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Weaver S, Dávila-Conn V, Ji D, Verdonk H, Ávila-Ríos S, Leigh Brown AJ, Wertheim JO, Kosakovsky Pond SL. AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS. bioRxiv 2024:2024.03.11.584522. [PMID: 38559140 PMCID: PMC10979987 DOI: 10.1101/2024.03.11.584522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic distance threshold used to connect sequences in the transmission network is a key parameter informing the properties of inferred networks. Using a distance threshold that is too high can result in a network with many spurious links, making it difficult to interpret. Conversely, a distance threshold that is too low can result in a network with too few links, which may not capture key insights into clusters of public health concern. Published research using the HIV-TRACE software package frequently uses the default threshold of 0.015 substitutions/site for HIV pol gene sequences, but in many cases, investigators heuristically select other threshold parameters to better capture the underlying dynamics of the epidemic they are studying. Here, we present a general heuristic scoring approach for tuning a distance threshold adaptively, which seeks to prevent the formation of giant clusters. We prioritize the ratio of the sizes of the largest and the second largest cluster, maximizing the number of clusters present in the network. We apply our scoring heuristic to outbreaks with different characteristics, such as regional or temporal variability, and demonstrate the utility of using the scoring mechanism's suggested distance threshold to identify clusters exhibiting risk factors that would have otherwise been more difficult to identify. For example, while we found that a 0.015 substitutions/site distance threshold is typical for US-like epidemics, recent outbreaks like the CRF07_BC subtype among men who have sex with men (MSM) in China have been found to have a lower optimal threshold of 0.005 to better capture the transition from injected drug use (IDU) to MSM as the primary risk factor. Alternatively, in communities surrounding Lake Victoria in Uganda, where there has been sustained hetero-sexual transmission for many years, we found that a larger distance threshold is necessary to capture a more risk factor-diverse population with sparse sampling over a longer period of time. Such identification may allow for more informed intervention action by respective public health officials.
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Affiliation(s)
- Steven Weaver
- Center for Viral Evolution, Temple University, Philadelphia, PA, USA
| | - Vanessa Dávila-Conn
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Daniel Ji
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA 92093, USA
| | - Hannah Verdonk
- Center for Viral Evolution, Temple University, Philadelphia, PA, USA
| | - Santiago Ávila-Ríos
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Andrew J Leigh Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Hallmark CJ, Luswata C, Del Vecchio N, Hayford C, Mora R, Carr M, McNeese M, Benbow N, Schneider JA, Wertheim JO, Fujimoto K. Predictors of HIV Molecular Cluster Membership and Implications for Partner Services. AIDS Res Hum Retroviruses 2023; 39:241-252. [PMID: 36785940 PMCID: PMC10171944 DOI: 10.1089/aid.2022.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Public health surveillance data used in HIV molecular cluster analyses lack contextual information that is available from partner services (PS) data. Integrating these data sources in retrospective analyses can enrich understanding of the risk profile of people in clusters. In this study, HIV molecular clusters were identified and matched to information on partners and other information gleaned at the time of diagnosis, including coinfection with syphilis. We aimed to produce a more complete understanding of molecular cluster membership in Houston, Texas, a city ranking ninth nationally in rate of new HIV diagnoses that may benefit from retrospective matched analyses between molecular and PS data to inform future intervention. Data from PS were matched to molecular HIV records of people newly diagnosed from 2012 to 2018. By conducting analyses in HIV-TRACE (TRAnsmission Cluster Engine) using viral genetic sequences, molecular clusters were detected. Multivariable logistic regression models were used to estimate the association between molecular cluster membership and completion of a PS interview, number of named partners, and syphilis coinfection. Using data from 4,035 people who had a viral genetic sequence and matched PS records, molecular cluster membership was not significantly associated with completion of a PS interview. Among those with sequences who completed a PS interview (n = 3,869), 45.3% (n = 1,753) clustered. Molecular cluster membership was significantly associated with naming 1 or 3+ partners compared with not naming any partners [adjusted odds ratio, aOR: 1.27 (95% confidence interval, CI: 1.08-1.50), p = .003 and aOR: 1.38 (95% CI: 1.06-1.81), p = .02]. Alone, coinfection with syphilis was not significantly associated with molecular cluster membership. Syphilis coinfection was associated with molecular cluster membership when coupled with incarceration [aOR: 1.91 (95% CI: 1.08-3.38), p = .03], a risk for treatment interruption. Enhanced intervention among those with similar profiles, such as people coinfected with other risks, may be warranted.
