1
|
Zhang F, Yang Y, Liang N, Liang H, Chen Y, Lin Z, Chen T, Tan W, Yang Y, Huang R, Yao L, Chen F, Huang X, Ye L, Liang H, Liang B. Transmission network and phylogenetic analysis reveal older male-centered transmission of CRF01_AE and CRF07_BC in Guangxi, China. Emerg Microbes Infect 2023; 12:2147023. [PMID: 36369697 PMCID: PMC9809400 DOI: 10.1080/22221751.2022.2147023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In China, the number of newly reported HIV infections in older people is increasing rapidly. However, clear information on the impact of older people on HIV transmission is limited. This study aims to reveal the local HIV transmission patterns, especially how older people affect virus transmission. Subtype analysis based on available pol sequences obtained from HIV patients revealed that CRF01_AE and CRF08_BC were predominant in patients aged <50 years, whereas CRF01_AE was predominant in older people aged ≥50 years (χ2 = 29.299, P < 0.001). A total of 25 patients (5.2%, 25/484) were identified with recent HIV infection (RHI). Transmission network analysis found 267 genetically linked individuals forming 55 clusters (2-63 individuals), including 5 large transmission clusters and 12 transmission clusters containing RHI. Bayesian phylogenetic analysis suggested that transmission events in CRF01_AE and CRF07_BC were centred on older males, while transmission events in CRF08_BC were centred on younger males. Multivariable logistic regression analysis showed that older people were more likely to cluster within networks (AOR = 2.303, 95% CI: 1.012-5.241) and that RHI was a significant factor associated with high linkage (AOR = 3.468, 95% CI: 1.315-9.146). This study provides molecular evidence that older males play a central role in the local transmission of CRF01_AE and CRF07_BC in Guangxi. Given the current widespread of CRF01_AE and CRF07_BC in Guangxi, there is a need to recommend HIV screening as part of free national medical examinations for older people to improve early detection, timely treatment, and further reduce second-generation transmission.
Collapse
Affiliation(s)
- Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, People’s Republic of China
| | - Yao Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China
| | - Na Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China
| | - Huayue Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China
| | - Yongzheng Chen
- Qinzhou Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Zhaosen Lin
- Qinzhou Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Tongbi Chen
- Qinzhou Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Wenling Tan
- Lingshan County Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Yuan Yang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, People’s Republic of China
| | - Rongye Huang
- Qinzhou Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Lin Yao
- Lingshan County Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Fuling Chen
- Lingshan County Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Xingzhen Huang
- Lingshan County Center for Disease Control and Prevention, Qinzhou, People’s Republic of China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, People’s Republic of China,Li Ye Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning530021, Guangxi, People’s Republic of China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, People’s Republic of China,Hao Liang
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, People’s Republic of China, Bingyu Liang
| |
Collapse
|
2
|
Jackman KMP, Tilchin C, Wagner J, Flinn RE, Trent M, Latkin C, Ruhs S, Fields EL, Hamill MM, Mahaffey C, Greenbaum A, Jennings JM. Desires for Individual- and Interpersonal-Level Patient Portal Use for HIV Prevention Among Urban Sexual Minority Men: Cross-sectional Study. JMIR Form Res 2023; 7:e43550. [PMID: 36826983 PMCID: PMC9994643 DOI: 10.2196/43550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Gay, bisexual, and other sexual minority men have expressed the acceptability of patient portals as tools for supporting HIV prevention behaviors, including facilitating disclosure of HIV and other sexually transmitted infection (STI/HIV) laboratory test results to sex partners. However, these studies, in which Black or African American sexual minority men were undersampled, failed to determine the relationship of reported history of discussing HIV results with sex partners and anticipated willingness to disclose web-based STI/HIV test results using a patient portal. OBJECTIVE Among a sample of predominantly Black sexual minority men, this study aimed to (1) determine preferences for patient portal use for HIV prevention and (2) test the associations between reported history of discussing HIV results and anticipated willingness to disclose web-based STI/HIV test results with most recent main and nonmain partners using patient portals. METHODS Data come from audio-computer self-assisted interview survey data collected during the 3-month visit of a longitudinal cohort study. Univariate analysis assessed patient portal preferences by measuring the valuation rankings of several portal features. Multiple Poisson regression models with robust error variance determined the associations between history of discussing HIV results and willingness to disclose those results using web-based portals by partner type, and to examine criterion validity of the enhancing dyadic communication (EDC) scale to anticipated willingness. RESULTS Of the 245 participants, 71% (n=174) were Black and 22% (n=53) were White. Most participants indicated a willingness to share web-based STI/HIV test results with their most recent main partner. Slightly fewer, nonetheless a majority, indicated a willingness to share web-based test results with their most recent nonmain partner. All but 2 patient portal features were valued as high or moderately high priority by >80% of participants. Specifically, tools to help manage HIV (n=183, 75%) and information about pre- and postexposure prophylaxis (both 71%, n=173 and n=175, respectively) were the top-valuated features to include in patient portals for HIV prevention. Discussing HIV test results was significantly associated with increased prevalence of willingness to disclose web-based test results with main (adjusted prevalence ratio [aPR] 1.46, 95% CI 1.21-1.75) and nonmain partners (aPR 1.54, 95% CI 1.23-1.93). CONCLUSIONS Our findings indicate what features Black sexual minority men envision may be included in the patient portal's design to optimize HIV prevention, further supporting the criterion validity of the EDC scale. Efforts should be made to support Black sexual minority men's willingness to disclose STI/HIV testing history and status with partners overall as it is associated significantly with a willingness to disclose testing results digitally via patient portals. Future studies should consider discussion behaviors regarding past HIV test results with partners when tailoring interventions that leverage patient portals in disclosure events.
Collapse
Affiliation(s)
- Kevon-Mark P Jackman
- Division of Adolescent and Young Adult Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Carla Tilchin
- Center for Child and Community Health Research, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Health, Behavior, and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jessica Wagner
- Center for Child and Community Health Research, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Ryan E Flinn
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Maria Trent
- Division of Adolescent and Young Adult Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Carl Latkin
- Department of Health, Behavior, and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Sebastian Ruhs
- Chase Brexton Health Services, Baltimore, MD, United States
| | - Errol L Fields
- Division of Adolescent and Young Adult Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Health, Behavior, and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Matthew M Hamill
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, United States.,STI/HIV Program, Baltimore City Health Department, Baltimore, MD, United States
| | - Carlos Mahaffey
- Department of Public Health, College of Health and Human Sciences, Purdue University, West Lafayette, IN, United States
| | - Adena Greenbaum
- STI/HIV Program, Baltimore City Health Department, Baltimore, MD, United States
| | - Jacky M Jennings
- Center for Child and Community Health Research, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Health, Behavior, and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| |
Collapse
|
3
|
Liu M, Chato C, Poon AFY. From components to communities: bringing network science to clustering for molecular epidemiology. Virus Evol 2023; 9:vead026. [PMID: 37187604 PMCID: PMC10175948 DOI: 10.1093/ve/vead026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/30/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Defining clusters of epidemiologically related infections is a common problem in the surveillance of infectious disease. A popular method for generating clusters is pairwise distance clustering, which assigns pairs of sequences to the same cluster if their genetic distance falls below some threshold. The result is often represented as a network or graph of nodes. A connected component is a set of interconnected nodes in a graph that are not connected to any other node. The prevailing approach to pairwise clustering is to map clusters to the connected components of the graph on a one-to-one basis. We propose that this definition of clusters is unnecessarily rigid. For instance, the connected components can collapse into one cluster by the addition of a single sequence that bridges nodes in the respective components. Moreover, the distance thresholds typically used for viruses like HIV-1 tend to exclude a large proportion of new sequences, making it difficult to train models for predicting cluster growth. These issues may be resolved by revisiting how we define clusters from genetic distances. Community detection is a promising class of clustering methods from the field of network science. A community is a set of nodes that are more densely inter-connected relative to the number of their connections to external nodes. Thus, a connected component may be partitioned into two or more communities. Here we describe community detection methods in the context of genetic clustering for epidemiology, demonstrate how a popular method (Markov clustering) enables us to resolve variation in transmission rates within a giant connected component of HIV-1 sequences, and identify current challenges and directions for further work.
