of results by OLA-Simple and Miseq was used to generate receiver-operating characteristic curves. RESULTS OLA-Simple PCR amplified 59 of 60 specimens and successfully genotyped 287 of 295 codons, with eight of 295 (2.7%) indeterminate results. Compared to MiSeq, OLA-Simple gave five of 295 (1.7%) false-positive and four of 295 (1.4%) false-negative results. Excluding indeterminate results, OLA-Simple classified mutant with an accuracy of 97.4 and 98.8% when using thresholds at 10 and 25% mutant within an individual's HIV quasispecies, respectively. CONCLUSIONS Compared to MiSeq, OLA-Simple detected HIVDR with high sensitivity and accuracy. OLA-Simple could expand access to affordable and rapid HIVDR testing to guide appropriate ART choices in populations using NNRTI-based ART.
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Matías-Florentino M, Chaillon A, Ávila-Ríos S, Mehta SR, Paz-Juárez HE, Becerril-Rodríguez MA, del Arenal-Sánchez SJ, Piñeirúa-Menéndez A, Ruiz V, Iracheta-Hernández P, Macías-González I, Tena-Sánchez J, Badial-Hernández F, González-Rodríguez A, Reyes-Terán G. Pretreatment HIV drug resistance spread within transmission clusters in Mexico City. J Antimicrob Chemother 2020; 75:656-667. [PMID: 31819984 PMCID: PMC7021100 DOI: 10.1093/jac/dkz502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade. OBJECTIVES To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR. PATIENTS AND METHODS 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 (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants. RESULTS Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). 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 = 0.93, 95% CI 0.88-0.98, P = 0.003). CONCLUSIONS Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.
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Affiliation(s)
- Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Antoine Chaillon
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Sanjay R Mehta
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Héctor E Paz-Juárez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Manuel A Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Silvia J del Arenal-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Alicia Piñeirúa-Menéndez
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Verónica Ruiz
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Patricia Iracheta-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Israel Macías-González
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Jehovani Tena-Sánchez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Florentino Badial-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Andrea González-Rodríguez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
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Girón‐Callejas A, García‐Morales C, Mendizabal‐Burastero R, Román M, Tapia‐Trejo D, Pérez‐García M, Quiroz‐Morales VS, Juárez SI, Ravasi G, Vargas C, Gutiérrez R, Romero L, Solórzano A, Sajquim E, Northbrook S, Ávila‐Ríos S, Reyes‐Terán G. High levels of pretreatment and acquired HIV drug resistance in Nicaragua: results from the first nationally representative survey, 2016. J Int AIDS Soc 2019; 22:e25429. [PMID: 31860167 PMCID: PMC6924533 DOI: 10.1002/jia2.25429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 11/04/2019] [Accepted: 11/20/2019] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION A nationally representative HIV drug resistance (HIVDR) survey in Nicaragua was conducted to estimate the prevalence of pretreatment HIVDR (PDR) among antiretroviral therapy (ART) initiators and acquired HIVDR among people living with HIV (PLHIV) who had received ART for 12 ± 3 months (ADR12) and ≥48 months (ADR48). METHODS A nationwide cross-sectional survey with a two-stage cluster sampling was conducted from March to November 2016. Nineteen of 45 total ART clinics representing >90% of the national cohort of adults on ART were included. ART initiators were defined as PLHIV initiating or reinitiating first-line ART. HIVDR was assessed for protease, reverse transcriptase and integrase Sanger sequences using the Stanford HIVdb algorithm. Viral load (VL) suppression was defined as <1000 copies/mL. Results were weighted according to the survey design. RESULTS AND DISCUSSION A total of 638 participants were enrolled (PDR: 171; ADR12: 114; ADR48: 353). The proportion of ART initiators with prior exposure to antiretrovirals (ARVs) was 12.3% (95% CI: 5.8% to 24.3%). PDR prevalence to any drug was 23.4% (95% CI: 14.4% to 35.6%), and 19.3% (95% CI: 12.2% to 29.1%) to non-nucleoside reverse transcriptase inhibitors (NNRTI). NNRTI PDR was higher in ART initiators with previous ARV exposure compared with those with no exposure (76.2% vs. 11.0%, p < 0.001). Protease inhibitors (PI) and integrase strand transfer inhibitors PDR was not observed. VL suppression rate was 77.8% (95% CI: 67.1% to 85.8%) in ADR12 and 70.3% (95% CI: 66.7% to 73.8%) in ADR48. ADR12 prevalence to any drug among PLHIV without VL suppression was 85.1% (95% CI: 66.1% to 94.4%), 82.4% to NNRTI and 70.2% to nucleoside reverse transcriptase inhibitors (NRTI). ADR48 prevalence to any drug among PLHIV without VL suppression was 75.5% (95% CI: 63.5% to 84.5 %), 70.7% to NNRTI, 59.4% to NRTI and 4.6% to PI. CONCLUSIONS Despite implementation challenges yielding low-precision HIVDR estimates, high rates of NNRTI PDR were observed in Nicaragua, suggesting consideration of non-NNRTI-based first-line regimens for ART initiators. Strengthened HIVDR monitoring, systematic VL testing, and improved ART adherence support are also warranted.
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Affiliation(s)
| | - Claudia García‐Morales
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | | | | | - Daniela Tapia‐Trejo
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Marissa Pérez‐García
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Verónica S Quiroz‐Morales
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Sandra I Juárez
- U.S. Centers for Disease Control and PreventionGuatemala CityGuatemala
| | | | - Carlos Vargas
- Universidad del Valle de GuatemalaGuatemala CityGuatemala
| | | | - Luz Romero
- Universidad del Valle de GuatemalaManaguaNicaragua
| | | | - Edgar Sajquim
- Universidad del Valle de GuatemalaGuatemala CityGuatemala
| | - Sanny Northbrook
- U.S. Centers for Disease Control and PreventionGuatemala CityGuatemala
| | - Santiago Ávila‐Ríos
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Gustavo Reyes‐Terán
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
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