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Novitsky V, Steingrimsson J, Howison M, Dunn CW, Gillani FS, Fulton J, Bertrand T, Howe K, Bhattarai L, Ronquillo G, MacAskill M, Bandy U, Hogan J, Kantor R. Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic. AIDS 2023; 37:389-399. [PMID: 36695355 PMCID: PMC9881752 DOI: 10.1097/qad.0000000000003426] [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] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Molecular epidemiology is a powerful tool to characterize HIV epidemics and prioritize public health interventions. Typically, HIV clusters are assumed to have uniform patterns over time. We hypothesized that assessment of cluster evolution would reveal distinct cluster behavior, possibly improving molecular epidemic characterization, towards disrupting HIV transmission. DESIGN Retrospective cohort. METHODS Annual phylogenies were inferred by cumulative aggregation of all available HIV-1 pol sequences of individuals with HIV-1 in Rhode Island (RI) between 1990 and 2020, representing a statewide epidemic. Molecular clusters were detected in annual phylogenies by strict and relaxed cluster definition criteria, and the impact of annual newly-diagnosed HIV-1 cases to the structure of individual clusters was examined over time. RESULTS Of 2153 individuals, 31% (strict criteria) - 47% (relaxed criteria) clustered. Longitudinal tracking of individual clusters identified three cluster types: normal, semi-normal and abnormal. Normal clusters (83-87% of all identified clusters) showed predicted growing/plateauing dynamics, with approximately three-fold higher growth rates in large (15-18%) vs. small (∼5%) clusters. Semi-normal clusters (1-2% of all clusters) temporarily fluctuated in size and composition. Abnormal clusters (11-16% of all clusters) demonstrated collapses and re-arrangements over time. Borderline values of cluster-defining parameters explained dynamics of non-normal clusters. CONCLUSIONS Comprehensive tracing of molecular HIV clusters over time in a statewide epidemic identified distinct cluster types, likely missed in cross-sectional analyses, demonstrating that not all clusters are equal. This knowledge challenges current perceptions of consistent cluster behavior over time and could improve molecular surveillance of local HIV epidemics to better inform public health strategies.
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Affiliation(s)
| | | | - Mark Howison
- Research Improving People’s Lives, Providence, RI, USA
| | | | | | | | | | | | | | | | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
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2
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Syphilis as Re-Emerging Disease, Antibiotic Resistance, and Vulnerable Population: Global Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11121546. [PMID: 36558880 PMCID: PMC9785152 DOI: 10.3390/pathogens11121546] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Syphilis is a sexually transmitted disease that has become a public health problem, especially in vulnerable populations. A systematic review and time-free meta-analysis of the publications on the molecular detection of syphilis and mutations associated with antibiotic resistance, CORE group, and syphilis genotypes in PubMed databases, Scielo, and Cochrane was performed, and the last search was conducted in June 2022. Proportions were calculated, and standard errors and confidence intervals were reported for all results of interest. We included 41 articles for quantitative extraction and data synthesis. An increase was observed in the proportion of subjects diagnosed with syphilis and the presence of the A2058G mutation during the 2018−2021 period compared to 2006 (70% 95%CI 50−87 vs. 58% 95%CI 12−78), and we observed that the greater the proportion of the population participating in men who have sex with men (MSM) (<50% and >50%) syphilis increased (78% 95%CI 65−90 vs. 33% 95%CI 19−49). In conclusion, we suggest that there are a set of characteristics that are contributing to the resurgence of syphilis and the selective pressure of bacteria. The MSM population could be a vulnerable factor for this scenario and the global presence of A2058G and A2059G mutations that confer resistance to macrolides.
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3
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Mazrouee S, Hallmark CJ, Mora R, Del Vecchio N, Carrasco Hernandez R, Carr M, McNeese M, Fujimoto K, Wertheim JO. Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection. Sci Rep 2022; 12:19230. [PMID: 36357480 PMCID: PMC9648870 DOI: 10.1038/s41598-022-21924-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Detection of viral transmission clusters using molecular epidemiology is critical to the response pillar of the Ending the HIV Epidemic initiative. Here, we studied whether inference with an incomplete dataset would influence the accuracy of the reconstructed molecular transmission network. We analyzed viral sequence data available from ~ 13,000 individuals with diagnosed HIV (2012-2019) from Houston Health Department surveillance data with 53% completeness (n = 6852 individuals with sequences). We extracted random subsamples and compared the resulting reconstructed networks versus the full-size network. Increasing simulated completeness was associated with an increase in the number of detected clusters. We also subsampled based on the network node influence in the transmission of the virus where we measured Expected Force (ExF) for each node in the network. We simulated the removal of nodes with the highest and then lowest ExF from the full dataset and discovered that 4.7% and 60% of priority clusters were detected respectively. These results highlight the non-uniform impact of capturing high influence nodes in identifying transmission clusters. Although increasing sequence reporting completeness is the way to fully detect HIV transmission patterns, reaching high completeness has remained challenging in the real world. Hence, we suggest taking a network science approach to enhance performance of molecular cluster detection, augmented by node influence information.
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Affiliation(s)
- Sepideh Mazrouee
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
| | | | | | | | - Rocio Carrasco Hernandez
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, México
| | | | | | - Kayo Fujimoto
- Department of Health Promotion and Behavioral Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, USA
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4
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Gore DJ, Schueler K, Ramani S, Uvin A, Phillips G, McNulty M, Fujimoto K, Schneider J. HIV Response Interventions that Integrate HIV Molecular Cluster and Social Network Analysis: A Systematic Review. AIDS Behav 2022; 26:1750-1792. [PMID: 34779940 PMCID: PMC9842229 DOI: 10.1007/s10461-021-03525-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/19/2023]
Abstract
Due to improved efficiency and reduced cost of viral sequencing, molecular cluster analysis can be feasibly utilized alongside existing human immunodeficiency virus (HIV) prevention strategies. The goal of this paper is to elucidate how HIV molecular cluster and social network analyses are being integrated to implement HIV response interventions. We searched PubMed, Scopus, PsycINFO, and Cochrane Library databases for studies incorporating both HIV molecular cluster and social network data. We identified 32 articles that combined analyses of HIV molecular sequences and social or sexual networks. All studies were descriptive. Six studies described network interventions informed by molecular and social data but did not fully evaluate their efficacy. There is no current standard for incorporating molecular and social network analyses to inform interventions or data demonstrating its utility. More research must be conducted to delineate benefits and best practices for leveraging molecular data for network-based interventions.
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Affiliation(s)
- Daniel J Gore
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kellie Schueler
- Department of Obstetrics and Gynecology, University of California San Diego, San Diego, CA, USA
| | - Santhoshini Ramani
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA
| | - Arno Uvin
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA
| | - Gregory Phillips
- Department of Medical Social Sciences, Northwestern University, Chicago, IL, USA
| | - Moira McNulty
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kayo Fujimoto
- Department of Health Promotion & Behavioral Sciences, University of Texas Health Sciences Center, Houston, TX, USA
| | - John Schneider
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
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5
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Steingrimsson JA, Fulton J, Howison M, Novitsky V, Gillani FS, Bertrand T, Civitarese A, Howe K, Ronquillo G, Lafazia B, Parillo Z, Marak T, Chan PA, Bhattarai L, Dunn C, Bandy U, Scott NA, Hogan JW, Kantor R. Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public health interventions. BMJ Open 2022; 12:e060184. [PMID: 35450916 PMCID: PMC9024226 DOI: 10.1136/bmjopen-2021-060184] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/29/2022] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION HIV continues to have great impact on millions of lives. Novel methods are needed to disrupt HIV transmission networks. In the USA, public health departments routinely conduct contact tracing and partner services and interview newly HIV-diagnosed index cases to obtain information on social networks and guide prevention interventions. Sequence clustering methods able to infer HIV networks have been used to investigate and halt outbreaks. Incorporation of such methods into routine, not only outbreak-driven, contact tracing and partner services holds promise for further disruption of HIV transmissions. METHODS AND ANALYSIS Building on a strong academic-public health collaboration in Rhode Island, we designed and have implemented a state-wide prospective study to evaluate an intervention that incorporates real-time HIV molecular clustering information with routine contact tracing and partner services. We present the rationale and study design of our approach to integrate sequence clustering methods into routine public health interventions as well as related important ethical considerations. This prospective study addresses key questions about the benefit of incorporating a clustering analysis triggered intervention into the routine workflow of public health departments, going beyond outbreak-only circumstances. By developing an intervention triggered by, and incorporating information from, viral sequence clustering analysis, and evaluating it with a novel design that avoids randomisation while allowing for methods comparison, we are confident that this study will inform how viral sequence clustering analysis can be routinely integrated into public health to support the ending of the HIV pandemic in the USA and beyond. ETHICS AND DISSEMINATION The study was approved by both the Lifespan and Rhode Island Department of Health Human Subjects Research Institutional Review Boards and study results will be published in peer-reviewed journals.
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Affiliation(s)
- Jon A Steingrimsson
- Biostatistics, Brown University School of Public Health, Providence, Rhode Island, USA
| | - John Fulton
- Department of Behavioral and Social Sciences, Brown University, Providence, Rhode Island, USA
| | - Mark Howison
- Research Improving People's Lives, Providence, Rhode Island, USA
| | - Vlad Novitsky
- Department of Medicine, Brown University, Providence, Rhode Island, USA
| | - Fizza S Gillani
- Department of Medicine, Brown University, Providence, Rhode Island, USA
| | - Thomas Bertrand
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Anna Civitarese
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Katharine Howe
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | | | - Benjamin Lafazia
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Zoanne Parillo
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Theodore Marak
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Philip A Chan
- Department of Medicine, Brown University, Providence, Rhode Island, USA
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Lila Bhattarai
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Casey Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Utpala Bandy
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | | | - Joseph W Hogan
- Biostatistics, Brown University School of Public Health, Providence, Rhode Island, USA
| | - Rami Kantor
- Department of Medicine, Brown University, Providence, Rhode Island, USA
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6
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Nguyen VT, Jatta A, Mayer R, Meier JL. Evaluation of Undiagnosed HIV Estimates Computed from the CD4 Depletion Model in a Rural, Medium-low HIV Prevalence State. AIDS Behav 2022; 26:613-622. [PMID: 34355286 DOI: 10.1007/s10461-021-03419-1] [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] [Accepted: 07/31/2021] [Indexed: 11/25/2022]
Abstract
The CD4 depletion model estimates diagnosis delays by approximating infection date from CD4 T-cell count at diagnosis, and back-calculation can compute the proportion of undiagnosed PLWHA. The model assumes the immigration of PLWHA to the U.S. is negligible and counts as a transmission event, which may be impractical outside high prevalence states. Duration of U.S. residency among foreign-born PLWHA and diagnosis delays were compared. The impact on estimates of undiagnosed PLWHA was tested through simulation with different proportions of foreign-born people assumed to have acquired HIV abroad. In 67% of foreign-born people, the mean (SD) years of delay (9.9 (6.3)) exceeded the duration of U.S. residency (2.0 (1.9)). Additionally, inaccuracies in the estimates for proportions of undiagnosed PLWHA were pronounced when foreign-born people who acquired HIV abroad comprised 30% of diagnoses. The CD4 model inadvertently misclassified some diagnoses as in-state transmission events. Consequently, simulated results demonstrated inaccuracies and unstable calculations.