Collapse
Affiliation(s)
- Molly Liu
- Department of Pathology and Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044, London, ON N6A 5C1, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044, London, ON N6A 5C1, Canada
| | | |
Collapse
|
4
|
Progress and challenges in virus genomic epidemiology. Trends Parasitol 2021; 37:1038-1049. [PMID: 34620561 DOI: 10.1016/j.pt.2021.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
Genomic epidemiology, which links pathogen genomes with associated metadata to understand disease transmission, has become a key component of outbreak response. Decreasing costs of genome sequencing and increasing computational power provide opportunities to generate and analyse large viral genomic datasets that aim to uncover the spatial scales of transmission, the demographics contributing to transmission patterns, and to forecast epidemic trends. Emerging sources of genomic data and associated metadata provide new opportunities to further unravel transmission patterns. Key challenges include how to integrate genomic data with metadata from multiple sources, how to generate efficient computational algorithms to cope with large datasets, and how to establish sampling frameworks to enable robust conclusions.
Collapse
|
5
|
Yang J, Han Z, Xu H, Xing H, Xu P, Cheng W, Gu Y, Lyu F. Identifying the Key Nodes of HIV Molecular Transmission Network Among Men Who Have Sex with Men - Guangzhou, Guangdong Province, China, 2015-2017. China CDC Wkly 2021; 3:803-807. [PMID: 34594994 PMCID: PMC8477060 DOI: 10.46234/ccdcw2021.198] [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: 05/10/2021] [Accepted: 09/15/2021] [Indexed: 11/24/2022] Open
Abstract
What is already known about this topic? Identifying the most influential spreaders in human immunodeficiency virus (HIV) transmission networks is crucial for developing effective prevention strategies. What is added by this report? This study identified key nodes of the HIV molecular transmission network among men who have sex with men (MSM) by utilizing linkages between sequences to reconstruct the transmission network at the molecular level. What are the implications for public health practice? This study could act as an important supplement of laboratory results to epidemiological studies and suggests that interdisciplinary research could inspire new ideas for finding breakthroughs on HIV/acquired immunodeficiency syndrome (AIDS) prevention and control.
Collapse
Affiliation(s)
- Juan Yang
- The National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhigang Han
- Department of HIV/AIDS Control and Prevention, Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Huifang Xu
- Department of HIV/AIDS Control and Prevention, Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Hui Xing
- The National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Peng Xu
- The National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weibin Cheng
- Department of HIV/AIDS Control and Prevention, Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yuzhou Gu
- Department of HIV/AIDS Control and Prevention, Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Fan Lyu
- The National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
6
|
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.
Collapse
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
| | | | | | | |
Collapse
|
7
|
Basodi S, Baykal PI, Zelikovsky A, Skums P, Pan Y. Analysis of heterogeneous genomic samples using image normalization and machine learning. BMC Genomics 2020; 21:405. [PMID: 33349236 PMCID: PMC7751093 DOI: 10.1186/s12864-020-6661-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analysis of heterogeneous populations such as viral quasispecies is one of the most challenging bioinformatics problems. Although machine learning models are becoming to be widely employed for analysis of sequence data from such populations, their straightforward application is impeded by multiple challenges associated with technological limitations and biases, difficulty of selection of relevant features and need to compare genomic datasets of different sizes and structures. RESULTS We propose a novel preprocessing approach to transform irregular genomic data into normalized image data. Such representation allows to restate the problems of classification and comparison of heterogeneous populations as image classification problems which can be solved using variety of available machine learning tools. We then apply the proposed approach to two important problems in molecular epidemiology: inference of viral infection stage and detection of viral transmission clusters using next-generation sequencing data. The infection staging method has been applied to HCV HVR1 samples collected from 108 recently and 257 chronically infected individuals. The SVM-based image classification approach achieved more than 95% accuracy for both recently and chronically HCV-infected individuals. Clustering has been performed on the data collected from 33 epidemiologically curated outbreaks, yielding more than 97% accuracy. CONCLUSIONS Sequence image normalization method allows for a robust conversion of genomic data into numerical data and overcomes several issues associated with employing machine learning methods to viral populations. Image data also help in the visualization of genomic data. Experimental results demonstrate that the proposed method can be successfully applied to different problems in molecular epidemiology and surveillance of viral diseases. Simple binary classifiers and clustering techniques applied to the image data are equally or more accurate than other models.
Collapse
Affiliation(s)
- Sunitha Basodi
- Department of Computer Science, Georgia State University, 25 Park Place NE, Atlanta, GA, 30303, USA.
| | - Pelin Icer Baykal
- Department of Computer Science, Georgia State University, 25 Park Place NE, Atlanta, GA, 30303, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, 25 Park Place NE, Atlanta, GA, 30303, USA.,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 11991, Russia
| | - Pavel Skums
- Department of Computer Science, Georgia State University, 25 Park Place NE, Atlanta, GA, 30303, USA
| | - Yi Pan
- Department of Computer Science, Georgia State University, 25 Park Place NE, Atlanta, GA, 30303, USA
| |
Collapse
|
8
|
Jean Louis F, Domercant JW, Ignacio C, Gianella S, Galbaud G, Leonard M, Smith DM, Chaillon A. High Prevalence of HIV-1 Drug Resistance and Dynamics of Transmission Among High-Risk Populations in Port-au-Prince, Haiti. J Acquir Immune Defic Syndr 2020; 85:416-422. [PMID: 33136738 PMCID: PMC7592887 DOI: 10.1097/qai.0000000000002475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/05/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND In low HIV prevalence settings, understanding the transmission dynamics and the impact of drug resistance is critical to curb down the epidemic. This study aims to explore the prevalence and dynamics of transmission of HIV drug-resistance mutations (DRMs) among key populations in Haiti. SETTINGS Eligible participants (naive, treated) were selected from 7 key population friendly health care centers in Port-au-Prince, Haiti, from September 2018 to July 2019. METHODS A total of 119 HIV-1 pol sequences were analyzed from men having sex with men (MSM), female sex workers (FSWs), and their sexual partners. Screening for HIV DRMs was performed using the Stanford University Drug Resistance Database. Phylogenetic and network analyses using HIV-TRACE software were performed to infer putative relationships and shared DRMs. RESULTS Of the 119 participants, 62.2% were men (74/119), and 75.7% of them (56/74) reported MSM as a main risk factor. The overall DRM prevalence was 58.8% (70/119). A DRM was observed in 37.5% of MSM (21/56), 82.2% of FSWs (37/45), and 66.7% (12/18) among FSWs' clients. In a multivariate model, age and FSWs were significant predictors for DRMs (P = 0.001). Transmission network analysis found 24 of the 119 (20.2%) genetically linked individuals forming 8 clusters. Clustering participants were mostly MSM (15/24; 62.5%). Five clusters (62.5%) had shared DRMs, and K103N and M184V were the main shared mutations. CONCLUSIONS High prevalence of HIV DRMs was observed among MSM, FSWs, and their clients in Port-au-Prince, Haiti. Network analysis revealed frequent DRM transmission among genetically linked individuals, highlighting the need for appropriate interventions to limit HIV transmission in these high-risk populations.
Collapse
Affiliation(s)
| | | | - Caroline Ignacio
- Division of Infectious Diseases, University of California San Diego, San Diego, CA
| | - Sara Gianella
- Division of Infectious Diseases, University of California San Diego, San Diego, CA
| | | | | | | | | |
Collapse
|
9
|
Novitsky V, Zahralban-Steele M, Moyo S, Nkhisang T, Maruapula D, McLane MF, Leidner J, Bennett K, Wirth KE, Gaolathe T, Kadima E, Chakalisa U, Pretorius Holme M, Lockman S, Mmalane M, Makhema J, Gaseitsiwe S, DeGruttola V, Essex M. Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial. J Infect Dis 2020; 222:1670-1680. [PMID: 32492145 PMCID: PMC7936922 DOI: 10.1093/infdis/jiaa276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/26/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Phylogenetic mapping of HIV-1 lineages circulating across defined geographical locations is promising for better understanding HIV transmission networks to design optimal prevention interventions. METHODS We obtained near full-length HIV-1 genome sequences from people living with HIV (PLWH), including participants on antiretroviral treatment in the Botswana Combination Prevention Project, conducted in 30 Botswana communities in 2013-2018. Phylogenetic relationships among viral sequences were estimated by maximum likelihood. RESULTS We obtained 6078 near full-length HIV-1C genome sequences from 6075 PLWH. We identified 984 phylogenetically distinct HIV-1 lineages (molecular HIV clusters) circulating in Botswana by mid-2018, with 2-27 members per cluster. Of these, dyads accounted for 62%, approximately 32% (n = 316) were found in single communities, and 68% (n = 668) were spread across multiple communities. Men in clusters were approximately 3 years older than women (median age 42 years, vs 39 years; P < .0001). In 65% of clusters, men were older than women, while in 35% of clusters women were older than men. The majority of identified viral lineages were spread across multiple communities. CONCLUSIONS A large number of circulating phylogenetically distinct HIV-1C lineages (molecular HIV clusters) suggests highly diversified HIV transmission networks across Botswana communities by 2018.