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Affiliation(s)
- Camden J. Hallmark
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Houston Health Department, Houston, Texas, USA
| | - Charles Luswata
- Houston Health Department, Houston, Texas, USA
- Department of Health Promotion and Behavioral Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Natascha Del Vecchio
- Department of Medicine and Public Health Sciences and the Chicago Center for HIV Elimination, University of Chicago, Chicago, Illinois, USA
| | - Christina Hayford
- Third Coast Center for AIDS Research, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Nanette Benbow
- Third Coast Center for AIDS Research, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - John A. Schneider
- Department of Medicine and Public Health Sciences and the Chicago Center for HIV Elimination, University of Chicago, Chicago, Illinois, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Kayo Fujimoto
- Department of Health Promotion and Behavioral Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
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Labarile M, Loosli T, Zeeb M, Kusejko K, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Battegay M, Rauch A, Calmy A, Notter J, Bernasconi E, Fux C, Günthard HF, Pasin C, Kouyos RD, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Quantifying and Predicting Ongoing Human Immunodeficiency Virus Type 1 Transmission Dynamics in Switzerland Using a Distance-Based Clustering Approach. J Infect Dis 2023; 227:554-564. [PMID: 36433831 DOI: 10.1093/infdis/jiac457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Despite effective prevention approaches, ongoing human immunodeficiency virus 1 (HIV-1) transmission remains a public health concern indicating a need for identifying its drivers. METHODS We combined a network-based clustering method using evolutionary distances between viral sequences with statistical learning approaches to investigate the dynamics of HIV transmission in the Swiss HIV Cohort Study and to predict the drivers of ongoing transmission. RESULTS We found that only a minority of clusters and patients acquired links to new infections between 2007 and 2020. While the growth of clusters and the probability of individual patients acquiring new links in the transmission network was associated with epidemiological, behavioral, and virological predictors, the strength of these associations decreased substantially when adjusting for network characteristics. Thus, these network characteristics can capture major heterogeneities beyond classical epidemiological parameters. When modeling the probability of a newly diagnosed patient being linked with future infections, we found that the best predictive performance (median area under the curve receiver operating characteristic AUCROC = 0.77) was achieved by models including characteristics of the network as predictors and that models excluding them performed substantially worse (median AUCROC = 0.54). CONCLUSIONS These results highlight the utility of molecular epidemiology-based network approaches for analyzing and predicting ongoing HIV transmission dynamics. This approach may serve for real-time prospective assessment of HIV transmission.