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Affiliation(s)
- V T Nguyen
- College of Public Health, University of Iowa, Iowa City, IA, USA.
- VA Connecticut Health Care System, West Haven, CT, USA.
- Yale University, Epidemiology & Public Health, PO Box 208034, New Haven, CT, 06520-8034, USA.
| | - A Jatta
- Iowa Department of Public Health, Bureau of HIV, STD, and Hepatitis, Des Moines, IA, USA
| | - R Mayer
- Iowa Department of Public Health, Bureau of HIV, STD, and Hepatitis, Des Moines, IA, USA
| | - J L Meier
- College of Public Health, University of Iowa, Iowa City, IA, USA
- College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa City Veterans Affairs Medical Center, Iowa City, IA, USA
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7
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Alexiev I, Mavian C, Paisie T, Ciccozzi M, Dimitrova R, Gancheva A, Kostadinova A, Seguin-Devaux C, Salemi M. Analysis of the Origin and Dissemination of HIV-1 Subtype C in Bulgaria. Viruses 2022; 14:v14020263. [PMID: 35215855 PMCID: PMC8875591 DOI: 10.3390/v14020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 subtype C is the most abundant strain of HIV-1 infections worldwide and was found in the first known patients diagnosed with HIV/AIDS in Bulgaria in 1986. However, there is limited information on the molecular-epidemiological characteristics of this strain in the epidemic of the country. In this study, we analyze the evolutionary history of the introduction and dissemination of HIV-1 subtype C in Bulgaria using global phylogenetic analysis, Bayesian coalescent-based approach, and molecular clock methods. All available samples with HIV-1 subtype C from individuals diagnosed with HIV/AIDS between 1986 and 2017 were analyzed. Men and women were equally represented, and 24.3% of patients reported being infected abroad. The global phylogenetic analysis indicated multiple introductions of HIV-1 subtype C from various countries of the world. The reconstruction of a Bayesian time-scaled phylogenies showed that several Bulgarian strains segregated together in clusters, while others were intermixed in larger clades containing strains isolated from both European and non-European countries. The time-scale of HIV-1 subtype C introductions in Bulgaria demonstrates the early introduction of these viruses in the country. Our in-depth phylogenetic and phylogeographic analyses are compatible with a scenario of multiple early introductions in the country followed by limited local distribution in the subsequent years. HIV-1 subtype C was introduced in the early years of the epidemic, originating from different countries of the world. Due to the comprehensive measures for prevention and control in the early years of the epidemic in Bulgaria, HIV-1 subtype C was not widely disseminated among the general population of the country.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
- Correspondence: ; Tel.: +359-2-9318071
| | - Carla Mavian
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Taylor Paisie
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico, 00128 Rome, Italy;
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Luxembourg, Luxembourg;
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
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8
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Novitsky V, Steingrimsson J, Gillani FS, Howison M, Aung S, Solomon M, Won CY, Brotherton A, Shah R, Dunn C, Fulton J, Bertrand T, Civitarese A, Howe K, Marak T, Chan P, Bandy U, Alexander-Scott N, Hogan J, Kantor R. Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA. Open Forum Infect Dis 2022; 9:ofab587. [PMID: 34988256 PMCID: PMC8709897 DOI: 10.1093/ofid/ofab587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Background HIV-1 transmitted drug resistance (TDR) remains a global challenge that can impact care, yet its comprehensive assessment is limited and heterogenous. We longitudinally characterized statewide TDR in Rhode Island. Methods Demographic and clinical data from treatment-naïve individuals were linked to protease, reverse transcriptase, and integrase sequences routinely obtained over 2004-2020. TDR extent, trends, impact on first-line regimens, and association with transmission networks were assessed using the Stanford Database, Mann-Kendall statistic, and phylogenetic tools. Results In 1123 individuals, TDR to any antiretroviral increased from 8% (2004) to 26% (2020), driven by non-nucleotide reverse transcriptase inhibitor (NNRTI; 5%-18%) and, to a lesser extent, nucleotide reverse transcriptase inhibitor (NRTI; 2%-8%) TDR. Dual- and triple-class TDR rates were low, and major integrase strand transfer inhibitor resistance was absent. Predicted intermediate to high resistance was in 77% of those with TDR, with differential suppression patterns. Among all individuals, 34% were in molecular clusters, some only with members with TDR who shared mutations. Among clustered individuals, people with TDR were more likely in small clusters. Conclusions In a unique (statewide) assessment over 2004-2020, TDR increased; this was primarily, but not solely, driven by NNRTIs, impacting antiretroviral regimens. Limited TDR to multiclass regimens and pre-exposure prophylaxis are encouraging; however, surveillance and its integration with molecular epidemiology should continue in order to potentially improve care and prevention interventions.
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Affiliation(s)
| | | | | | - Mark Howison
- Research Improving People's Life, Providence, Rhode Island, USA
| | - Su Aung
- Brown University, Providence, Rhode Island, USA
| | | | - Cindy Y Won
- Brown University, Providence, Rhode Island, USA
| | | | - Rajeev Shah
- Brown University, Providence, Rhode Island, USA
| | - Casey Dunn
- Yale University, New Haven, Connecticut, USA
| | - John Fulton
- Brown University, Providence, Rhode Island, USA
| | - Thomas Bertrand
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Anna Civitarese
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Katharine Howe
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Theodore Marak
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Philip Chan
- Brown University, Providence, Rhode Island, USA.,Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Utpala Bandy
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | | | | | - Rami Kantor
- Brown University, Providence, Rhode Island, USA
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9
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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. SOCIAL 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] [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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10
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Novitsky V, Steingrimsson J, Howison M, Dunn C, Gillani FS, Manne A, Li Y, Spence M, Parillo Z, Fulton J, Marak T, Chan P, Bertrand T, Bandy U, Alexander-Scott N, Hogan J, Kantor R. Longitudinal typing of molecular HIV clusters in a statewide epidemic. AIDS 2021; 35:1711-1722. [PMID: 34033589 PMCID: PMC8373695 DOI: 10.1097/qad.0000000000002953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND HIV molecular epidemiology is increasingly integrated into public health prevention. We conducted cluster typing to enhance characterization of a densely sampled statewide epidemic towards informing public health. METHODS We identified HIV clusters, categorized them into types, and evaluated their dynamics between 2004 and 2019 in Rhode Island. We grouped sequences by diagnosis year, assessed cluster changes between paired phylogenies, t0 and t1, representing adjacent years and categorized clusters as stable (cluster in t0 phylogeny = cluster in t1 phylogeny) or unstable (cluster in t0 ≠ cluster in t1). Unstable clusters were further categorized as emerging (t1 phylogeny only) or growing (larger in t1 phylogeny). We determined proportions of each cluster type, of individuals in each cluster type, and of newly diagnosed individuals in each cluster type, and assessed trends over time. RESULTS A total of 1727 individuals with available HIV-1 subtype B pol sequences were diagnosed in Rhode Island by 2019. Over time, stable clusters and individuals in them dominated the epidemic, increasing over time, with reciprocally decreasing unstable clusters and individuals in them. Conversely, proportions of newly diagnosed individuals in unstable clusters significantly increased. Within unstable clusters, proportions of emerging clusters and of individuals in them declined; whereas proportions of newly diagnosed individuals in growing clusters significantly increased over time. CONCLUSION Distinct molecular cluster types were identified in the Rhode Island epidemic. Cluster dynamics demonstrated increasing stable and decreasing unstable clusters driven by growing, rather than emerging clusters, suggesting consistent in-state transmission networks. Cluster typing could inform public health beyond conventional approaches and direct interventions.
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Affiliation(s)
| | | | - Mark Howison
- Research Improving People’s Life, Providence, RI, USA
| | | | | | | | | | | | | | | | | | - Philip Chan
- Brown University, Providence, RI, USA
- Rhode Island Department of Health, Providence, RI, USA
| | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
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11
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Hughes SD, Woods WJ, O'Keefe KJ, Delgado V, Pipkin S, Scheer S, Truong HHM. Integrating Phylogenetic Biomarker Data and Qualitative Approaches: An example of HIV Transmission Clusters as a Sampling Frame for Semistructured Interviews and Implications for the COVID-19 Era. JOURNAL OF MIXED METHODS RESEARCH 2021; 15:327-347. [PMID: 38883973 PMCID: PMC11178346 DOI: 10.1177/15586898211012786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mixed methods studies of human disease that combine surveillance, biomarker, and qualitative data can help elucidate what drives epidemiological trends. Viral genetic data are rarely coupled with other types of data due to legal and ethical concerns about patient privacy. We developed a novel approach to integrate phylogenetic and qualitative methods in order to better target HIV prevention efforts. The overall aim of our mixed methods study was to characterize HIV transmission clusters. We combined surveillance data with HIV genomic data to identify cases whose viruses share enough similarities to suggest a recent common source of infection or participation in linked transmission chains. Cases were recruited through a multi-phase process to obtain consent for recruitment to semi-structured interviews. Through linkage of viral genetic sequences with epidemiological data, we identified individuals in large transmission clusters, which then served as a sampling frame for the interviews. In this article, we describe the multi-phase process and the limitations and challenges encountered. Our approach contributes to the mixed methods research field by demonstrating that phylogenetic analysis and surveillance data can be harnessed to generate a sampling frame for subsequent qualitative data collection, using an explanatory sequential design. The process we developed also respected protections of patient confidentiality. The novel method we devised may offer an opportunity to implement a sampling frame that allows for the recruitment and interview of individuals in high-transmission clusters to better understand what contributes to spread of other infectious diseases, including COVID-19.