Collapse
Affiliation(s)
- Vlad Novitsky
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Melissa Zahralban-Steele
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tapiwa Nkhisang
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Mary Fran McLane
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jean Leidner
- Goodtables Data Consulting LLC, Norman, Oklahoma, USA
| | - Kara Bennett
- Bennett Statistical Consulting Inc, Ballston Lake, New York, USA
| | - Kathleen E Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Molly Pretorius Holme
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Joseph Makhema
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Victor DeGruttola
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - M Essex
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Abstract
OBJECTIVE We investigated the duration of HIV transmission clusters. DESIGN Fifty-four individuals newly infected at enrollment in the ALIVE cohort were included, all of whom had sequences at an intake visit (T1) and from a second (T2) and/or a third (T3) follow-up visit, median 2.9 and 5.4 years later, respectively. METHODS Sequences were generated using the 454 DNA sequencing platform for portions of HIV pol and env (HXB2 positions 2717-3230; 7941-8264). Genetic distances were calculated using tn93 and sequences were clustered over a range of thresholds (1--5%) using HIV-TRACE. Analyses were performed separately for individuals with pol sequences for T1 + T2 (n = 40, 'Set 1') and T1 + T3 (n = 25; 'Set 2'), and env sequences for T1 + T2 (n = 47, 'Set 1'), and T1 + T3 (n = 30; 'Set 2'). RESULTS For pol, with one exception, a single cluster contained more than 75% of samples at all thresholds, and cluster composition was at least 90% concordant between time points/thresholds. For env, two major clusters (A and B) were observed at T1 and T2/T3, although cluster composition concordance between time points/thresholds was low (<60%) at lower thresholds for both sets 1 and 2. In addition, several individuals were included in clusters at T2/T3, although not at T1. CONCLUSION Caution should be used in applying a single threshold in population studies where seroconversion dates are unknown. However, the retention of some clusters even after 5 + years is evidence for the robustness of the clustering approach in general.
Collapse
|
11
|
Networks Among Racial and Ethnic Minority Men Who Have Sex With Men in HIV Research in the United States: A Concept Analysis. J Assoc Nurses AIDS Care 2020; 31:379-391. [PMID: 31985510 DOI: 10.1097/jnc.0000000000000160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In the past 10 years, research has proliferated investigating the effects of sexual and social networks on the transmission of HIV, especially among racial/ethnic minority men who have sex with men (MSM). This research, however, has been inconsistent in its application of social network theory leading to variations in the measurement of networks and a lack of clarity in the interpretation of results from studies of network data. Efforts to delineate how networks are defined, measured, and interpreted are needed to advance the science of HIV prevention and promote health equity. The aims of this article are to review the literature around networks among racial/ethnic minority MSM, use concept analysis methods to clarify the definition and scope of the concept of networks, and to develop a network typology that can be used to guide measurement and interpretation of networks for HIV research with racial/ethnic minority MSM.
Collapse
|
12
|
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.
Collapse
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
| | | |
Collapse
|
13
|
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.
Collapse
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
| | | |
Collapse
|
14
|
Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinformatics 2020; 35:1852-1861. [PMID: 30395173 DOI: 10.1093/bioinformatics/bty921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The ability to simulate epidemics as a function of model parameters allows insights that are unobtainable from real datasets. Further, reconstructing transmission networks for fast-evolving viruses like Human Immunodeficiency Virus (HIV) may have the potential to greatly enhance epidemic intervention, but transmission network reconstruction methods have been inadequately studied, largely because it is difficult to obtain 'truth' sets on which to test them and properly measure their performance. RESULTS We introduce FrAmework for VIral Transmission and Evolution Simulation (FAVITES), a robust framework for simulating realistic datasets for epidemics that are caused by fast-evolving pathogens like HIV. FAVITES creates a generative model to produce contact networks, transmission networks, phylogenetic trees and sequence datasets, and to add error to the data. FAVITES is designed to be extensible by dividing the generative model into modules, each of which is expressed as a fixed API that can be implemented using various models. We use FAVITES to simulate HIV datasets and study the realism of the simulated datasets. We then use the simulated data to study the impact of the increased treatment efforts on epidemiological outcomes. We also study two transmission network reconstruction methods and their effectiveness in detecting fast-growing clusters. AVAILABILITY AND IMPLEMENTATION FAVITES is available at https://github.com/niemasd/FAVITES, and a Docker image can be found on DockerHub (https://hub.docker.com/r/niemasd/favites). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Niema Moshiri
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, USA
| | | | | | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC San Diego, La Jolla, USA
| |
Collapse
|
15
|
Gibson KM, Jair K, Castel AD, Bendall ML, Wilbourn B, Jordan JA, Crandall KA, Pérez-Losada M. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep 2020; 10:1989. [PMID: 32029767 PMCID: PMC7004982 DOI: 10.1038/s41598-020-58410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/31/2019] [Indexed: 11/08/2022] Open
Abstract
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
Collapse
Grants
- P30 AI117970 NIAID NIH HHS
- U01 AI069503 NIAID NIH HHS
- UM1 AI069503 NIAID NIH HHS
- This study was supported by the DC Cohort Study (U01 AI69503-03S2), a supplement from the Women’s Interagency Study for HIV-1 (410722_GR410708), a DC D-CFAR pilot award, and a 2015 HIV-1 Phylodynamics Supplement award from the District of Columbia for AIDS Research, an NIH funded program (AI117970), which is supported by the following NIH Co-Funding and Participating Institutes and Centers: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, NIGMS, NIDDK and OAR. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
Collapse
Affiliation(s)
- Keylie M Gibson
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
| | - Kamwing Jair
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Amanda D Castel
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Matthew L Bendall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Brittany Wilbourn
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Jeanne A Jordan
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| |
Collapse
|
16
|
How are transgender women acquiring HIV? Insights from phylogenetic transmission clusters in San Francisco. AIDS 2019; 33:2073-2079. [PMID: 31335804 DOI: 10.1097/qad.0000000000002318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We explored potential HIV transmission typologies that involve transgender women to obtain insights on sexual and needle-sharing networks as sources of HIV infection. DESIGN San Francisco residents diagnosed with HIV in care at public facilities who had available viral pol sequences from June 2001 to January 2016 were included in the analysis. METHODS Viral sequence data were matched to the San Francisco HIV/AIDS Case Registry to obtain demographic and risk classification information. Transmission clusters with at least two cases were identified by bootstrap values at least 90% and mean pairwise genetic distances 0.025 or less substitutions per site. RESULTS Transgender women represented 275 of 5200 patients; 86 were present in 70 clusters. Four typologies were hypothesized: first, transgender women in clusters with MSM; second, transgender women who inject drugs in clusters with cisgender women and men who inject drugs; third, multiple transgender women in clusters with one man; and fourth, multiple transgender women who do not inject drugs in clusters with men and cisgender women who inject drugs. CONCLUSION Transmission patterns of transgender women may stand apart from MSM epidemics. Transgender women clustered with people who inject drugs, and with men who have sex with transgender women and cisgender women. Aggregation of transgender women into the category of MSM may obscure understanding of how they acquire HIV and to whom they may transmit infection. Phylogenetic insights strengthen the case that HIV prevention programs for MSM may not be applicable to transgender women or their partners.
Collapse
|
17
|
Han AX, Parker E, Maurer-Stroh S, Russell CA. Inferring putative transmission clusters with Phydelity. Virus Evol 2019; 5:vez039. [PMID: 31616568 PMCID: PMC6785678 DOI: 10.1093/ve/vez039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Current phylogenetic clustering approaches for identifying pathogen transmission clusters are limited by their dependency on arbitrarily defined genetic distance thresholds for within-cluster divergence. Incomplete knowledge of a pathogen’s underlying dynamics often reduces the choice of distance threshold to an exploratory, ad hoc exercise that is difficult to standardise across studies. Phydelity is a new tool for the identification of transmission clusters in pathogen phylogenies. It identifies groups of sequences that are more closely related than the ensemble distribution of the phylogeny under a statistically principled and phylogeny-informed framework, without the introduction of arbitrary distance thresholds. Relative to other distance threshold- and model-based methods, Phydelity outputs clusters with higher purity and lower probability of misclassification in simulated phylogenies. Applying Phydelity to empirical datasets of hepatitis B and C virus infections showed that Phydelity identified clusters with better correspondence to individuals that are more likely to be linked by transmission events relative to other widely used non-parametric phylogenetic clustering methods without the need for parameter calibration. Phydelity is generalisable to any pathogen and can be used to identify putative direct transmission events. Phydelity is freely available at https://github.com/alvinxhan/Phydelity.