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Affiliation(s)
- Marco Labarile
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Manuel Battegay
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Christoph Fux
- Department of Infectious Diseases, Kantonsspital Aarau, Aarau, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Lee F, Khanna AS, Hallmark CJ, Lavingia R, McNeese M, Zhao J, McNeese ML, Khuwaja S, Ardestani BM, Collier N, Ozik J, Hotton AL, Harawa NT, Schneider JA, Fujimoto K. Expanding Medicaid to Reduce Human Immunodeficiency Virus Transmission in Houston, Texas: Insights From a Modeling Study. Med Care 2023; 61:12-19. [PMID: 36477617 PMCID: PMC9733589 DOI: 10.1097/mlr.0000000000001772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CONTEXT Medicaid expansion has been nationally shown to improve engagement in the human immunodeficiency virus (HIV) treatment and prevention continua, which are vital steps to stopping the HIV epidemic. New HIV infections in the United States are disproportionately concentrated among young Black men who have sex with men (YBMSM). Houston, TX, is the most populous city in the Southern United States with a racially/ethnically diverse population that is located in 1 of 11 US states that have not yet expanded Medicaid coverage as of 2021. METHODS An agent-based model that incorporated the sexual networks of YBMSM was used to simulate improved antiretroviral treatment and pre-exposure prophylaxis (PrEP) engagement through Medicaid expansion in Houston, TX. Analyses considered the HIV incidence (number of new infections and as a rate metric) among YBMSM over the next 10 years under Medicaid expansion as the primary outcome. Additional scenarios, involving viral suppression and PrEP uptake above the projected levels achieved under Medicaid expansion, were also simulated. RESULTS The baseline model projected an HIV incidence rate of 4.96 per 100 person years (py) and about 368 new annual HIV infections in the 10th year. Improved HIV treatment and prevention continua engagement under Medicaid expansion resulted in a 14.9% decline in the number of annual new HIV infections in the 10th year. Increasing viral suppression by an additional 15% and PrEP uptake by 30% resulted in a 44.0% decline in new HIV infections in the 10th year, and a 27.1% decline in cumulative infections across the 10 years of the simulated intervention. FINDINGS Simulation results indicate that Medicaid expansion has the potential to reduce HIV incidence among YBMSM in Houston. Achieving HIV elimination objectives, however, might require additional effective measures to increase antiretroviral treatment and PrEP uptake beyond the projected improvements under expanded Medicaid.
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Affiliation(s)
- Francis Lee
- Chicago Center for HIV Elimination,Department of Medicine, The University of Chicago, Chicago, IL
| | - Aditya S. Khanna
- Center for Alcohol and Addiction Studies,Department of Behavioral and Social Sciences, Brown University School of Public Health, Providence, RI
| | | | - Richa Lavingia
- Department of Medicine, Epidemiology, and Population Sciences, Baylor College of Medicine, Houston, Texas
| | - Marlene McNeese
- Division of Disease Prevention and Control, Houston Health Department
| | - Jing Zhao
- Department of Medicine, Epidemiology, and Population Sciences, Baylor College of Medicine, Houston, Texas
| | | | - Salma Khuwaja
- Division of Disease Prevention and Control, Houston Health Department
| | - Babak M. Ardestani
- Chicago Center for HIV Elimination,Department of Medicine, The University of Chicago, Chicago, IL
| | - Nicholson Collier
- Decision and Infrastructure Sciences Division, Argonne National Laboratory, Lemont, IL
| | - Jonathan Ozik
- Decision and Infrastructure Sciences Division, Argonne National Laboratory, Lemont, IL
| | - Anna L. Hotton
- Chicago Center for HIV Elimination,Department of Medicine, The University of Chicago, Chicago, IL
| | - Nina T. Harawa
- Departments of Medicine and Epidemiology, University of California,Department of Psychiatry, Charles R. Drew University of Medicine and Science, Los Angeles, CA
| | - John A. Schneider
- Chicago Center for HIV Elimination,Department of Medicine, The University of Chicago, Chicago, IL
| | - Kayo Fujimoto
- Department of Health Promotion and Behavioral Sciences, School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX
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5
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Fujimoto K, Paraskevis D, Kuo JC, Hallmark CJ, Zhao J, Hochi A, Kuhns LM, Hwang LY, Hatzakis A, Schneider JA. Integrated molecular and affiliation network analysis: Core-periphery social clustering is associated with HIV transmission patterns. Soc Networks 2022; 68:107-117. [PMID: 34262236 PMCID: PMC8274587 DOI: 10.1016/j.socnet.2021.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This study investigates the two-mode core-periphery structures of venue affiliation networks of younger Black men who have sex with men (YBMSM). We examined the association between these structures and HIV phylogenetic clusters, defined as members who share highly similar HIV strains that are regarded as a proxy for sexual affiliation networks. Using data from 114 YBMSM who are living with HIV in two large U.S. cities, we found that HIV phylogenetic clustering patterns were associated with social clustering patterns whose members share affiliation with core venues that overlap with those of YBMSM. Distinct HIV transmission patterns were found in each city, a finding that can help to inform tailored venue-based and network intervention strategies.