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Affiliation(s)
| | | | - Kara J O'Keefe
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Viva Delgado
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Sharon Pipkin
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Susan Scheer
- San Francisco Department of Public Health, San Francisco, CA, USA
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12
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Fujimoto K, Bahl J, Wertheim JO, Del Vecchio N, Hicks JT, Damodaran L, Hallmark CJ, Lavingia R, Mora R, Carr M, Yang B, Schneider JA, Hwang LY, McNeese M. Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context. Sci Rep 2021; 11:3325. [PMID: 33558579 PMCID: PMC7870963 DOI: 10.1038/s41598-021-82673-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/22/2021] [Indexed: 12/30/2022] Open
Abstract
This study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. Using 6332 HIV-1 pol sequences from persons newly diagnosed with HIV during the period 2010–2018, we reconstructed HIV-1 transmission clusters, using the HIV-TRAnsmission Cluster Engine (HIV-TRACE); inferred demographic and risk parameters on HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and modeled the degree of network connectivity by using generalized estimating equations (GEE). Our results indicate that Hispanics/Latinos are most vulnerable to the structure of transmission clusters and serve as a bridge population, acting as recipients of transmissions from Whites (3.0 state changes/year) and from Blacks (2.6 state changes/year) as well as sources of transmissions to Whites (1.8 state changes/year) and to Blacks (1.2 state changes/year). There were high rates of transmission and high network connectivity between younger and older Hispanics/Latinos as well as between younger and older Blacks. Prevention and intervention efforts are needed for transmission clusters that involve younger racial/ethnic minorities, in particular Hispanic/Latino youth, to reduce onward transmission of HIV in Houston.
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Affiliation(s)
- Kayo Fujimoto
- Department of Health Promotion and Behavioral Sciences, The University of Texas Health Science Center at Houston, 7000 Fannin Street, UCT 2514, Houston, TX, 77030, USA.
| | - Justin Bahl
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Natascha Del Vecchio
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joseph T Hicks
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | | | - Camden J Hallmark
- Division of Disease Prevention and Control, Houston Health Department, Houston, TX, USA
| | - Richa Lavingia
- Department of Health Promotion and Behavioral Sciences, The University of Texas Health Science Center at Houston, 7000 Fannin Street, UCT 2514, Houston, TX, 77030, USA
| | - Ricardo Mora
- Division of Disease Prevention and Control, Houston Health Department, Houston, TX, USA
| | - Michelle Carr
- Division of Disease Prevention and Control, Houston Health Department, Houston, TX, USA
| | - Biru Yang
- Division of Disease Prevention and Control, Houston Health Department, Houston, TX, USA
| | | | - Lu-Yu Hwang
- Department of Epidemiology, Human Genetics, and Environmental Science, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Marlene McNeese
- Division of Disease Prevention and Control, Houston Health Department, Houston, TX, USA
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13
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Fan Q, Zhang J, Luo M, Yao J, Ge R, Yan Y, Ding X, Chen W, Pan X. Analysis of the Driving Factors of Active and Rapid Growth Clusters Among CRF07_BC-Infected Patients in a Developed Area in Eastern China. Open Forum Infect Dis 2021; 8:ofab051. [PMID: 33728360 PMCID: PMC7944347 DOI: 10.1093/ofid/ofab051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/29/2021] [Indexed: 11/22/2022] Open
Abstract
Background The purpose of this study was to research the molecular transmission and genetic evolutionary characteristics among CRF07_BC-infected patients in a developed area in Eastern China. Methods Plasma samples from newly diagnosed HIV-1-positive patients from 2015–2018 and basic demographic and epidemiological information were obtained. Pol sequences from CRF07_BC-infected patients were selected for phylogenetic, molecular transmission network, and Bayesian evolutionary analyses. Results Pol sequences were successfully obtained from 258 samples of CRF07_BC. Phylogenetic analysis revealed 2 distinct lineages: lineage 1 (66.3%, 171/258), primarily from men who have sex with men (MSM) and some heterosexual individuals, and lineage 2 (33.7%, 87/258), primarily from heterosexual individuals. Under an optimal genetic distance of 0.01 substitutions/site, 163 individuals (63.2%, 163/258) formed 23 groups comprising 6 clusters and 17 dyads in the networks. A distinctly large and rapidly growing cluster (C1) containing 105 individuals was identified, in which MSM with ≥4 links had quite a high transmission risk (low educational background, active sexual behavior, low sexual protection awareness, etc.). According to Bayesian analyses, most C1 clades formed from 2005 to 2009, most of which were closely geographically related to CRF07_BC epidemic strains from Anhui province. Conclusions Here, we elucidated the local transmission characteristics and epidemic pattern of HIV-1 CRF07_BC, revealing that MSM (especially with ≥4 links) may be a significant driver in the formation of active and rapid growth networks in regional CRF07_BC epidemics. Thus, unique region– and risk group–specific transmission network analysis based on a molecular approach can provide critical and insightful information for more effective intervention strategies to limit future HIV-1 transmission.
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Affiliation(s)
- Qin Fan
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jiafeng Zhang
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Mingyu Luo
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jiaming Yao
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Rui Ge
- Division of AIDS/TB Prevention and Control, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing, China
| | - Yong Yan
- Division of AIDS/TB Prevention and Control, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing, China
| | - Xiaobei Ding
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Wanjun Chen
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaohong Pan
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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14
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Factors Associated With Human Immunodeficiency Virus Infections Linked in Genetic Clusters But Disconnected in Partner Tracing. Sex Transm Dis 2020; 47:80-87. [PMID: 31934954 DOI: 10.1097/olq.0000000000001094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Successful partner notification can improve community-level outcomes by increasing the proportion of persons living with human immunodeficiency virus (HIV) who are linked to HIV care and virally suppressed, but it is resource intensive. Understanding where HIV transmission pathways may be undetected by routine partner notification may help improve case finding strategies. METHODS We combined partner notification interview and HIV sequence data for persons diagnosed with HIV in Wake County, NC in 2012 to 2013 to evaluate partner contact networks among persons with HIV pol gene sequences 2% or less pairwise genetic distance. We applied a set of multivariable generalized estimating equations to identify correlates of disparate membership in genetic versus partner contact networks. RESULTS In the multivariable model, being in a male-male pair (adjusted odds ratio [AOR], 16.7; P = 0.01), chronic HIV infection status (AOR, 4.5; P < 0.01), and increasing percent genetic distance between each dyad member's HIV pol gene sequence (AOR, 8.3 per each 1% increase, P < 0.01) were all associated with persons with HIV clustering but not being identified in the partner notification network component. Having anonymous partners or other factors typically associated with risk behavior were not associated. CONCLUSIONS Based on genetic networks, partnerships which may be stigmatized, may have occurred farther back in time or may have an intervening partner were more likely to be unobserved in the partner contact network. The HIV genetic cluster information contributes to public health understanding of HIV transmission networks in these settings where partner identifying information is not available.
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15
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Shiino T, Hachiya A, Hattori J, Sugiura W, Yoshimura K. Nation-Wide Viral Sequence Analysis of HIV-1 Subtype B Epidemic in 2003–2012 Revealed a Contribution of Men Who Have Sex With Men to the Transmission Cluster Formation and Growth in Japan. FRONTIERS IN REPRODUCTIVE HEALTH 2020; 2:531212. [PMID: 36304701 PMCID: PMC9580810 DOI: 10.3389/frph.2020.531212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
Background: To better understand the epidemiology of human immunodeficiency virus type 1 (HIV-1) subtype B transmission in Japan, phylodynamic analysis of viral pol sequences was conducted on individuals newly diagnosed as HIV-1 seropositive. Methodology: A total of 5,018 patients newly diagnosed with HIV-1 infection and registered in the Japanese Drug Resistance HIV Surveillance Network from 2003 to 2012 were enrolled in the analysis. Using the protease-reverse transcriptase nucleotide sequences, their subtypes were determined, and phylogenetic relationships among subtype B sequences were inferred using three different methods: distance-matrix, maximum likelihood, and Bayesian Markov chain Monte Carlo. Domestically spread transmission clusters (dTCs) were identified based on the following criteria: >95% in interior branch test, >95% in Bayesian posterior probability and <10% in depth-first searches for sub-tree partitions. The association between dTC affiliation and individuals' demographics was analyzed using univariate and multivariate analyses. Results: Among the cases enrolled in the analysis, 4,398 (87.6%) were classified as subtype B. Many of them were Japanese men who had sex with men (MSM), and 3,708 (84.3%) belonged to any of 312 dTCs. Among these dTCs, 243 (77.9%) were small clusters with <10 individuals, and the largest cluster consisted of 256 individuals. Most dTCs had median time of the most recent common ancestor between 1995 and 2005, suggesting that subtype B infection was spread among MSMs in the second half of the 1990s. Interestingly, many dTCs occurred within geographical regions. Comparing with singleton cases, TCs included more MSM, young person, and individuals with high CD4+ T-cell count at the first consultation. Furthermore, dTC size was significantly correlated with gender, age, transmission risks, recent diagnosis and relative population size of the region mainly distributed. Conclusions: Our study clarified that major key population of HIV-1 subtype B epidemic in Japan is local MSM groups. The study suggests that HIV-1 subtype B spread via episodic introductions into the local MSM groups, some of the viruses spread to multiple regions. Many cases in dTC were diagnosed during the early phase of infection, suggesting their awareness to HIV risks.
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Affiliation(s)
- Teiichiro Shiino
- Surveillance and Information Division, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Teiichiro Shiino
| | - Atsuko Hachiya
- Division of Biological Information Analysis, Department of Clinical Research Management, Crinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Junko Hattori
- Division of Biological Information Analysis, Department of Clinical Research Management, Crinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Wataru Sugiura
- Division of Biological Information Analysis, Department of Clinical Research Management, Crinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhisa Yoshimura
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Research Institute Director, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
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16
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Liu M, Han X, Zhao B, An M, He W, Wang Z, Qiu Y, Ding H, Shang H. Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes. Front Microbiol 2020; 11:604993. [PMID: 33281803 PMCID: PMC7691493 DOI: 10.3389/fmicb.2020.604993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/27/2020] [Indexed: 01/20/2023] Open
Abstract
This study reconstructed molecular networks of human immunodeficiency virus (HIV) transmission history in an area affected by an epidemic of multiple HIV-1 subtypes and assessed the efficacy of strengthened early antiretroviral therapy (ART) and regular interventions in preventing HIV spread. We collected demographic and clinical data of 2221 treatment-naïve HIV-1–infected patients in a long-term cohort in Shenyang, Northeast China, between 2008 and 2016. HIV pol gene sequencing was performed and molecular networks of CRF01_AE, CRF07_BC, and subtype B were inferred using HIV-TRACE with separate optimized genetic distance threshold. We identified 168 clusters containing ≥ 2 cases among CRF01_AE-, CRF07_BC-, and subtype B-infected cases, including 13 large clusters (≥ 10 cases). Individuals in large clusters were characterized by younger age, homosexual behavior, more recent infection, higher CD4 counts, and delayed/no ART (P < 0.001). The dynamics of large clusters were estimated by proportional detection rate (PDR), cluster growth predictor, and effective reproductive number (Re). Most large clusters showed decreased or stable during the study period, indicating that expansion was slowing. The proportion of newly diagnosed cases in large clusters declined from 30 to 8% between 2008 and 2016, coinciding with an increase in early ART within 6 months after diagnosis from 24 to 79%, supporting the effectiveness of strengthened early ART and continuous regular interventions. In conclusion, molecular network analyses can thus be useful for evaluating the efficacy of interventions in epidemics with a complex HIV profile.