Collapse
Affiliation(s)
- Alvin X Han
- Protein Sequence Analysis Group, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, 138671 Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), 21 Lower Kent Ridge, 119077 Singapore.,Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam-Zuidoost, The Netherlands
| | - Edyth Parker
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam-Zuidoost, The Netherlands.,Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK
| | - Sebastian Maurer-Stroh
- Protein Sequence Analysis Group, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, 138671 Singapore.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam-Zuidoost, The Netherlands
| |
Collapse
|
18
|
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.
Collapse
|
19
|
Wu J, Zhang Y, Shen Y, Wang X, Xing H, Yang X, Ding X, Hu B, Li H, Han J, Li J, Su B, Liu Y, Li L. Phylogenetic analysis highlights the role of older people in the transmission of HIV-1 in Fuyang, Anhui Province, China. BMC Infect Dis 2019; 19:562. [PMID: 31248372 PMCID: PMC6598234 DOI: 10.1186/s12879-019-4187-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/12/2019] [Indexed: 01/16/2023] Open
Abstract
Background The proportion of older HIV-1 infected people in China has increased rapidly in recent years. Elucidation of the transmission characteristics of this high-risk population subgroup is helpful for the development of tailored interventions. Methods A phylogenetic analysis was performed that uses available HIV-1 pol sequences amplified with nested RT-PCR from plasma samples of all newly diagnosed participants spanning from October 2017 to September 2018 in Fuyang, Anhui Province. Transmission clusters were identified as two or more sequences that shared a corresponding node with an aLRT-SH value ≥90 in the maximum-likelihood phylogenetic tree and had an overall mean genetic distance of ≤1.5%. A local transmission cluster was defined as a cluster that had more than 80% of its sequences from Fuyang. The role of older people in local HIV-1 transmission was determined using an integration of molecular and demographic data. Results Of 362 available sequences, 14 subtypes, and 28 local transmission clusters were identified. It was found that the proportion of older people in the local transmission cluster (69/77, 89.61%) was much higher than that of younger people (46/114, 40.35%) (χ2 test, P < 0.001). In the pretreatment drug resistance analysis, the proportion of sequences with PDRMs in the local transmission cluster was not significantly different between the older people group (57.14%, 4/7) and non-old-aged group (11.11%, 1/9) (Fisher’s exact test, P > 0.05). Conclusion By combining phylogenetic analyses with demographic data, more detailed information was provided about the local transmission structure in Fuyang. These findings suggested that older people play an important role in local transmission, and more tailored interventions for this population subgroup are urgently needed.
Collapse
Affiliation(s)
- Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaohui Yang
- Fuyang Center for Disease Control and Prevention, Fuyang, 236069, China
| | - Xinping Ding
- Fuyang Center for Disease Control and Prevention, Fuyang, 236069, China
| | - Bing Hu
- Fuyang Center for Disease Control and Prevention, Fuyang, 236069, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China.
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| |
Collapse
|
20
|
Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Mol Biol Evol 2019; 35:1812-1819. [PMID: 29401317 DOI: 10.1093/molbev/msy016] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoe-leather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, that is, on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from www.github.com/veg/hivtrace, along with the accompanying result visualization module from www.github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens.
Collapse
Affiliation(s)
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Andrew J Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA
| |
Collapse
|
21
|
Abeler-Dörner L, Grabowski MK, Rambaut A, Pillay D, Fraser C. PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa. Curr Opin HIV AIDS 2019; 14:173-180. [PMID: 30946141 PMCID: PMC6629166 DOI: 10.1097/coh.0000000000000542] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW The HIV epidemic in sub-Saharan Africa is far from being under control and the ambitious UNAIDS targets are unlikely to be met by 2020 as declines in per-capita incidence being largely offset by demographic trends. There is an increasing number of proven and specific HIV prevention tools, but little consensus on how best to deploy them. RECENT FINDINGS Traditionally, phylogenetics has been used in HIV research to reconstruct the history of the epidemic and date zoonotic infections, whereas more recent publications focus on HIV diversity and drug resistance. However, it is also the most powerful method of source attribution available for the study of HIV transmission. The PANGEA (Phylogenetics And Networks for Generalized Epidemics in Africa) consortium has generated over 18 000 NGS HIV sequences from five countries in sub-Saharan Africa. Using phylogenetic methods, we will identify characteristics of individuals or groups, which are most likely to be at risk of infection or at risk of infecting others. SUMMARY Combining phylogenetics, phylodynamics and epidemiology will allow PANGEA to highlight where prevention efforts should be focussed to reduce the HIV epidemic most effectively. To maximise the public health benefit of the data, PANGEA offers accreditation to external researchers, allowing them to access the data and join the consortium. We also welcome submissions of other HIV sequences from sub-Saharan Africa to the database.
Collapse
Affiliation(s)
- Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mary K. Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
22
|
Wertheim JO, Chato C, Poon AFY. Comparative analysis of HIV sequences in real time for public health. Curr Opin HIV AIDS 2019; 14:213-220. [PMID: 30882486 DOI: 10.1097/coh.0000000000000539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW The purpose of this study is to summarize recent advances in public health applications of comparative methods for HIV-1 sequence analysis in real time, including genetic clustering methods. RECENT FINDINGS Over the past 2 years, several groups have reported the deployment of established genetic clustering methods to guide public health decisions for HIV prevention in 'near real time'. However, it remains unresolved how well the readouts of comparative methods like clusters translate to events that are actionable for public health. A small number of recent studies have begun to elucidate the linkage between clusters and HIV-1 incidence, whereas others continue to refine and develop new comparative methods for such applications. SUMMARY Although the use of established methods to cluster HIV-1 sequence databases has become a widespread activity, there remains a critical gap between clusters and public health value.
Collapse
Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, California, USA
| | | | - Art F Y Poon
- Department of Pathology and Laboratory Medicine
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| |
Collapse
|
23
|
Tran NK, Welles SL. Four Decades of Epidemiologic Science on HIV Infection and Disease, and Its Impact on Public Health Practice and Policy for Sexual and Gender Minority Persons. Dela J Public Health 2019; 5:64-71. [PMID: 34467031 PMCID: PMC8396754 DOI: 10.32481/djph.2019.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Even at the cusp of the second decade of the new millennia, HIV continues to be a significant public health challenge for sexual and gender minorities (SGM). Men who have sex with men and transgender women, in particular, continue to report higher rates of HIV incidence compared to their heterosexual counterparts, while facing significant barriers to comprehensive sexual healthcare. In Delaware, HIV infection impacts a substantial number of individuals with approximately 14.5 incident cases per 100,000. This ranks Delaware as the 14th highest for HIV incidence among U.S. states. However, the largest healthcare provider in Delaware, Christiana Care Health System, has created many health initiatives to support the health needs of SGM and those living with HIV. The current sustained rate of HIV infection indicates the need for enhanced epidemiologic work to identify HIV cases in subgroups of diverse sexuality and gender identity, collaboration within and across research institution and community organizations, as well as engagement in creative solutions that target the multiple levels of factors contributing to HIV incidence. In addition, it is imperative that local agencies and health organizations continue to support these communities of SGM individuals during the current sociopolitical climate of the national U.S. government.