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Affiliation(s)
- Kayo Fujimoto
- Department of Health Promotion, The University of Texas Health Science Center at Houston, 7000 Fannin Street, UCT 2514, Houston, TX 77030
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Jacky C. Kuo
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston, 7000 Fannin Street, Houston, TX 77030
| | | | - Jing Zhao
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
| | - Andre Hochi
- Department of Health Promotion, The University of Texas Health Science Center at Houston, 7000 Fannin Street, UCT 2514, Houston, TX 77030
| | - Lisa M Kuhns
- Division of Adolescent Medicine, Ann & Robert H. Lurie Children’s Hospital, and Northwestern University, Feinberg School of Medicine, Department of Pediatrics, 225 E. Chicago Avenue, #161, Chicago, IL 60611
| | - Lu-Yu Hwang
- Department of Epidemiology, Human Genetics, and Environmental Science, The University of Texas Health Science Center at Houston, 7000 Fannin Street, Houston, TX 77030
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - John A. Schneider
- Department of Medicine and Public Health Sciences and the Chicago Center for HIV Elimination, University of Chicago, 5837 South Maryland Avenue MC 5065, Chicago, IL 60637
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Sivay MV, Totmenin AV, Zyryanova DP, Osipova IP, Nalimova TM, Gashnikova MP, Ivlev VV, Meshkov IO, Chokmorova UZ, Narmatova E, Motorov U, Akmatova Z, Asybalieva N, Bekbolotov AA, Kadyrbekov UK, Maksutov RA, Gashnikova NM. Characterization of HIV-1 Epidemic in Kyrgyzstan. Front Microbiol 2021; 12:753675. [PMID: 34721358 PMCID: PMC8554114 DOI: 10.3389/fmicb.2021.753675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Kyrgyzstan has one of the highest rates of HIV-1 spread in Central Asia. In this study, we used molecular–epidemiological approaches to examine the HIV-1 epidemic in Kyrgyzstan. Samples were obtained from HIV-positive individuals who visited HIV/AIDS clinics. Partial pol gene sequences were used to identify HIV-1 subtypes and drug resistance mutations (DRMs) and to perform phylogenetic analysis. Genetic diversity and history reconstruction of the major HIV-1 subtypes were explored using BEAST. This study includes an analysis of 555 HIV-positive individuals. The study population was equally represented by men and women aged 1–72 years. Heterosexual transmission was the most frequent, followed by nosocomial infection. Men were more likely to acquire HIV-1 during injection drug use and while getting clinical services, while women were more likely to be infected through sexual contacts (p < 0.01). Heterosexual transmission was the more prevalent among individuals 25–49 years old; individuals over 49 years old were more likely to be persons who inject drugs (PWID). The major HIV-1 variants were CRF02_AG, CRF63_02A, and sub-subtype A6. Major DRMs were detected in 26.9% of the study individuals; 62.2% of those had DRMs to at least two antiretroviral (ARV) drug classes. Phylogenetic analysis revealed a well-defined structure of CRF02_AG, indicating locally evolving sub-epidemics. The lack of well-defined phylogenetic structure was observed for sub-subtype A6. The estimated origin date of CRF02_AG was January 1997; CRF63_02A, April 2004; and A6, June 1995. A rapid evolutionary dynamic of CRF02_AG and A6 among Kyrgyz population since the mid-1990s was observed. We observed the high levels of HIV-1 genetic diversity and drug resistance in the study population. Complex patterns of HIV-1 phylogenetics in Kyrgyzstan were found. This study highlights the importance of molecular–epidemiological analysis for HIV-1 surveillance and treatment implementation to reduce new HIV-1 infections.