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Affiliation(s)
- Mingchen Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wei He
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhen Wang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yu Qiu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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17
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Novitsky V, Steingrimsson JA, Howison M, Gillani FS, Li Y, Manne A, Fulton J, Spence M, Parillo Z, Marak T, Chan PA, Bertrand T, Bandy U, Alexander-Scott N, Dunn CW, Hogan J, Kantor R. Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters. Sci Rep 2020; 10:18547. [PMID: 33122765 PMCID: PMC7596705 DOI: 10.1038/s41598-020-75560-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023] Open
Abstract
Public health interventions guided by clustering of HIV-1 molecular sequences may be impacted by choices of analytical approaches. We identified commonly-used clustering analytical approaches, applied them to 1886 HIV-1 Rhode Island sequences from 2004-2018, and compared concordance in identifying molecular HIV-1 clusters within and between approaches. We used strict (topological support ≥ 0.95; distance 0.015 substitutions/site) and relaxed (topological support 0.80-0.95; distance 0.030-0.045 substitutions/site) thresholds to reflect different epidemiological scenarios. We found that clustering differed by method and threshold and depended more on distance than topological support thresholds. Clustering concordance analyses demonstrated some differences across analytical approaches, with RAxML having the highest (91%) mean summary percent concordance when strict thresholds were applied, and three (RAxML-, FastTree regular bootstrap- and IQ-Tree regular bootstrap-based) analytical approaches having the highest (86%) mean summary percent concordance when relaxed thresholds were applied. We conclude that different analytical approaches can yield diverse HIV-1 clustering outcomes and may need to be differentially used in diverse public health scenarios. Recognizing the variability and limitations of commonly-used methods in cluster identification is important for guiding clustering-triggered interventions to disrupt new transmissions and end the HIV epidemic.
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Affiliation(s)
| | | | - Mark Howison
- Research Improving People's Life, Providence, RI, USA
| | | | | | | | | | | | | | | | - Philip A Chan
- Brown University, Providence, RI, USA
- Rhode Island Department of Health, Providence, RI, USA
| | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
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18
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Sacks-Davis R, Chibo D, Peach E, Aleksic E, Crowe SM, El Hayek C, Marukutira T, Higgins N, Stoove M, Hellard M. Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia. PLoS One 2020; 15:e0237469. [PMID: 32870911 PMCID: PMC7462279 DOI: 10.1371/journal.pone.0237469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 01/28/2023] Open
Abstract
Background It is estimated that approximately half of new HIV diagnoses among heterosexual migrants in Victoria, Australia, were acquired post-migration. We investigated the characteristics of phylogenetic clusters in notified cases of HIV among heterosexual migrants. Methods Partial HIV pol sequences obtained from routine clinical genotype tests were linked to Victorian HIV notifications with the following exposures listed on the notification form: heterosexual sexual contact, injecting drug use, bisexual sexual contact, male-to male sexual contact or heterosexual sexual contact in combination with injecting drug use, unknown exposure. Those with heterosexual sexual contact as the only exposure were the focus of this study, with the other exposures included to better understand transmission networks. Additional reference sequences were extracted from the Los Alamos database. Maximum likelihood methods were used to infer the phylogeny and the robustness of the resulting tree was assessed using bootstrap analysis. Phylogenetic clusters were defined on the basis of bootstrap and genetic distance. Results HIV pol sequences were available for 332 of 445 HIV notifications attributed to only heterosexual sexual contact in Victoria from 2005–2014. Forty-three phylogenetic clusters containing at least one heterosexual migrant were detected, 30 (70%) of which were pairs. The characteristics of these phylogenetic clusters varied considerably by cluster size. Pairs were more likely to be composed of people living with HIV from a single country of birth (p = 0.032). Larger clusters (n≥3) were more likely to contain people born in Australian/New Zealand (p = 0.002), migrants from more than one country of birth (p = 0.013) and viral subtype-B, the most common subtype in Australia (p = 0.006). Pairs were significantly more likely to contain females (p = 0.037) and less likely to include HIV diagnoses with male-to-male sexual contact reported as a possible exposure (p<0.001) compared to larger clusters (n≥3). Conclusion Migrants appear to be at elevated risk of HIV acquisition, in part due to intimate relationships between migrants from the same country of origin, and in part due to risks associated with the broader Australian HIV epidemic. However, there was no evidence of large transmission clusters driven by heterosexual transmission between migrants. A multipronged approach to prevention of HIV among migrants is warranted.
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Affiliation(s)
- Rachel Sacks-Davis
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- * E-mail:
| | - Doris Chibo
- Victorian Infectious Disease Reference Laboratory, Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Eman Aleksic
- Burnet Institute, Melbourne, Victoria, Australia
| | - Suzanne M. Crowe
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Carol El Hayek
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Tafireyi Marukutira
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Nasra Higgins
- Department of Health and Human Services, Melbourne, Victoria, Australia
| | - Mark Stoove
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Margaret Hellard
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Hepatitis Services, Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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19
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Kantor R, Fulton JP, Steingrimsson J, Novitsky V, Howison M, Gillani F, Li Y, Manne A, Parillo Z, Spence M, Marak T, Chan P, Dunn CW, Bertrand T, Bandy U, Alexander-Scott N, Hogan JW. Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health. STATISTICAL COMMUNICATIONS IN INFECTIOUS DISEASES 2020; 12:20190019. [PMID: 34733405 PMCID: PMC8561650 DOI: 10.1515/scid-2019-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 10/22/2020] [Indexed: 11/15/2022]
Abstract
Great efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks.
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Affiliation(s)
| | | | | | | | - Mark Howison
- Research Improving People’s Life, Providence, RI, USA
| | | | | | | | | | | | | | - Philip Chan
- Brown University, Providence, RI, USA
- Rhode Island Department of Health, Providence, RI, USA
| | | | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
| | - Nicole Alexander-Scott
- Brown University, Providence, RI, USA
- Rhode Island Department of Health, Providence, RI, USA
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20
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Rudolph AE, Martinez O, Davison R, Amuchi CB. Informed consent for HIV phylogenetic research: A case study of urban individuals living with HIV approached for enrollment in an HIV study. EHQUIDAD 2020; 2020:129-143. [PMID: 32954381 PMCID: PMC7497840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Phylogenetic analyses can provide insights on HIV tansmission dynamics. Country and state-level differences in HIV criminalization and disclosure laws and advances in next generation sequencing could impact perceived study risks. METHODS We present study opt-out rates and the reasons provided during enrollment for a study conducted in Boston (6/2017-8/2018). RESULTS Of 90 patients approached to participate, 45 did not consent to participate. Reasons for not participating included unwillingness to discuss their HIV status, privacy and confidentiality concerns, disinterest, and lack of time. CONLUSIONS Given low participation rates and concerns related to HIV disclosure, privacy, and confidentiality, these questions remain (1) should informed consent be required for all phylogenetic analyses, including deidentified and surveillance data? (2) what additional steps can researchers take to protect the privacy of individuals, particularly in contexts where HIV is criminalized or there have been civil/criminal cases investigating HIV transmission? And (3) what role can community members play to minimize the potential risks, particularly for those most marginalized? These questions require input from both researchers and community members living with HIV/AIDS.
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Affiliation(s)
- Abby E. Rudolph
- Department of Epidemiology and Biostatistics, Temple
University College of Public Health, Philadelphia, USA
| | - Omar Martinez
- School of Social Work, Temple University College of Public
Health, Philadelphia, USA
| | - Robin Davison
- School of Social Work, Temple University College of Public
Health, Philadelphia, USA
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21
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Zhang J, Yao J, Jiang J, Pan X, Luo M, Xia Y, Fan Q, Ding X, Ruan J, Handel A, Bahl J, Chen W, Zha L, Fu T. Migration interacts with the local transmission of HIV in developed trade areas: A molecular transmission network analysis in China. INFECTION GENETICS AND EVOLUTION 2020; 84:104376. [PMID: 32454244 DOI: 10.1016/j.meegid.2020.104376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 11/16/2022]
Abstract
The HIV-1 epidemic is a remarkable public health concern in China, especially in developed trade areas. We aimed to investigate the interaction of migration with the local transmission network in a typical trade area, Yiwu City, the world's largest commodity distribution center. Based on 390 pol sequences from 413 participants diagnosed between 2014 and 2016, putative transmission clusters and the underlying demographic and behavioral characteristics were analyzed. Recent infection status was determined by HIV-1 limiting antigen avidity enzyme immunoassay to identify active clusters. Multiple subtypes were identified, with a predominance of CRF01_AE (47.4%) and CRF07_BC (40.8%), followed by 9 other subtypes and 8 URFs. Multivariable analyses revealed that individuals in clusters were more likely to be local residents, infected through heterosexual behaviors, and infected with CRF01_AE (P < .05). Of men who have sex with men (MSM), 81% were linked to other MSM, and only 3% were linked to heterosexual women. Of heterosexual women, 67% were linked to heterosexual men, and 11% to MSM. Yiwu residents were more likely to link to locals than that of migrants (43% vs 20%, P < .001). By contrast, local MSM and migrant MSM all had high percentages of linkage to migrant MSM (57% vs 69%, P = .069). Our findings reveal that migration promotes the dissemination and dynamic change of HIV, which are interwoven between locals and migrants. The results highlight the far-reaching influence of migrant MSM on the local HIV transmission network.
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Affiliation(s)
- Jiafeng Zhang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Jiaming Yao
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Jun Jiang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Xiaohong Pan
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China.
| | - Mingyu Luo
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Yan Xia
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Qin Fan
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Xiaobei Ding
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Jianjun Ruan
- Yiwu Municipal Center for Disease Control and Prevention, Yiwu 322000, China
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, Health Informatics Institute, Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Justin Bahl
- Center for the Ecology of Infectious Diseases, Department of Infectious Disease, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Duke-NUS Graduate Medical School, Singapore
| | - Wanjun Chen
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Lianqi Zha
- Yiwu Municipal Center for Disease Control and Prevention, Yiwu 322000, China
| | - Tao Fu
- Yiwu Municipal Center for Disease Control and Prevention, Yiwu 322000, China.