Collapse
Affiliation(s)
- Nguyen K Tran
- Department of Epidemiology & Biostatistics, Drexel University Dornsife School of Public Health, Philadelphia, PA
| | - Seth L Welles
- Department of Epidemiology & Biostatistics, Drexel University Dornsife School of Public Health, Philadelphia, PA
| |
Collapse
|
24
|
Rhee SY, Magalis BR, Hurley L, Silverberg MJ, Marcus JL, Slome S, Kosakovsky Pond SL, Shafer RW. National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort. Open Forum Infect Dis 2019; 6:ofz135. [PMID: 31041344 PMCID: PMC6483754 DOI: 10.1093/ofid/ofz135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/12/2019] [Indexed: 11/14/2022] Open
Abstract
Background Recent advances in high-throughput molecular epidemiology are transforming the analysis of viral infections. Methods Human immunodeficiency virus (HIV)-1 pol sequences from a Northern Californian cohort (NCC) of 4553 antiretroviral-naive individuals sampled between 1998 and 2016 were analyzed together with 140 000 previously published global pol sequences. The HIV-TRAnsmission Cluster Engine (HIV-TRACE) was used to infer a transmission network comprising links between NCC and previously published sequences having a genetic distance ≤1.5%. Results Twenty-five percent of NCC sequences were included in 264 clusters linked to a published sequence, and approximately one third of these (8.0% of the total) were linked to 1 or more non-US sequences. The largest cluster, containing 512 NCC sequences (11.2% of the total), comprised the subtype B lineage that traced its origin to the earliest North American sequences. Approximately 5 percent of NCC sequences belonged to a non-B subtype, and these were more likely to cluster with a non-US sequence. Twenty-two NCC sequences belonged to 1 of 4 large clusters containing sequences from rapidly growing regional epidemics: CRF07_BC (East Asia), subtype A6 (former Soviet Union), a Japanese subtype B lineage, and an East/Southeast Asian CRF01_AE lineage. Bayesian phylogenetics suggested that most non-B sequences resulted from separate introductions but that local spread within the largest CRF01_AE cluster occurred twice. Conclusions The NCC contains national and international links to previously published sequences including many to the subtype B strain that originated in North America and several to rapidly growing Asian epidemics. Despite their rapid regional growth, the Asian epidemic strains demonstrated limited NCC spread.
Collapse
Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, California
| | | | - Leo Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | - Julia L Marcus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Sally Slome
- Department of Infectious Diseases, Kaiser Permanente Northern California, Oakland
| | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, California
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
West BS. Social Networks of Substance-Using Populations: Key Issues and Promising New Approaches for HIV. Curr HIV/AIDS Rep 2019; 16:48-56. [PMID: 30659477 PMCID: PMC6420834 DOI: 10.1007/s11904-019-00425-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE OF REVIEW This paper presents recent literature on substance using networks and HIV, highlighting renewed and emerging themes in the field. The goal is to draw attention to research that holds considerable promise for advancing our understanding of the role of networks in shaping behaviors, while also providing critical information for the development of interventions, programs, and policies to reduce HIV and other drug-related harms. RECENT FINDINGS Recent research advances our understanding of networks and HIV, including among understudied populations, and provides new insight into how risk environments shape the networks and health of substance-using populations. In particular, the integration of network approaches with molecular epidemiology, research on space and place, and intervention methods provides exciting new avenues of investigation. Continued advances in network research are critical to supporting the health and rights of substance-using populations and ensuring the development of high-impact HIV programs and policies.
Collapse
Affiliation(s)
- Brooke S West
- School of Social Work, Columbia University, 1255 Amsterdam Avenue, New York, NY, 10027, USA.
- Division of Infectious Diseases and Global Public Health in the School of Medicine, University of California San Diego, San Diego, CA, USA.
| |
Collapse
|
27
|
Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
Collapse
Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
| |
Collapse
|
28
|
Mutenherwa F, Wassenaar DR, de Oliveira T. Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research. J Empir Res Hum Res Ethics 2018; 14:61-77. [PMID: 30486713 DOI: 10.1177/1556264618809608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The use of phylogenetics in HIV molecular epidemiology has considerably increased our ability to understand the origin, spread, and characteristics of HIV epidemics. Despite its potential to advance knowledge on HIV transmission dynamics, the ethical issues associated with HIV molecular epidemiology have received minimal attention. In-depth interviews were conducted with scientists from diverse backgrounds to explore their perspectives on ethical issues associated with phylogenetic analysis of HIV genetic data as applied to HIV transmission dynamics studies. The Emanuel framework was used as the analytical framework. Favorable risk-benefit ratio and informed consent were the most invoked ethical principles and fair participant selection the least. Fear of loss of privacy and disclosure of HIV transmission were invariably cited as key ethical concerns. As HIV sequence data become increasingly available, comprehensive guidelines should be developed to guide its access, sharing and use, cognizant of the potential harms that may result.
Collapse
Affiliation(s)
- Farirai Mutenherwa
- 1 University of KwaZulu-Natal, South Africa.,2 KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Tulio de Oliveira
- 1 University of KwaZulu-Natal, South Africa.,2 KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,3 Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| |
Collapse
|
29
|
Coltart CEM, Hoppe A, Parker M, Dawson L, Amon JJ, Simwinga M, Geller G, Henderson G, Laeyendecker O, Tucker JD, Eba P, Novitsky V, Vandamme AM, Seeley J, Dallabetta G, Harling G, Grabowski MK, Godfrey-Faussett P, Fraser C, Cohen MS, Pillay D. Ethical considerations in global HIV phylogenetic research. Lancet HIV 2018; 5:e656-e666. [PMID: 30174214 PMCID: PMC7327184 DOI: 10.1016/s2352-3018(18)30134-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/28/2018] [Accepted: 06/06/2018] [Indexed: 01/01/2023]
Abstract
Phylogenetic analysis of pathogens is an increasingly powerful way to reduce the spread of epidemics, including HIV. As a result, phylogenetic approaches are becoming embedded in public health and research programmes, as well as outbreak responses, presenting unique ethical, legal, and social issues that are not adequately addressed by existing bioethics literature. We formed a multidisciplinary working group to explore the ethical issues arising from the design of, conduct in, and use of results from HIV phylogenetic studies, and to propose recommendations to minimise the associated risks to both individuals and groups. We identified eight key ethical domains, within which we highlighted factors that make HIV phylogenetic research unique. In this Review, we endeavoured to provide a framework to assist researchers, public health practitioners, and funding institutions to ensure that HIV phylogenetic studies are designed, done, and disseminated in an ethical manner. Our conclusions also have broader relevance for pathogen phylogenetics.
Collapse
Affiliation(s)
| | - Anne Hoppe
- Division of Infection and Immunity, University College London, London, UK.
| | - Michael Parker
- The Wellcome Centre for Ethics and Humanities (Ethox), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liza Dawson
- Division of AIDS, National Institutes of Health, Bethesda, MD, USA
| | - Joseph J Amon
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | | | - Gail Geller
- Berman Institute of Bioethics and School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Gail Henderson
- Center for Genomics and Society, Department of Social Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph D Tucker
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Patrick Eba
- Community Support, Social Justice and Inclusion Department, Geneva, Switzerland; School of Law, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven-University of Leuven, Leuven, Belgium; Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Janet Seeley
- Africa Health Research Institute, KwaZulu-Natal, South Africa; Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Guy Harling
- Institute for Global Health, University College London, London, UK; Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - M Kate Grabowski
- Department of Pathology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Rakai Community Cohort Study, Rakai Health Sciences Program, Kalisizo, Uganda
| | - Peter Godfrey-Faussett
- Joint United Nations Programme on HIV/AIDS, Geneva, Switzerland; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Myron S Cohen
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK; Africa Health Research Institute, KwaZulu-Natal, South Africa
| |
Collapse
|
30
|
Bae JM. Introduction of Phylodynamics for Controlling the HIV/AIDS Epidemic in Korea. J Prev Med Public Health 2018; 51:326-328. [PMID: 30514063 PMCID: PMC6283738 DOI: 10.3961/jpmph.18.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
As over 1000 new cases of HIV/AIDS occur in Korea annually, preventive health programs against HIV/AIDS are urgently needed. Since phylodynamic studies have been suggested as a way to understand how infectious diseases are transmitted and evolve, phylodynamic inferences can be a useful tool for HIV/AIDS research. In particular, phylodynamic models are helpful for dating the origins of an epidemic and estimating its basic reproduction number. Thus, the introduction of phylodynamics would be a highly valuable step towards controlling the HIV/AIDS epidemic in Korea.