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Affiliation(s)
- Mariya V Sivay
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Alexei V Totmenin
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Daria P Zyryanova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Irina P Osipova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Tatyana M Nalimova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Mariya P Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Vladimir V Ivlev
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | | | - Umut Z Chokmorova
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Elmira Narmatova
- Osh Regional Center of AIDS Treatment and Prevention, Osh, Kyrgyzstan
| | - Ulukbek Motorov
- Osh Regional Center of AIDS Treatment and Prevention, Osh, Kyrgyzstan
| | - Zhyldyz Akmatova
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Nazgul Asybalieva
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Aybek A Bekbolotov
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Ulan K Kadyrbekov
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Rinat A Maksutov
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Natalya M Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
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7
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Dávila‐Conn V, García‐Morales C, Matías‐Florentino M, López‐Ortiz E, Paz‐Juárez HE, Beristain‐Barreda Á, Cárdenas‐Sandoval M, Tapia‐Trejo D, López‐Sánchez DM, Becerril‐Rodríguez M, García‐Esparza P, Macías‐González I, Iracheta‐Hernández P, Weaver S, Wertheim JO, Reyes‐Terán G, González‐Rodríguez A, Ávila‐Ríos S. Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020. J Int AIDS Soc 2021; 24:e25836. [PMID: 34762774 PMCID: PMC8583431 DOI: 10.1002/jia2.25836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022] Open
Abstract
INTRODUCTION Molecular surveillance systems could provide public health benefits to focus strategies to improve the HIV care continuum. Here, we infer the HIV genetic network of Mexico City in 2020, and identify actively growing clusters that could represent relevant targets for intervention. METHODS All new diagnoses, referrals from other institutions, as well as persons returning to care, enrolling at the largest HIV clinic in Mexico City were invited to participate in the study. The network was inferred from HIV pol sequences, using pairwise genetic distance methods, with a locally hosted, secure version of the HIV-TRACE tool: Seguro HIV-TRACE. Socio-demographic, clinical and behavioural metadata were overlaid across the network to design focused prevention interventions. RESULTS A total of 3168 HIV sequences from unique individuals were included. One thousand and one-hundred and fifty (36%) sequences formed 1361 links within 386 transmission clusters in the network. Cluster size varied from 2 to 14 (63% were dyads). After adjustment for covariates, lower age (adjusted odds ratio [aOR]: 0.37, p<0.001; >34 vs. <24 years), being a man who has sex with men (MSM) (aOR: 2.47, p = 0.004; MSM vs. cisgender women), having higher viral load (aOR: 1.28, p<0.001) and higher CD4+ T cell count (aOR: 1.80, p<0.001; ≥500 vs. <200 cells/mm3 ) remained associated with higher odds of clustering. Compared to MSM, cisgender women and heterosexual men had significantly lower education (none or any elementary: 59.1% and 54.2% vs. 16.6%, p<0.001) and socio-economic status (low income: 36.4% and 29.0% vs. 18.6%, p = 0.03) than MSM. We identified 10 (2.6%) clusters with constant growth, for prioritized intervention, that included intersecting sexual risk groups, highly connected nodes and bridge nodes between possible sub-clusters with high growth potential. CONCLUSIONS HIV transmission in Mexico City is strongly driven by young MSM with higher education level and recent infection. Nevertheless, leveraging network inference, we identified actively growing clusters that could be prioritized for focused intervention with demographic and risk characteristics that do not necessarily reflect the ones observed in the overall clustering population. Further studies evaluating different models to predict growing clusters are warranted. Focused interventions will have to consider structural and risk disparities between the MSM and the heterosexual populations.
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Affiliation(s)
- Vanessa Dávila‐Conn
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Claudia García‐Morales
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | | | - Eduardo López‐Ortiz
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Héctor E. Paz‐Juárez
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Ángeles Beristain‐Barreda
- 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
| | - Dulce M. López‐Sánchez
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Manuel Becerril‐Rodríguez
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Pedro García‐Esparza
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | | | | | - Steven Weaver
- Institute for Genomics and Evolutionary MedicineTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Joel O. Wertheim
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Gustavo Reyes‐Terán
- Coordinating Commission of the National Institutes of Health and High Specialty HospitalsMexico CityMexico
| | | | - Santiago Ávila‐Ríos
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
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