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Vasylyeva TI, du Plessis L, Pineda-Peña AC, Kühnert D, Lemey P, Vandamme AM, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NR. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. J Infect Dis 2020; 220:233-243. [PMID: 30805610 PMCID: PMC6581889 DOI: 10.1093/infdis/jiz085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. METHODS Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. RESULTS We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. CONCLUSIONS The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
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Affiliation(s)
- Tetyana I Vasylyeva
- Department of Zoology, University of Oxford, United Kingdom.,New College, University of Oxford, United Kingdom
| | | | - Andrea C Pineda-Peña
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia.,Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Perpétua Gomes
- Laboratory of Molecular Biology, LMCBM, SPC, Hospital de Egas Moniz-Centro Hospitalar de Lisboa Ocidental, Lisbon.,Center for Interdisciplinary Research Egas Moniz, CiiEM, Almada, Portugal
| | - Ricardo J Camacho
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
| | - Ana B Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom
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23
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Genetic clustering analysis for HIV infection among MSM in Nigeria: implications for intervention. AIDS 2020; 34:227-236. [PMID: 31634185 DOI: 10.1097/qad.0000000000002409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The HIV epidemic continues to grow among MSM in countries across sub-Saharan Africa including Nigeria. To inform prevention efforts, we used a phylogenetic cluster method to characterize HIV genetic clusters and factors associated with cluster formation among MSM living with HIV in Nigeria. METHODS We analyzed HIV-1 pol sequences from 417 MSM living with HIV enrolled in the TRUST/RV368 cohort between 2013 and 2017 in Abuja and Lagos, Nigeria. A genetically linked cluster was defined among participants whose sequences had pairwise genetic distance of 1.5% or less. Binary and multinomial logistic regressions were used to estimate adjusted odds ratios (AORs) and 95% confidence intervals (CIs) for factors associated with HIV genetic cluster membership and size. RESULTS Among 417 MSM living with HIV, 153 (36.7%) were genetically linked. Participants with higher viral load (AOR = 1.72 95% CI: 1.04-2.86), no female partners (AOR = 3.66; 95% CI: 1.97-6.08), and self-identified as male sex (compared with self-identified as bigender) (AOR = 3.42; 95% CI: 1.08-10.78) had higher odds of being in a genetic cluster. Compared with unlinked participants, MSM who had high school education (AOR = 23.84; 95% CI: 2.66-213.49), were employed (AOR = 3.41; 95% CI: 1.89-10.70), had bacterial sexually transmitted infections (AOR = 3.98; 95% CI: 0.89-17.22) and were not taking antiretroviral therapy (AOR = 6.61; 95% CI: 2.25-19.37) had higher odds of being in a large cluster (size > 4). CONCLUSION Comprehensive HIV prevention packages should include behavioral and biological components, including early diagnosis and treatment of both HIV and bacterial sexually transmitted infections to optimally reduce the risk of HIV transmission and acquisition.
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Verhofstede C, Mortier V, Dauwe K, Callens S, Deblonde J, Dessilly G, Delforge ML, Fransen K, Sasse A, Stoffels K, Van Beckhoven D, Vanroye F, Vaira D, Vancutsem E, Van Laethem K. Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing. Viruses 2019; 11:v11121096. [PMID: 31779195 PMCID: PMC6950120 DOI: 10.3390/v11121096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of ≥3 members. The percentage of early diagnosed (≤4 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for >4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.
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Affiliation(s)
- Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
- Correspondence:
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
| | - Steven Callens
- Aids Reference Center, Department of Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Jessika Deblonde
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Géraldine Dessilly
- Aids Reference Laboratory, Medical Microbiology Unit, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Marie-Luce Delforge
- Aids Reference Laboratory, Université Libre de Bruxelles, 1050 Brussels, Belgium;
| | - Katrien Fransen
- HIV/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.F.); (F.V.)
| | - André Sasse
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Karolien Stoffels
- Aids Reference Laboratory, Centre Hospitalier Universitaire St. Pierre, 1000 Brussels, Belgium;
| | - Dominique Van Beckhoven
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Fien Vanroye
- HIV/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.F.); (F.V.)
| | - Dolores Vaira
- Aids Reference Laboratory, Centre Hospitalier Universitaire de Liège, 4000 Liège, Belgium;
| | - Ellen Vancutsem
- Aids Reference Laboratory, Vrije Universiteit Brussel VUB, 1090 Brussels, Belgium;
| | - Kristel Van Laethem
- Aids Reference Laboratory, University Hospital Leuven, 3000 Leuven, Belgium;
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
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25
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Leveraging Phylogenetics to Understand HIV Transmission and Partner Notification Networks. J Acquir Immune Defic Syndr 2019; 78:367-375. [PMID: 29940601 DOI: 10.1097/qai.0000000000001695] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Partner notification is an important component of public health test and treat interventions. To enhance this essential function, we assessed the potential for molecular methods to supplement routine partner notification and corroborate HIV networks. METHODS All persons diagnosed with HIV infection in Wake County, NC, during 2012-2013 and their disclosed sexual partners were included in a sexual network. A data set containing HIV-1 pol sequences collected in NC during 1997-2014 from 15,246 persons was matched to HIV-positive persons in the network and used to identify putative transmission clusters. Both networks were compared. RESULTS The partner notification network comprised 280 index cases and 383 sexual partners and high-risk social contacts (n = 131 HIV-positive). Of the 411 HIV-positive persons in the partner notification network, 181 (44%) did not match to a HIV sequence, 61 (15%) had sequences but were not identified in a transmission cluster, and 169 (41%) were identified in a transmission cluster. More than half (59%) of transmission clusters bridged sexual network partnerships that were not recognized in the partner notification; most of these clusters were dominated by men who have sex with men. CONCLUSIONS Partner notification and HIV sequence analysis provide complementary representations of the existent partnerships underlying the HIV transmission network. The partner notification network components were bridged by transmission clusters, particularly among components dominated by men who have sex with men. Supplementing the partner notification network with phylogenetic data highlighted avenues for intervention.
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Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data. J Acquir Immune Defic Syndr 2019; 79:543-550. [PMID: 30222659 DOI: 10.1097/qai.0000000000001856] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Detecting recent and rapid spread of HIV can help prioritize prevention and early treatment for those at highest risk of transmission. HIV genetic sequence data can identify transmission clusters, but previous approaches have not distinguished clusters of recent, rapid transmission. We assessed an analytic approach to identify such clusters in the United States. METHODS We analyzed 156,553 partial HIV-1 polymerase sequences reported to the National HIV Surveillance System and inferred transmission clusters using 2 genetic distance thresholds (0.5% and 1.5%) and 2 periods for diagnoses (all years and 2013-2015, ie, recent diagnoses). For rapidly growing clusters (with ≥5 diagnoses during 2015), molecular clock phylogenetic analysis estimated the time to most recent common ancestor for all divergence events within the cluster. Cluster transmission rates were estimated using these phylogenies. RESULTS A distance threshold of 1.5% identified 103 rapidly growing clusters using all diagnoses and 73 using recent diagnoses; at 0.5%, 15 clusters were identified using all diagnoses and 13 using recent diagnoses. Molecular clock analysis estimated that the 13 clusters identified at 0.5% using recent diagnoses had been diversifying for a median of 4.7 years, compared with 6.5-13.2 years using other approaches. The 13 clusters at 0.5% had a transmission rate of 33/100 person-years, compared with previous national estimates of 4/100 person-years. CONCLUSIONS Our approach identified clusters with transmission rates 8 times those of previous national estimates. This method can identify groups involved in rapid transmission and help programs effectively direct and prioritize limited public health resources.
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Kafando A, Serhir B, Doualla-Bell F, Fournier E, Sangaré MN, Martineau C, Sylla M, Chamberland A, El-Far M, Charest H, Tremblay CL. A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses. AIDS Res Hum Retroviruses 2019; 35:906-919. [PMID: 31407606 PMCID: PMC6806616 DOI: 10.1089/aid.2019.0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.
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Affiliation(s)
- Alexis Kafando
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Bouchra Serhir
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Mohamed Ndongo Sangaré
- Département de Médecine Sociale et Préventive, École de Santé Publique, Université de Montréal, Montréal, Canada
| | - Christine Martineau
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Mohamed Sylla
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Annie Chamberland
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Mohamed El-Far
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Hugues Charest
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Cécile L. Tremblay
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
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German D, Grabowski MK, Beyrer C. Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men. Sex Health 2019; 14:89-96. [PMID: 27584826 DOI: 10.1071/sh16056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/29/2016] [Indexed: 12/14/2022]
Abstract
The multidimensional nature and continued evolution of HIV epidemics among men who have sex with men (MSM) requires innovative intervention approaches. Strategies are needed that recognise the individual, social and structural factors driving HIV transmission; that can pinpoint networks with heightened transmission risk; and that can help target intervention in real time. HIV phylogenetics is a rapidly evolving field with strong promise for informing innovative responses to the HIV epidemic among MSM. Currently, HIV phylogenetic insights are providing new understandings of characteristics of HIV epidemics involving MSM, social networks influencing transmission, characteristics of HIV transmission clusters involving MSM, targets for antiretroviral and other prevention strategies and dynamics of emergent epidemics. Maximising the potential of HIV phylogenetics for HIV responses among MSM will require attention to key methodological challenges and ethical considerations, as well as resolving key implementation and scientific questions. Enhanced and integrated use of HIV surveillance, sociobehavioural and phylogenetic data resources are becoming increasingly critical for informing public health approaches to HIV among MSM.