Collapse
Affiliation(s)
- Jong-Myon Bae
- Department of Preventive Medicine, Jeju National University School of Medicine, Jeju, Korea
| |
Collapse
|
31
|
Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y. QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinformatics 2018; 34:163-170. [PMID: 29304222 DOI: 10.1093/bioinformatics/btx402] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Motivation Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data, such as sampling times and exposure intervals. This impedes genomic analysis of outbreaks of highly mutable viruses associated with chronic infections, such as human immunodeficiency virus and hepatitis C virus, whose transmissions are often carried out through minor intra-host variants, while the additional epidemiological information often is either unavailable or has a limited use. Results The proposed framework QUasispecies Evolution, Network-based Transmission INference (QUENTIN) addresses the above challenges by evolutionary analysis of intra-host viral populations sampled by deep sequencing and Bayesian inference using general properties of social networks relevant to infection dissemination. This method allows inference of transmission direction even without the supporting case-specific epidemiological information, identify transmission clusters and reconstruct transmission history. QUENTIN was validated on experimental and simulated data, and applied to investigate HCV transmission within a community of hosts with high-risk behavior. It is available at https://github.com/skumsp/QUENTIN. Contact pskums@gsu.edu or alexz@cs.gsu.edu or rahul@sfsu.edu or yek0@cdc.gov. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Pavel Skums
- Department of Computer Science, Georgia State University.,Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | | | - Rahul Singh
- Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA
| | - Walker Gussler
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Zoya Dimitrova
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Sergey Knyazev
- Department of Computer Science, Georgia State University
| | - Igor Mandric
- Department of Computer Science, Georgia State University
| | - Sumathi Ramachandran
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - David Campo
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Deeptanshu Jha
- Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA
| | - Leonid Bunimovich
- School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30313, USA
| | | | - Connie Sexton
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA.,Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Siobhan O'Connor
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA.,Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Guo-Liang Xia
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Yury Khudyakov
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Kiessling AA. Retroviruses and reproduction revisited. J Assist Reprod Genet 2018; 35:1969-1972. [PMID: 30006789 PMCID: PMC6240540 DOI: 10.1007/s10815-018-1253-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/26/2018] [Indexed: 11/15/2022] Open
Abstract
Thanks to effective anti-HIV medications, deaths from acquired immunodeficiency disease (AIDS) have plummeted, although the incidence of new HIV infections has decreased little, approximately 36,000 annually in the USA. The CDC estimates 1.1 million persons, mostly men, are living with HIV in the USA, with approximately 14% unaware they are infected. Since the global blood supply is essentially free of HIV today, infected semen is fueling the pandemic (88% of new infections in the USA), with needle sharing among IV drug abusers (7% of new US infections) and female to male transmission (5% of new infections) accounting for the balance. In spite of the importance to disease prevention and strategies for safe conception, semen transmission of HIV is not well understood. Because anti-HIV therapy does not eliminate HIV from semen, the Centers for Disease Control (CDC) for the past 25 years has espoused condom use as the safest approach to prevent HIV transmission, as well as other sexually transmitted diseases. A few months ago, however, an MMWR was circulated by the CDC that suggested condomless sex might be safe if the HIV-infected partner’s medications achieved an undetectable viral load in his blood. This new opinion was based on reports by three teams of investigators cited in the MMWR: “All three studies observed no HIV transmission to the uninfected partner while the partner with HIV was virologically suppressed with ART.” Unfortunately, this CDC statement does not fully describe the data presented in the studies, and abandoning condom use puts uninfected partners, including women seeking to conceive, at risk for infection by HIV and other STDs.
Collapse
Affiliation(s)
- Ann A Kiessling
- Bedford Research Foundation, 124 South Road, Bedford, MA, 01730, USA.
| |
Collapse
|
34
|
Sivay MV, Hudelson SE, Wang J, Agyei Y, Hamilton EL, Selin A, Dennis A, Kahn K, Gomez-Olive FX, MacPhail C, Hughes JP, Pettifor A, Eshleman SH, Grabowski MK. HIV-1 diversity among young women in rural South Africa: HPTN 068. PLoS One 2018; 13:e0198999. [PMID: 29975689 PMCID: PMC6033411 DOI: 10.1371/journal.pone.0198999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/21/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND South Africa has one of the highest rates of HIV-1 (HIV) infection world-wide, with the highest rates among young women. We analyzed the molecular epidemiology and evolutionary history of HIV in young women attending high school in rural South Africa. METHODS Samples were obtained from the HPTN 068 randomized controlled trial, which evaluated the effect of cash transfers for school attendance on HIV incidence in women aged 13-20 years (Mpumalanga province, 2011-2015). Plasma samples from HIV-infected participants were analyzed using the ViroSeq HIV-1 Genotyping assay. Phylogenetic analysis was performed using 200 pol gene study sequences and 2,294 subtype C reference sequences from South Africa. Transmission clusters were identified using Cluster Picker and HIV-TRACE, and were characterized using demographic and other epidemiological data. Phylodynamic analyses were performed using the BEAST software. RESULTS The study enrolled 2,533 young women who were followed through their expected high school graduation date (main study); some participants had a post-study assessment (follow-up study). Two-hundred-twelve of 2,533 enrolled young women had HIV infection. HIV pol sequences were obtained for 94% (n = 201/212) of the HIV-infected participants. All but one of the sequences were HIV-1 subtype C; the non-C subtype sequence was excluded from further analysis. Median pairwise genetic distance between the subtype C sequences was 6.4% (IQR: 5.6-7.2). Overall, 26% of study sequences fell into 21 phylogenetic clusters with 2-6 women per cluster. Thirteen (62%) clusters included women who were HIV-infected at enrollment. Clustering was not associated with study arm, demographic or other epidemiological factors. The estimated date of origin of HIV subtype C in the study population was 1958 (95% highest posterior density [HPD]: 1931-1980), and the median estimated substitution rate among study pol sequences was 1.98x10-3 (95% HPD: 1.15x10-3-2.81x10-3) per site per year. CONCLUSIONS Phylogenetic analysis suggests that multiple HIV subtype C sublineages circulate among school age girls in South Africa. There were no substantive differences in the molecular epidemiology of HIV between control and intervention arms in the HPTN 068 trial.
Collapse
Affiliation(s)
- Mariya V. Sivay
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Sarah E. Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Jing Wang
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Yaw Agyei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | | | - Amanda Selin
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Ann Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F. Xavier Gomez-Olive
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Catherine MacPhail
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Health and Society, University of Wollongong, New South Wales, Australia
| | - James P. Hughes
- University of Washington, Seattle, WA, United States of America
| | - Audrey Pettifor
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mary Kathryn Grabowski
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| |
Collapse
|
35
|
Patiño-Galindo JÁ, González-Candelas F. Molecular evolution methods to study HIV-1 epidemics. Future Virol 2018; 13:399-404. [PMID: 29967650 DOI: 10.2217/fvl-2017-0159] [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] [Received: 12/25/2017] [Accepted: 04/04/2018] [Indexed: 01/17/2023]
Abstract
Nucleotide sequences of HIV isolates are obtained routinely to evaluate the presence of resistance mutations to antiretroviral drugs. But, beyond their clinical use, these and other viral sequences include a wealth of information that can be used to better understand and characterize the epidemiology of HIV in relevant populations. In this review, we provide a brief overview of the main methods used to analyze HIV sequences, the data bases where reference sequences can be obtained, and some caveats about the possible applications for public health of these analyses, along with some considerations about their limitations and correct usage to derive robust and reliable conclusions.
Collapse
Affiliation(s)
- Juan Á Patiño-Galindo
- Department of Systems Biology, Columbia University, New York, NY 10032, USA.,Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Fernando González-Candelas
- Joint Research Unit "Infección y Salud Pública" FISABIO-Salud Pública/Universitat de València-Institute for Integrative Systems Biology (ISysBio, CSIC-UV) Valencia, Spain.,CIBER in Epidemiology & Public Health, Valencia, Spain.,Joint Research Unit "Infección y Salud Pública" FISABIO-Salud Pública/Universitat de València-Institute for Integrative Systems Biology (ISysBio, CSIC-UV) Valencia, Spain.,CIBER in Epidemiology & Public Health, Valencia, Spain
| |
Collapse
|
36
|
Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach. PLoS One 2017; 12:e0186928. [PMID: 29084239 PMCID: PMC5662216 DOI: 10.1371/journal.pone.0186928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/10/2017] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic studies are a valuable tool to understand viral transmission patterns and the role of immigration in HIV-1 spread. We analyzed the spatio-temporal relationship of different HIV-1 non-B subtype variants over time using phylogenetic analysis techniques. We collected 693 pol (PR+RT) sequences that were sampled from 2005 to 2012 from naïve patients in different hospitals in southern Spain. We used REGA v3.0 to classify them into subtypes and recombinant forms, which were confirmed by phylogenetic analysis through maximum likelihood (ML) using RAxML. For the main HIV-1 non-B variants, publicly available, genetically similar sequences were sought using HIV-BLAST. The presence of HIV-1 lineages circulating in our study population was established using ML and Bayesian inference (BEAST v1.7.5) and transmission networks were identified. We detected 165 (23.4%) patients infected with HIV-1 non-B variants: 104 (63%) with recombinant viruses in pol: CRF02_AG (71, 43%), CRF14_BG (8, 4.8%), CRF06_cpx (5, 3%) and nine other recombinant forms (11, 6.7%) and unique recombinants (9, 5.5%). The rest (61, 37%) were infected with non-recombinant subtypes: A1 (30, 18.2%), C (7, [4.2%]), D (3, [1.8%]), F1 (9, 5.5%) and G (12, 7.3%). Most patients infected with HIV-1 non-B variants were men (63%, p < 0.001) aged over 35 (73.5%, p < 0.001), heterosexuals (92.2%, p < 0.001), from Africa (59.5%, p < 0.001) and living in the El Ejido area (62.4%, p<0.001). We found lineages of epidemiological relevance (mainly within Subtype A1), imported primarily through female sex workers from East Europe. We detected 11 transmission clusters of HIV-1 non-B Subtypes, which included patients born in Spain in half of them. We present the phylogenetic profiles of the HIV-1 non-B variants detected in southern Spain, and explore their putative geographical origins. Our data reveals a high HIV-1 genetic diversity likely due to the import of viral lineages that circulate in other countries. The highly immigrated El Ejido area acts as a gateway through which different subtypes are introduced into other regions, hence the importance of setting up epidemiological control measures to prevent future outbreaks.
Collapse
Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, the United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| |
Collapse
|
37
|
Le Vu S, Ratmann O, Delpech V, Brown AE, Gill ON, Tostevin A, Fraser C, Volz EM. Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases. Epidemics 2017; 23:1-10. [PMID: 29089285 DOI: 10.1016/j.epidem.2017.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 11/26/2022] Open
Abstract
Phylogenetic clustering of HIV sequences from a random sample of patients can reveal epidemiological transmission patterns, but interpretation is hampered by limited theoretical support and statistical properties of clustering analysis remain poorly understood. Alternatively, source attribution methods allow fitting of HIV transmission models and thereby quantify aspects of disease transmission. A simulation study was conducted to assess error rates of clustering methods for detecting transmission risk factors. We modeled HIV epidemics among men having sex with men and generated phylogenies comparable to those that can be obtained from HIV surveillance data in the UK. Clustering and source attribution approaches were applied to evaluate their ability to identify patient attributes as transmission risk factors. We find that commonly used methods show a misleading association between cluster size or odds of clustering and covariates that are correlated with time since infection, regardless of their influence on transmission. Clustering methods usually have higher error rates and lower sensitivity than source attribution method for identifying transmission risk factors. But neither methods provide robust estimates of transmission risk ratios. Source attribution method can alleviate drawbacks from phylogenetic clustering but formal population genetic modeling may be required to estimate quantitative transmission risk factors.
Collapse
Affiliation(s)
- Stéphane Le Vu
- Department of Infectious Disease Epidemiology and the NIHR HPRU on Modeling Methodology, Imperial College London, United Kingdom.
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, United Kingdom
| | - Valerie Delpech
- HIV and STI Department of Public Health England's Centre for Infectious Disease Surveillance and Control, London, United Kingdom
| | - Alison E Brown
- HIV and STI Department of Public Health England's Centre for Infectious Disease Surveillance and Control, London, United Kingdom
| | - O Noel Gill
- HIV and STI Department of Public Health England's Centre for Infectious Disease Surveillance and Control, London, United Kingdom
| | - Anna Tostevin
- Department of Infection and Population Health and the NIHR HPRU in Blood Borne and Sexually Transmitted Infections, University College London, United Kingdom
| | - Christophe Fraser
- Li Ka Shing Centre for Health Information and Discovery, Oxford University, United Kingdom
| | - Erik M Volz
- Department of Infectious Disease Epidemiology and the NIHR HPRU on Modeling Methodology, Imperial College London, United Kingdom
| |
Collapse
|
38
|
Kiwuwa-Muyingo S, Nazziwa J, Ssemwanga D, Ilmonen P, Njai H, Ndembi N, Parry C, Kitandwe PK, Gershim A, Mpendo J, Neilsen L, Seeley J, Seppälä H, Lyagoba F, Kamali A, Kaleebu P. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS One 2017; 12:e0185818. [PMID: 29023474 PMCID: PMC5638258 DOI: 10.1371/journal.pone.0185818] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. METHODS Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. RESULTS Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]). CONCLUSIONS A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.
Collapse
Affiliation(s)
- Sylvia Kiwuwa-Muyingo
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Jamirah Nazziwa
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Pauliina Ilmonen
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Harr Njai
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Nicaise Ndembi
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Chris Parry
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Asiki Gershim
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Leslie Neilsen
- International AIDS Vaccine Initiative, New York, United States of America
| | - Janet Seeley
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Heikki Seppälä
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Fred Lyagoba
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| |
Collapse
|
39
|
Patiño-Galindo JÁ, Torres-Puente M, Bracho MA, Alastrué I, Juan A, Navarro D, Galindo MJ, Ocete D, Ortega E, Gimeno C, Belda J, Domínguez V, Moreno R, González-Candelas F. The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters. Sci Rep 2017; 7:11584. [PMID: 28912478 PMCID: PMC5599654 DOI: 10.1038/s41598-017-10286-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups. The HIV epidemic in the CV is dominated by subtype B infections among local men who have sex with men (MSM). 270 transmission clusters were identified (>57% of the dataset), 12 of which included ≥10 patients; 11 of subtype B (9 affecting MSMs) and one (n = 21) of CRF14, affecting predominately intravenous drug users (IDUs). Dated phylogenies revealed these large clusters to have originated from the mid-80s to the early 00 s. Subtype B is more likely to form transmission clusters than non-B variants and MSMs to cluster than other risk groups. Multinomial analyses revealed an association between non-B variants, which are not established in the local population yet, and different foreign groups.
Collapse
Affiliation(s)
- Juan Ángel Patiño-Galindo
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain.,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Manoli Torres-Puente
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain
| | - María Alma Bracho
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain.,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | | | - Amparo Juan
- Unidad Prevención del SIDA y otras ITS, Valencia, 46017, Spain
| | - David Navarro
- Hospital Clínico Universitario, Valencia, 46010, Spain.,Dpto. Microbiología, Universidad de Valencia, 46080, Valencia, Spain
| | | | - Dolores Ocete
- Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Enrique Ortega
- Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Concepción Gimeno
- Dpto. Microbiología, Universidad de Valencia, 46080, Valencia, Spain.,Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Josefina Belda
- Unidad Prevención del SIDA y otras ITS, Alicante, 03010, Spain
| | | | | | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain. .,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain.
| |
Collapse
|
40
|
Caro-Pérez N, Martínez-Rebollar M, Gregori J, Quer J, González P, Gambato M, García-González N, González-Candelas F, Costa J, Esteban JI, Mallolas J, Forns X, Laguno M, Pérez-Del-Pulgar S. Phylogenetic analysis of an epidemic outbreak of acute hepatitis C in HIV-infected patients by ultra-deep pyrosequencing. J Clin Virol 2017; 92:42-47. [PMID: 28521213 DOI: 10.1016/j.jcv.2017.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/29/2017] [Accepted: 05/06/2017] [Indexed: 01/18/2023]
Abstract
BACKGROUND The incidence of acute hepatitis C (AHC) among HIV-infected men who have sex with men (MSM) has increased significantly in the last 10 years. Several studies point to a social and sexual network of HIV-positive MSM that extends internationally. OBJECTIVES The aim of our study was to investigate the dynamics of HCV transmission in an outbreak of AHC in HIV-infected MSM in Barcelona by ultra-deep pyrosequencing. STUDY DESIGN Between 2008 and 2013, 113 cases of AHC in HIV-infected MSM were diagnosed in the Infectious Diseases Unit, Hospital Clínic, Barcelona. Massive sequencing was performed using the Roche 454 GS Junior platform. To define possible transmission networks, maximum likelihood phylogenetic trees were constructed, and levels of genetic diversity within and among patients were compared. RESULTS Among the 70 cases analyzed, we have identified 16 potential clusters of transmission: 8 for genotype 1a (23 cases involved), 1 for genotype 1b (3 cases) and 7 for genotype 4d (27 cases). Although the initial phylogenetic reconstruction suggested a local transmission cluster of HCV gt4d, our approach based on low genetic differentiation did not corroborate it. Indeed, gt4d strains formed 4 independent groups related to patients from other countries. CONCLUSIONS Frequent clustering of HIV-positive MSM shows that HCV infection has spread through a local network in Barcelona. This outbreak is related to a large international HCV transmission network among MSM. Public health efforts are needed to reduce HCV transmission among this high-risk group.