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Affiliation(s)
- Danielle German
- Johns Hopkins Bloomberg School of Public Health, Department of Health, Behavior and Society, 624N. Broadway, Baltimore, MD 21205, USA
| | - Mary Kate Grabowski
- Johns Hopkins Bloomberg School of Public Health, Department of Health, Behavior and Society, 624N. Broadway, Baltimore, MD 21205, USA
| | - Chris Beyrer
- Johns Hopkins Bloomberg School of Public Health, Department of Health, Behavior and Society, 624N. Broadway, Baltimore, MD 21205, USA
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29
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Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany. J Virol 2019; 93:JVI.02238-18. [PMID: 30944175 DOI: 10.1128/jvi.02238-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/13/2019] [Indexed: 12/15/2022] Open
Abstract
HIV-1 non-B infections have been increasing in Europe for several years. In Germany, subtype A belongs to the most abundant non-B subtypes showing an increasing prevalence of 8.3% among new infections in 2016. Here we trace the origin and examine the current spread of the German HIV-1 subtype A epidemic. Bayesian coalescence and birth-death analyses were performed with 180 German HIV-1 pol sequences and 528 related and publicly available sequences to reconstruct the population dynamics and fluctuations for each of the transmission groups. Our reconstructions indicate two distinct sources of the German subtype A epidemic, with an Eastern European and an Eastern African lineage both cocirculating in the country. A total of 13 German-origin clusters were identified; among these, 6 clusters showed recent activity. Introductions leading to further countrywide spread originated predominantly from Eastern Africa when introduced before 2005. Since 2005, however, spreading introductions have occurred exclusively within the Eastern European clade. Moreover, we observed changes in the main route of subtype A transmission. The beginning of the German epidemic (1985 to 1995) was dominated by heterosexual transmission of the Eastern African lineage. Since 2005, transmissions among German men who have sex with men (MSM) have been increasing and have been associated with the Eastern European lineage. Infections among people who inject drugs dominated between 1998 and 2005. Our findings on HIV-1 subtype A infections provide new insights into the spread of this virus and extend the understanding of the HIV epidemic in Germany.IMPORTANCE HIV-1 subtype A is the second most prevalent subtype worldwide, with a high prevalence in Eastern Africa and Eastern Europe. However, an increase of non-B infections, including subtype A infections, has been observed in Germany and other European countries. There has simultaneously been an increased flow of refugees into Europe and especially into Germany, raising the question of whether the surge in non-B infections resulted from this increased immigration or whether German transmission chains are mainly involved. This study is the first comprehensive subtype A study from a western European country analyzing in detail its phylogenetic origin, the impact of various transmission routes, and its current spread. The results and conclusions presented provide new and substantial insights for virologists, epidemiologists, and the general public health sector. In this regard, they should be useful to those authorities responsible for developing public health intervention strategies to combat the further spread of HIV/AIDS.
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Dasgupta S, France AM, Brandt MG, Reuer J, Zhang T, Panneer N, Hernandez AL, Oster AM. Estimating Effects of HIV Sequencing Data Completeness on Transmission Network Patterns and Detection of Growing HIV Transmission Clusters. AIDS Res Hum Retroviruses 2019; 35:368-375. [PMID: 30403157 DOI: 10.1089/aid.2018.0181] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
HIV nucleotide sequence data can identify clusters of persons with genetically similar strains suggesting transmission. We simulated the effect of lowered data completeness, defined by the percent of persons with diagnosed HIV with a reported sequence, on transmission patterns and detection of growing HIV transmission clusters. We analyzed HIV surveillance data for persons with HIV diagnosed during 2008-2014 who resided in Michigan or Washington. We calculated genetic distances, constructed the inferred transmission network for each jurisdiction, and compared transmission network characteristics and detection of growing transmission clusters in the full dataset with artificially reduced datasets. Simulating lower levels of completeness resulted in decreased percentages of persons linked to a cluster from high completeness (full dataset) to low completeness (5%) (Michigan: 54%-18%; Washington, 46%-16%). Patterns of transmission between certain populations remained robust as data completeness level was reduced. As data completeness was artificially decreased, sensitivity of cluster detection substantially diminished in both states. In Michigan, sensitivity decreased from 100% with the full dataset, to 62% at 50% completeness and 21% at 25% completeness. In Washington, sensitivity decreased from 100% with the full dataset, to 71% at 50% completeness and 29% at 25% completeness. Lower sequence data completeness limits the ability to detect clusters that may benefit from investigation; however, inferences can be made about transmission patterns even with low data completeness, given sufficient numbers. Data completeness should be prioritized, as lack of or delays in detection of transmission clusters could result in additional infections.
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Affiliation(s)
- Sharoda Dasgupta
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anne Marie France
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mary-Grace Brandt
- Michigan Department of Health and Human Services, Southfield, Michigan
| | - Jennifer Reuer
- Washington State Department of Health, Tumwater, Washington
| | | | - Nivedha Panneer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Angela L. Hernandez
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alexandra M. Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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Jovanović L, Šiljić M, Ćirković V, Salemović D, Pešić-Pavlović I, Todorović M, Ranin J, Jevtović D, Stanojević M. Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach. Front Microbiol 2019; 10:287. [PMID: 30858834 PMCID: PMC6397891 DOI: 10.3389/fmicb.2019.00287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/04/2019] [Indexed: 12/04/2022] Open
Abstract
Previous molecular studies of Serbian HIV epidemic identified the dominance of subtype B and presence of clusters related HIV-1 transmission, in particular among men who have sex with men (MSM). In order to get a deeper understanding of the complexities of HIV sub-epidemics in Serbia, epidemic trends, temporal origin and phylodynamic characteristics in general population and subpopulations were analyzed by means of mathematical modeling, phylogenetic analysis and latent class analysis (LCA). Fitting of the logistic curve of trends for a cumulative annual number of new HIV cases in 1984–2016, in general population and MSM transmission group, was performed. Both datasets fitted the logistic growth model, showing the early exponential phase of the growth curve. According to the suggested model, in the year 2030, the number of newly diagnosed HIV cases in Serbia will continue to grow, in particular in the MSM transmission group. Further, a detailed phylogenetic analysis was performed on 385 sequences from the period 1997–2015. Identification of transmission clusters, estimation of population growth (Ne), of the effective reproductive number (Re) and time of the most recent common ancestor (tMRCA) were estimated employing Bayesian and maximum likelihood methods. A substantial proportion of 53% of subtype B sequences was found within transmission clusters/network. Phylodynamic analysis revealed Re over one during the whole period investigated, with the steepest slopes and a recent tMRCA for MSM transmission group subtype B clades, in line with a growing trend in the number of transmissions in years approaching the end of the study period. Contrary, heterosexual clades in both studied subtypes – B and C – showed modest growth and stagnation. LCA analysis identified five latent classes, with transmission clusters dominantly present in 2/5 classes, linked to MSM transmission living in the capital city and with the high prevalence of co-infection with HBV and/or other STIs.Presented findings imply that HIV epidemic in Serbia is still in the exponential growth phase, in particular, related to the MSM transmission, with estimated steep growth curve until 2030. The obtained results imply that an average new HIV patient in Serbia is a young man with concomitant sexually transmitted infection.
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Affiliation(s)
- Luka Jovanović
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marina Šiljić
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Valentina Ćirković
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Dubravka Salemović
- Infectious and Tropical Diseases University Hospital, Clinical Centre of Serbia, Belgrade, Serbia
| | - Ivana Pešić-Pavlović
- Virology Laboratory, Microbiology Department, Clinical Centre of Serbia, Belgrade, Serbia
| | - Marija Todorović
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jovan Ranin
- Infectious and Tropical Diseases University Hospital, Clinical Centre of Serbia, Belgrade, Serbia
| | - Djordje Jevtović
- Infectious and Tropical Diseases University Hospital, Clinical Centre of Serbia, Belgrade, Serbia
| | - Maja Stanojević
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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Grande KM, Schumann CL, Bañez Ocfemia MC, Vergeront JM, Wertheim JO, Oster AM. Transmission Patterns in a Low HIV-Morbidity State - Wisconsin, 2014-2017. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2019; 68:149-152. [PMID: 30763299 PMCID: PMC6375656 DOI: 10.15585/mmwr.mm6806a5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Public health interviews (i.e., partner services), during which persons with diagnosed human immunodeficiency virus (HIV) infection name their sexual or needle-sharing partners (named partners), are used to identify HIV transmission networks to guide and prioritize HIV prevention activities. HIV sequence data, generated from provider-ordered drug resistance testing, can be used to understand characteristics of molecular clusters, a group of sequences for which each sequence is highly similar (linked) to all other sequences, and assess whether named partners are plausible HIV transmission partners. Although molecular data in higher HIV-morbidity states have been analyzed (1-3), few analyses exist for lower morbidity states (4), such as Wisconsin, which reported 4.6 HIV diagnoses per 100,000 persons aged ≥13 years in 2016 (5). The Wisconsin Division of Public Health (DPH) analyzed HIV sequence data generated from provider-ordered drug resistance testing and collected through routine HIV surveillance to identify molecular clusters and describe demographic and transmission risk characteristics among pairs of persons whose sequences were highly genetically similar (i.e., molecular linkages). In addition, overlap between partner linkages identified during public health interviews and molecular linkages was assessed. Overall, characteristics of molecular clusters in Wisconsin mirrored those from states with more HIV diagnoses, particularly in that most molecular linkages were observed among persons of the same race (78.2% of non-Hispanic blacks [blacks] linked to other blacks), the same transmission risk (90.2% of men who have sex with men [MSM] linked to other MSM), and the same age group (59.2% of persons aged 20-29 years linked to other persons aged 20-29 years). Among named partner linkages identified during interviews in which both persons also had a reported sequence, overlap of named partner and molecular linkages was moderate: 33.8% of named partners were plausible transmission partners according to available molecular data. Analysis of HIV sequence data is a useful tool for characterizing transmission patterns not immediately apparent using traditional public health interview data, even in a state with lower HIV morbidity. Prevention recommendations generated from national data (e.g., targeting preexposure prophylaxis for HIV-negative persons at high risk and implementing measures to maintain viral suppression among persons with HIV infection) also are relevant in a lower HIV-morbidity state.
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Nicolás D, Ambrosioni J, de Lazzari E, Suarez A, Manzardo C, Agüero F, Mosquera MM, Costa J, Ligero C, Marcos MÁ, Sánchez-Palomino S, Fernández E, Plana M, Yerly S, Gatell JM, Miró JM. Epidemiological changes of acute/recent human immunodeficiency virus type 1 infection in Barcelona, Spain (1997-2015): a prospective cohort study. Clin Microbiol Infect 2018; 25:878-884. [PMID: 30472421 DOI: 10.1016/j.cmi.2018.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To describe the epidemiology of acute/recent human immunodeficiency virus (HIV) infection over two decades in Barcelona (Spain). METHODS Prospective, single-centre cohort including all patients with an acute/recent HIV infection (<180 days) since 1997. Patients were stratified into four periods. Phylogenetic analysis was performed to determine clusters of transmission. RESULTS A total of 346 consecutive acute/recently infected patients were included. The annual proportion of recent infections among total new HIV diagnoses increased over time from 1% (29 out of 1964) to 8% (112 out of 1474) (p <0.001). Proportion of men who have sex with men (MSM) in the cohort increased from 62% (18 out of 29) to 89% (100 out of 112) (p <0.001). The proportion of migrants showed a non-significant increasing trend (24% (7 of 29) to 40% (45 of 112)) likewise the non-B subtype (0% to 22% (22 of 112)). The mean time from infection to diagnosis was 53.6 days (interquartile range (IQR) 50-57), comparable among all periods. Mean time from infection to treatment decreased over the years from 575 (IQR 467-683) to 471 (IQR 394-549) days (p <0.001) without significant differences between migrants and non-migrants (133 (IQR 71-411) versus 208 (IQR 90-523) days p 0.089). Almost 50% (152 of 311) of recently infected individuals were included in a cluster of transmission, and 92% (137 of 149) of them were MSM. CONCLUSION The MSM population has progressively grown within acutely/recently infected patients in Barcelona, and is frequently involved in transmission clusters. Although the time between diagnosis and treatment has been reduced, the time between infection and diagnosis still needs to be shortened.