Collapse
Affiliation(s)
- Noelia Caro-Pérez
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | | | - Josep Gregori
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Patricia González
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Martina Gambato
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Neris García-González
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Josep Costa
- Microbiology Department, Centre Diagnòstic Biomèdic, Hospital Clínic, CIBERehd, Barcelona, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Josep Mallolas
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Montse Laguno
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Sofía Pérez-Del-Pulgar
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| |
Collapse
|
41
|
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.
Collapse
|
42
|
van de Laar TJ, Bezemer D, van Laethem K, Vandewalle G, de Smet A, van Wijngaerden E, Claas EC, van Sighem AI, Vandamme AM, Compernolle V, Zaaijer HL. Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus-infected donors in the Netherlands and Flanders. Transfusion 2017; 57:1235-1247. [PMID: 28375576 DOI: 10.1111/trf.14097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/14/2016] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Separate transmission networks for human immunodeficiency virus (HIV) coexist. Molecular typing of viral genomes can provide insight in HIV transmission routes in donors for whom risk behavior-based donor selection failed. STUDY DESIGN AND METHODS This study includes all HIV-infected Dutch and Flemish donors in the period 2005 to 2014 (n = 55). Part of the HIV polymerase (pol) gene was amplified, sequenced, and compared with more than 10,000 HIV strains obtained from HIV-infected Dutch and Flemish patients. The most likely transmission route was determined based on HIV phylogeny and the donor's self-reported risk behavior during the exit interview. RESULTS HIV-infected donors were predominantly male (69%), were repeat donors (73%), were born in the Netherlands or Belgium (95%), and harbored HIV Subtype B (68%). Seventy-five percent of HIV-infected male donors were part of robust phylogenetic clusters linked to male-to-male sex, while only 24% of HIV-infected male donors reported male-to-male sex during posttest counseling. Sex between men and women accounted for 13% of HIV infections in male donors and 93% of HIV infections in female donors based on phylogenetic analysis. Only 40% of HIV-infected female donors had HIV Subtype B; 65% of female donors reported a foreign partner and indeed HIV sequences interspersed with sequences from HIV-endemic areas abroad, in particular sub-Saharan Africa. CONCLUSION HIV typing helps to understand HIV transmission routes in donor populations. We found substantial underreporting of male-to-male sex among HIV-infected male donors. Donor education on HIV risk factors and the danger of window-period donations and a donor environment that encourages frank disclosure of sexual behavior will contribute to a decrease of HIV-infected donors.
Collapse
Affiliation(s)
- Thijs J van de Laar
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands
| | | | - Kristel van Laethem
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-Leuven University, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | | | - Annie de Smet
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Eric van Wijngaerden
- AIDS Reference Center, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology, KU Leuven-Leuven University, Leuven, Belgium
| | - Eric C Claas
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Molecular Biology, MC Slotervaart, Amsterdam, the Netherlands
| | | | - Anne-Mieke Vandamme
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-Leuven University, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Veerle Compernolle
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium.,Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hans L Zaaijer
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands.,Department of Medical Microbiology (CINIMA), Academic Medical Center/University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
43
|
Sallam M, Esbjörnsson J, Baldvinsdóttir G, Indriðason H, Björnsdóttir TB, Widell A, Gottfreðsson M, Löve A, Medstrand P. Molecular epidemiology of HIV-1 in Iceland: Early introductions, transmission dynamics and recent outbreaks among injection drug users. INFECTION GENETICS AND EVOLUTION 2017; 49:157-163. [PMID: 28082188 DOI: 10.1016/j.meegid.2017.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/19/2016] [Accepted: 01/02/2017] [Indexed: 10/20/2022]
|
44
|
Abstract
OBJECTIVE HIV-1 epidemics among MSM remain unchecked despite advances in treatment and prevention paradigms. This study combined viral phylogenetic and behavioural risk data to better understand underlying factors governing the temporal growth of the HIV epidemic among MSM in Quebec (2002-2015). METHODS Phylogenetic analysis of pol sequences was used to deduce HIV-1 transmission dynamics (cluster size, size distribution and growth rate) in first genotypes of treatment-naïve MSM (2002-2015, n = 3901). Low sequence diversity of first genotypes (0-0.44% mixed base calls) was used as an indication of early-stage infection. Behavioural risk data were obtained from the Montreal rapid testing site and primary HIV-1-infection cohorts. RESULTS Phylogenetic analyses uncovered high proportion of clustering of new MSM infections. Overall, 27, 45, 48, 53 and 57% of first genotypes within one (singleton, n = 1359), 2-4 (n = 692), 5-9 (n = 367), 10-19 (n = 405) and 20+ (n = 1277) cluster size groups were early infections (<0.44% diversity). Thirty viruses within large 20+ clusters disproportionately fuelled the epidemic, representing 13, 25 and 42% of infections, first genotyped in 2004-2007 (n = 1314), 2008-2011 (n = 1356) and 2012-2015 (n = 1033), respectively. Of note, 35, 21 and 14% of MSM belonging to 20+, 2-19 and one (singleton) cluster groups were under 30 years of age, respectively. Half of persons seen at the rapid testing site (2009-2011, n = 1781) were untested in the prior year. Poor testing propensity was associated with fewer reported partnerships. CONCLUSION Addressing the heterogeneity in transmission dynamics among HIV-1-infected MSM populations may help guide testing, treatment and prevention strategies.
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Patiño-Galindo JÁ, Torres-Puente M, Bracho MA, Alastrué I, Juan A, Navarro D, Galindo MJ, Gimeno C, Ortega E, González-Candelas F. Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain. PLoS One 2017; 12:e0171062. [PMID: 28152089 PMCID: PMC5289541 DOI: 10.1371/journal.pone.0171062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.
Collapse
Affiliation(s)
- Juan Ángel Patiño-Galindo
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
| | - Manoli Torres-Puente
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
| | - María Alma Bracho
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
| | | | - Amparo Juan
- Unidad Prevención del SIDA y otras ITS, Valencia, Spain
| | - David Navarro
- Hospital Clínico Universitario-Universidad de Valencia, Valencia, Spain
| | | | | | | | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
- * E-mail:
| |
Collapse
|
47
|
Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain. PLoS One 2016; 11:e0168099. [PMID: 28002469 PMCID: PMC5176287 DOI: 10.1371/journal.pone.0168099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/23/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain. PATIENTS & METHODS We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6. RESULTS Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations. CONCLUSIONS We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.
Collapse
Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | - Ana B. Lozano
- Servicio de Infecciosas, Hospital de Poniente, Almería, Spain
| | - Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| |
Collapse
|
48
|
Grabowski MK, Lessler J. Phylogenetic insights into age-disparate partnerships and HIV. Lancet HIV 2016; 4:e8-e9. [PMID: 27914876 DOI: 10.1016/s2352-3018(16)30184-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Mary Kathryn Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore MD 21205, USA.
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore MD 21205, USA
| |
Collapse
|
49
|
Abstract
For infectious diseases, a genetic cluster is a group of closely related infections that is usually interpreted as representing a recent outbreak of transmission. Genetic clustering methods are becoming increasingly popular for molecular epidemiology, especially in the context of HIV where there is now considerable interest in applying these methods to prioritize groups for public health resources such as pre-exposure prophylaxis. To date, genetic clustering has generally been performed with ad hoc algorithms, only some of which have since been encoded and distributed as free software. These algorithms have seldom been validated on simulated data where clusters are known, and their interpretation and similarities are not transparent to users outside of the field. Here, I provide a brief overview on the development and inter-relationships of genetic clustering methods, and an evaluation of six methods on data simulated under an epidemic model in a risk-structured population. The simulation analysis demonstrates that the majority of clustering methods are systematically biased to detect variation in sampling rates among subpopulations, not variation in transmission rates. I discuss these results in the context of previous work and the implications for public health applications of genetic clustering.
Collapse
Affiliation(s)
- Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| |
Collapse
|
50
|
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.
Collapse
|