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Affiliation(s)
- D Nicolás
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - J Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - E de Lazzari
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - A Suarez
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - C Manzardo
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - F Agüero
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - M M Mosquera
- Laboratory of Virology, Microbiology Service, Hospital Clinic Barcelona, CIBERehd, University of Barcelona, Barcelona, Spain
| | - J Costa
- Laboratory of Virology, Microbiology Service, Hospital Clinic Barcelona, CIBERehd, University of Barcelona, Barcelona, Spain
| | - C Ligero
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - M Á Marcos
- Laboratory of Virology, Microbiology Service, Hospital Clinic Barcelona, CIBERehd, University of Barcelona, Barcelona, Spain
| | - S Sánchez-Palomino
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - E Fernández
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - M Plana
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - S Yerly
- Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - J M Gatell
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - J M Miró
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
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Wang H, Yang Z, Zhu H, Mo Q, Tan H. High HIV-1 prevalence and viral diversity among entry-exit populations at frontier ports of China, 2012-2016: A cross-sectional molecular epidemiology study. INFECTION GENETICS AND EVOLUTION 2018; 65:231-237. [PMID: 30086369 DOI: 10.1016/j.meegid.2018.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
The cross border movement of populations would potentially increase the transmission and spread of various diseases including HIV/AIDS, which needed strict surveillance. In the current study, a total of 2,961,530 specimens were collected between 2012 and 2016 from the entry-exit populations at frontier ports of China for epidemiology and molecular epidemiology study. Results showed that HIV-1 prevalence rate among these populations was significantly higher than that of other general populations in China (p < .001). Epidemiological investigation indicated that most of the HIV-1 infected participants were male and young general population, in contrast to intravenous drug users as revealed by previous studies. There were significantly more female, Chinese, and migrant labors in southeastern ports than in northwestern ports (p < .05). Molecular epidemiology study revealed that three subtypes C/BC, CRF01_AE and B dominated, with the emerging of novel unique recombinant forms and drug-resistant viruses among this population. Overall, the results suggests and calls for the shift of HIV-1 prevention projects' focus and the continuous monitoring of HIV-1 molecular epidemiology among entry-exit populations. These findings are useful for the generation of evidence-based biomedical and behavioral prevention programs to HIV/AIDS.
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Affiliation(s)
- Haibo Wang
- State Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai 519020, China.
| | - Ze Yang
- State Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai 519020, China
| | - Hong Zhu
- Beijing International Travel Healthcare Center, Beijing 100000, China
| | - Qiuhua Mo
- State Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai 519020, China
| | - Hua Tan
- State Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai 519020, China
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Kostaki EG, Nikolopoulos GK, Pavlitina E, Williams L, Magiorkinis G, Schneider J, Skaathun B, Morgan E, Psichogiou M, Daikos GL, Sypsa V, Smyrnov P, Korobchuk A, Malliori M, Hatzakis A, Friedman SR, Paraskevis D. Molecular Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Infected Individuals in a Network-Based Intervention (Transmission Reduction Intervention Project): Phylogenetics Identify HIV-1-Infected Individuals With Social Links. J Infect Dis 2018; 218:707-715. [PMID: 29697829 PMCID: PMC6057507 DOI: 10.1093/infdis/jiy239] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/23/2018] [Indexed: 01/04/2023] Open
Abstract
Background The Transmission Reduction Intervention Project (TRIP) is a network-based intervention that aims at decreasing human immunodeficiency virus type 1 (HIV-1) spread. We herein explore associations between transmission links as estimated by phylogenetic analyses, and social network-based ties among persons who inject drugs (PWID) recruited in TRIP. Methods Phylogenetic trees were inferred from HIV-1 sequences of TRIP participants. Highly supported phylogenetic clusters (transmission clusters) were those fulfilling 3 different phylogenetic confidence criteria. Social network-based ties (injecting or sexual partners, same venue engagement) were determined based on personal interviews, recruitment links, and field observation. Results TRIP recruited 356 individuals (90.2% PWID) including HIV-negative controls; recently HIV-infected seeds; long-term HIV-infected seeds; and their social network members. Of the 150 HIV-infected participants, 118 (78.7%) were phylogenetically analyzed. Phylogenetic analyses suggested the existence of 13 transmission clusters with 32 sequences. Seven of these clusters included 14 individuals (14/32 [43.8%]) who also had social ties with at least 1 member of their cluster. This proportion was significantly higher than what was expected by chance. Conclusions Molecular methods can identify HIV-infected people socially linked with another person in about half of the phylogenetic clusters. This could help public health efforts to locate individuals in networks with high transmission rates.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | | | - Leslie Williams
- National Development and Research Institutes, New York, New York
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - John Schneider
- Departments of Medicine and Public Health Sciences, University of Chicago Medical Center, Center for AIDS Elimination, Illinois
| | - Britt Skaathun
- Departments of Medicine and Public Health Sciences, University of Chicago Medical Center, Center for AIDS Elimination, Illinois
| | - Ethan Morgan
- Departments of Medicine and Public Health Sciences, University of Chicago Medical Center, Center for AIDS Elimination, Illinois
| | - Mina Psichogiou
- Laikon General Hospital, First Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Greece
| | - Georgios L Daikos
- Laikon General Hospital, First Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Greece
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | | | - Meni Malliori
- Medical School, National and Kapodistrian University of Athens, Greece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
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Chan PA, Montgomery MC, Rose J, Tributino A, Crowley C, Medina MM, Patel R, Mayer K, Kantor R, Nunn AS. Statewide Evaluation of New HIV Diagnoses in Rhode Island: Implications for Prevention. Public Health Rep 2018; 133:489-496. [PMID: 29874149 DOI: 10.1177/0033354918777255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES Patterns of HIV transmission vary widely across demographic groups. Identifying and engaging these groups are necessary to prevent new infections and diagnose disease among people who are unaware of their infection. The objective of this study was to determine characteristics of newly diagnosed individuals across an entire state to determine patterns of HIV transmission. METHODS We evaluated data on people with new HIV diagnoses in Rhode Island from 2013 through 2015. We performed a latent class analysis (LCA) to identify underlying demographic and behavioral characteristics of people with newly diagnosed HIV. RESULTS Of 167 people with new HIV diagnoses interviewed in Rhode Island from 2013 through 2015, 132 (79%) were male, 84 (50%) were nonwhite, 112 (67%) were men who have sex with men (MSM), 112 (67%) were born in the United States, and 61 (37%) were born in Rhode Island. LCA revealed 2 major classes. Of the 98 people in class 1, 96% were male, 85% were MSM, 80% were white, 94% were born in the United States, and 80% believed they acquired HIV in Rhode Island. Class 2 was 63% male and 69% Hispanic/Latino; 29% were born in the United States, and 61% believed they acquired HIV in Rhode Island. CONCLUSIONS Most new HIV diagnoses in Rhode Island were among MSM born in the United States, and a substantial number were likely infected in-state. People with newly diagnosed HIV who were foreign-born, including Hispanic/Latino and heterosexual groups, were less likely to have acquired HIV in Rhode Island than were MSM. HIV prevention approaches, including pre-exposure prophylaxis, should be adapted to the needs of specific groups. Rhode Island offers lessons for other states focused on eliminating HIV transmission.
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Affiliation(s)
- Philip A Chan
- 1 Department of Medicine, Brown University, Providence, RI, USA
| | | | - Jennifer Rose
- 2 Department of Psychology, Wesleyan University, Middletown, CT, USA
| | - Alec Tributino
- 1 Department of Medicine, Brown University, Providence, RI, USA
| | | | - Martha M Medina
- 1 Department of Medicine, Brown University, Providence, RI, USA
| | - Rupa Patel
- 3 Department of Internal Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | | | - Rami Kantor
- 1 Department of Medicine, Brown University, Providence, RI, USA
| | - Amy S Nunn
- 5 Rhode Island Public Health Institute, Providence, RI, USA
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Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29522828 DOI: 10.1016/j.meegid.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.
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Mehta SR, Chaillon A, Gaines TL, Gonzalez-Zuniga PE, Stockman JK, Almanza-Reyes H, Chavez JR, Vera A, Wagner KD, Patterson TL, Scott B, Smith DM, Strathdee SA. Impact of Public Safety Policies on Human Immunodeficiency Virus Transmission Dynamics in Tijuana, Mexico. Clin Infect Dis 2018; 66:758-764. [PMID: 29045592 PMCID: PMC5848227 DOI: 10.1093/cid/cix884] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/09/2017] [Indexed: 11/15/2022] Open
Abstract
Background North Tijuana, Mexico is home to many individuals at high risk for transmitting and acquiring human immunodeficiency virus (HIV). Recently, policy shifts by local government impacted how these individuals were handled by authorities. Here we examined how this affected regional HIV transmission dynamics. Methods HIV pol sequences and associated demographic information were collected from 8 research studies enrolling persons in Tijuana and were used to infer viral transmission patterns. To evaluate the impact of recent policy changes on HIV transmission dynamics, qualitative interviews were performed on a subset of recently infected individuals. Results Between 2004 and 2016, 288 unique HIV pol sequences were obtained from individuals in Tijuana, including 46.4% from men who have sex with men, 42.1% from individuals reporting transactional sex, and 27.8% from persons who inject drugs (some individuals had >1 risk factor). Forty-two percent of sequences linked to at least 1 other sequence, forming 37 transmission clusters. Thirty-two individuals seroconverted during the observation period, including 8 between April and July 2016. Three of these individuals were putatively linked together. Qualitative interviews suggested changes in policing led individuals to shift locations of residence and injection drug use, leading to increased risk taking (eg, sharing needles). Conclusions Near real-time molecular epidemiologic analyses identified a cluster of linked transmissions temporally associated with policy shifts. Interviews suggested these shifts may have led to increased risk taking among individuals at high risk for HIV acquisition. With all public policy shifts, downstream impacts need to be carefully considered, as even well-intentioned policies can have major public health consequences.
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Affiliation(s)
- Sanjay R Mehta
- Departments of Medicine University of California, La Jolla
- Departments of Pathology, University of California, La Jolla
- San Diego Veterans Affairs Medical Center, California
| | | | - Tommi L Gaines
- Departments of Medicine University of California, La Jolla
| | | | | | - Horatio Almanza-Reyes
- Escuela de Ciencias de la Salud Valle de Las Palmas, Universidad Autónoma de Baja California, Tijuana, Baja California, México
| | - Jose Roman Chavez
- Escuela de Ciencias de la Salud Valle de Las Palmas, Universidad Autónoma de Baja California, Tijuana, Baja California, México
| | - Alicia Vera
- Departments of Medicine University of California, La Jolla
| | - Karla D Wagner
- School of Community Health Sciences, University of Nevada, Reno
| | | | - Brianna Scott
- Departments of Medicine University of California, La Jolla
| | - Davey M Smith
- Departments of Medicine University of California, La Jolla
- San Diego Veterans Affairs Medical Center, California
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Fujimoto K, Coghill LM, Weier CA, Hwang LY, Kim JY, Schneider JA, Metzker ML, Brown JM. Short Communication: Lack of Support for Socially Connected HIV-1 Transmission Among Young Adult Black Men Who Have Sex with Men. AIDS Res Hum Retroviruses 2017; 33:935-940. [PMID: 28398775 DOI: 10.1089/aid.2016.0228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We explore the phylogenetic relationships among HIV sequences sampled from young adult black men who have sex with men (YAB-MSM), who are connected through peer referral/social ties and who attend common venues. Using 196 viral sequences sampled from the peripheral blood mononuclear cells of 10 individuals, our preliminary phylogenetic results indicate that these socially connected YAB-MSM are infected with distantly related viruses and provide no evidence for viral transmission between network members. Our results suggest that HIV-prevention strategies that target young adult MSM should extend beyond their network members and local community.
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Affiliation(s)
- Kayo Fujimoto
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Lyndon M. Coghill
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | | | - Lu-Yu Hwang
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Ju Yeong Kim
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | | | | | - Jeremy M. Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
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van Griensven F, Guadamuz TE, de Lind van Wijngaarden JW, Phanuphak N, Solomon SS, Lo YR. Challenges and emerging opportunities for the HIV prevention, treatment and care cascade in men who have sex with men in Asia Pacific. Sex Transm Infect 2017; 93:356-362. [PMID: 28729520 DOI: 10.1136/sextrans-2016-052669] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/19/2017] [Accepted: 06/03/2017] [Indexed: 01/23/2023] Open
Abstract
In Asia Pacific, most countries have expanded HIV treatment guidelines to include all those with HIV infection and adopted antiretroviral treatment for prevention (TFP) as a blanket strategy for HIV control. Although the overall epidemic development associated with this focus is positive, the HIV epidemic in men who have sex with men (MSM) is continuing unperturbed without any signs of decline or reversal. This raises doubt about whether TFP as a blanket HIV prevention policy is the right approach. This paper reviews currently available biomedical HIV prevention strategies, national HIV prevention policies and guidelines from selected countries and published data on the HIV cascade in MSM. No evidence for efficacy of TFP in protecting MSM from HIV infection was found. The rationale for this approach is based on assumptions about biological plausibility and external validity of latency-based efficacy found in heterosexual couples. This is different from the route and timing of HIV transmission in MSM. New HIV infections in MSM principally occur in chains of acutely HIV-infected highly sexually active young men, in whom acquisition and transmission are correlated in space and time. By the time TFP renders its effects, most new HIV infections in MSM will have already occurred. On a global level, less than 6% of all reports regarding the HIV care cascade from 1990 to 2016 included MSM, and only 2.3% concerned MSM in low/middle-income countries. Only one report originated from Asia Pacific. Generally, HIV cascade data in MSM show a sobering picture of TFP in engaging and retaining MSM along the continuum. Widening the cascade with a preventive extension, including pre-exposure prophylaxis, the first proven efficacious and only biomedical HIV prevention strategy in MSM, will be instrumental in achieving HIV epidemic control in this group.
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Affiliation(s)
- Frits van Griensven
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Thomas E Guadamuz
- Department of Society and Health, Mahidol University, Nakorn Pathom, Thailand
| | | | - Nittaya Phanuphak
- Prevention Department, Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Sunil Suhas Solomon
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ying-Ru Lo
- HIV, Hepatitis and STI Unit, Regional Office for the Western Pacific, World Health Organization, Manila, Philippines
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Abstract
Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.
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The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data. INFECTION GENETICS AND EVOLUTION 2017; 52:100-105. [PMID: 28427935 DOI: 10.1016/j.meegid.2017.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 01/05/2023]
Abstract
Molecular epidemiology has become a key tool for tracking infectious disease epidemics. Here, the spread of the most prevalent HIV-1 subtypes in Northern Alberta, Canada, was characterized with a Bayesian phylogenetic approach using 1146 HIV-1 pol sequences collected between 2007 and 2013 for routine clinical management purposes. Available patient metadata were qualitatively interpreted and correlated with onwards transmission using Fisher exact tests and logistic regression. Most infections were from subtypes A (n=36), B (n=815) and C (n=211). Africa is the dominant origin location for subtypes A and C while the subtype B epidemic was seeded from the USA and Middle America and, from the early 1990s onwards, mostly by interprovincial spread. Subtypes A (77.8%) and C (74.0%) were usually heterosexually transmitted and circulate predominantly among Blacks (61.1% and 85% respectively). Subtype B was mostly found among Caucasians (48.6%) and First Nations (36.8%), and its modes of transmission were stratified by ethnic origin. Compared to subtypes A (5.6%) and C (3.8-10.0%), a larger portion of subtype B patients were found within putative provincial transmission networks (20.3-29.5%), and this almost doubled when focusing on nationwide transmission clusters (37.9-57.5%). No clear association between cluster membership and particular patient characteristics was found. This study reveals complex and multi-faceted transmission dynamics of the HIV-1 epidemic in this otherwise low HIV prevalence population in Northern Alberta, Canada. These findings can aid public health planning.
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Parczewski M, Leszczyszyn-Pynka M, Witak-Jędra M, Szetela B, Gąsiorowski J, Knysz B, Bociąga-Jasik M, Skwara P, Grzeszczuk A, Jankowska M, Barałkiewicz G, Mozer-Lisewska I, Łojewski W, Kozieł K, Grąbczewska E, Jabłonowska E, Urbańska A. Expanding HIV-1 subtype B transmission networks among men who have sex with men in Poland. PLoS One 2017; 12:e0172473. [PMID: 28234955 PMCID: PMC5325290 DOI: 10.1371/journal.pone.0172473] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/05/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Reconstruction of HIV transmission links allows to trace the spread and dynamics of infection and guide epidemiological interventions. The aim of this study was to characterize transmission networks among subtype B infected patients from Poland. MATERIAL AND METHODS Maximum likelihood phylogenenetic trees were inferred from 966 HIV-1 subtype B protease/reverse transcriptase sequences from patients followed up in nine Polish HIV centers. Monophyletic clusters were identified using 3% within-cluster distance and 0.9 bootstrap values. Interregional links for the clusters were investigated and time from infection to onward transmission estimated using Bayesian dated MCMC phylogeny. RESULTS Three hundred twenty one (33.2%) sequences formed 109 clusters, including ten clusters of ≥5 sequences (n = 81, 8.4%). Transmission networks were more common among MSM (234 sequences, 68.6%) compared to other infection routes (injection drug use: 28 (8.2%) and heterosexual transmissions: 59 (17.3%) cases, respectively [OR:3.5 (95%CI:2.6-4.6),p<0.001]. Frequency of clustering increased from 26.92% in 2009 to 50.6% in 2014 [OR:1.18 (95%CI:1.06-1.31),p = 0.0026; slope +2.8%/year] with median time to onward transmission within clusters of 1.38 (IQR:0.59-2.52) years. In multivariate models clustering was associated with both MSM transmission route [OR:2.24 (95%CI:1.38-3.65),p<0.001] and asymptomatic stage of HIV infection [OR:1.93 (95%CI:1.4-2.64),p<0.0001]. Additionally, interregional networks were linked to MSM transmissions [OR:4.7 (95%CI:2.55-8.96),p<0.001]. CONCLUSIONS Reconstruction of the HIV-1 subtype B transmission patterns reveals increasing degree of clustering and existence of interregional networks among Polish MSM. Dated phylogeny confirms the association between onward transmission and recent infections. High transmission dynamics among Polish MSM emphasizes the necessity for active testing and early treatment in this group.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Leszczyszyn-Pynka
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Witak-Jędra
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Jacek Gąsiorowski
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Brygida Knysz
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Monika Bociąga-Jasik
- Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł Skwara
- Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Anna Grzeszczuk
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Białystok, Poland
| | - Maria Jankowska
- Department of Infectious Diseases, Medical University in Gdańsk, Gdańsk, Poland
| | | | - Iwona Mozer-Lisewska
- Department of Infectious Diseases, Poznań University of Medical Sciences, Poznań, Poland
| | - Władysław Łojewski
- Department of Infectious Diseases, Regional Hospital in Zielona Gora, Zielona Góra, Poland
| | - Katarzyna Kozieł
- Department of Infectious Diseases, Regional Hospital in Zielona Gora, Zielona Góra, Poland
| | - Edyta Grąbczewska
- Department of Infectious Diseases and Hepatology Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Elżbieta Jabłonowska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
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Abstract
Effective HIV prevention requires knowledge of the structure and dynamics of the social networks across which infections are transmitted. These networks most commonly comprise chains of sexual relationships, but in some populations, sharing of contaminated needles is also an important, or even the main mechanism that connects people in the network. Whereas network data have long been collected during survey interviews, new data sources have become increasingly common in recent years, because of advances in molecular biology and the use of partner notification services in HIV prevention and treatment programmes. We review current and emerging methods for collecting HIV-related network data, as well as modelling frameworks commonly used to infer network parameters and map potential HIV transmission pathways within the network. We discuss the relative strengths and weaknesses of existing methods and models, and we propose a research agenda for advancing network analysis in HIV epidemiology. We make the case for a combination approach that integrates multiple data sources into a coherent statistical framework.
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