1
|
Polotan FGM, Salazar CRP, Morito HLE, Abulencia MFB, Pantoni RAR, Mercado ES, Hué S, Ditangco RA. Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018. Virus Evol 2023; 9:vead073. [PMID: 38131006 PMCID: PMC10735293 DOI: 10.1093/ve/vead073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The Philippines has had a rapidly growing human immunodeficiency virus (HIV) epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology. Partial polymerase sequences (n = 1144) collected between 2008 and 2018 from three island groups were collated from the Research Institute for Tropical Medicine drug resistance genotyping database. Estimation of the time to the most recent common ancestor (tMRCA), effective reproductive number (Re), effective viral population size (Ne), relative migration rates, and geographic spread of CRF01_AE was performed with BEAST. Re and Ne were compared between CRF01_AE and B. Most CRF01_AE sequences formed a single clade with a tMRCA of June 1996 [95 per cent highest posterior density (HPD): December 1991, October 1999]. An increasing CRF01_AE Ne was observed from the tMRCA to 2013. The CRF01_AE Re reached peaks of 2.46 [95 per cent HPD: 1.76, 3.27] in 2007 and 2.52 [95 per cent HPD: 1.83, 3.34] in 2015. A decrease of CRF01_AE Re occurred in the intervening years of 2007 to 2011, reaching as low as 1.43 [95 per cent HPD: 1.06, 1.90] in 2011, followed by a rebound. The CRF01_AE epidemic most likely started in Luzon and then spread to the other island groups of the country. Both CRF01_AE and Subtype B exhibited similar patterns of Re fluctuation over time. These results characterize the subtype-specific phylodynamic history of the largest CRF01_AE cluster in the Philippines, which contextualizes and may inform past, present, and future public health measures toward controlling the HIV epidemic in the Philippines.
Collapse
Affiliation(s)
- Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Carl Raymund P Salazar
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6700 EH, The Netherlands
| | - Hannah Leah E Morito
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Miguel Francisco B Abulencia
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Roslind Anne R Pantoni
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Edelwisa S Mercado
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Stéphane Hué
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
| | - Rossana A Ditangco
- AIDS Research Group, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| |
Collapse
|
2
|
Nascimento FF, Ragonnet-Cronin M, Golubchik T, Danaviah S, Derache A, Fraser C, Volz E. Evaluating whole HIV-1 genome sequence for estimation of incidence and migration in a rural South African community. Wellcome Open Res 2022; 7:174. [PMID: 37333843 PMCID: PMC10276198 DOI: 10.12688/wellcomeopenres.17891.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 09/21/2024] Open
Abstract
Background: South Africa has the largest number of people living with HIV (PLWHIV) in the world, with HIV prevalence and transmission patterns varying greatly between provinces. Transmission between regions is still poorly understood, but phylodynamics of HIV-1 evolution can reveal how many infections are attributable to contacts outside a given community. We analysed whole genome HIV-1 genetic sequences to estimate incidence and the proportion of transmissions between communities in Hlabisa, a rural South African community. Methods: We separately analysed HIV-1 for gag, pol, and env genes sampled from 2,503 PLWHIV. We estimated time-scaled phylogenies by maximum likelihood under a molecular clock model. Phylodynamic models were fitted to time-scaled trees to estimate transmission rates, effective number of infections, incidence through time, and the proportion of infections imported to Hlabisa. We also partitioned time-scaled phylogenies with significantly different distributions of coalescent times. Results: Phylodynamic analyses showed similar trends in epidemic growth rates between 1980 and 1990. Model-based estimates of incidence and effective number of infections were consistent across genes. Parameter estimates with gag were generally smaller than those estimated with pol and env. When estimating the proportions of new infections in Hlabisa from immigration or transmission from external sources, our posterior median estimates were 85% (95% credible interval (CI) = 78%-92%) for gag, 62% (CI = 40%-78%) for pol, and 77% (CI = 58%-90%) for env in 2015. Analysis of phylogenetic partitions by gene showed that most close global reference sequences clustered within a single partition. This suggests local evolving epidemics or potential unmeasured heterogeneity in the population. Conclusions: We estimated consistent epidemic dynamic trends for gag, pol and env genes using phylodynamic models. There was a high probability that new infections were not attributable to endogenous transmission within Hlabisa, suggesting high inter-connectedness between communities in rural South Africa.
Collapse
Affiliation(s)
| | | | | | - Siva Danaviah
- Africa Health Research Institute, Durban, South Africa
| | - Anne Derache
- Africa Health Research Institute, Durban, South Africa
| | | | - Erik Volz
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| |
Collapse
|
3
|
Spencer DC. SAHCS 2021 Conference Summary. South Afr J HIV Med 2022; 23:1371. [PMID: 35706547 PMCID: PMC9082288 DOI: 10.4102/sajhivmed.v23i1.1371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- David C Spencer
- Division of Infectious Diseases, Faculty of Medicine, University of the Witwatersrand, Johannesburg, South Africa
- Southern African HIV Clinicians Society, Johannesburg, South Africa
| |
Collapse
|
4
|
Bell GJ, Ncayiyana J, Sholomon A, Goel V, Zuma K, Emch M. Race, place, and HIV: The legacies of apartheid and racist policy in South Africa. Soc Sci Med 2022; 296:114755. [PMID: 35123373 PMCID: PMC8887645 DOI: 10.1016/j.socscimed.2022.114755] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/18/2021] [Accepted: 01/25/2022] [Indexed: 12/01/2022]
Abstract
Black South Africans accounted for 6.2 out of 6.4 million people living with HIV in South Africa in 2012, highlighting extreme racial disparities in HIV infection. These racial disparities are the result of structural and historical factors, specifically, the racist policies which were facilitated by segregation before, during, and after Apartheid. First, we describe the theoretical context of how racist policies and segregation are linked to HIV prevalence. Next, using data from a 2012 national survey of South Africans (SABSSM IV) and Statistics South Africa (StatsSA), we describe the race-specific geospatial distribution of HIV in South Africa, provide empirical evidence for the impact of Apartheid on important risk factors for HIV infection, and describe the relationship between these risk factors and HIV within racial groups. Using multilevel logistic regression, we find that segregation increases the odds of HIV infection among Black South Africans, even after adjusting for many covariates which are sometimes blamed, in place of structural factors, for a higher HIV prevalence in Black South Africans. We found that the estimated odds of infection in the most segregated municipality was 1.95 (95% CI: 1.15, 3.32) times the odds of infection in the least segregated municipality for Black South Africans. In addition to segregation, we also find other covariates to be differentially associated with HIV infection depending on race, such as gender, age, and sexual behavior. We also find that the HIV infection odds ratio comparing Black and Coloured (i.e., multiple ethnic groups with mixed ancestries from Africa, Asia, and Europe) South Africans varies over space. These results continue to build evidence for the influence of structural and historical factors on the modern geospatial and demographic distribution of HIV.
Collapse
Affiliation(s)
- Griffin J. Bell
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jabulani Ncayiyana
- Division of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Ari Sholomon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Varun Goel
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Khangelani Zuma
- Human Sciences Research Council, Research Methodology Centre, Pretoria, South Africa,School of Public Health, University of Witwatersrand, Johannesburg, South Africa
| | - Michael Emch
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
5
|
An M, Zheng C, Li H, Chen L, Yang Z, Gan Y, Han X, Zhao J, Shang H. Independent epidemic patterns of HIV-1 CRF01_AE lineages driven by mobile population in Shenzhen, an immigrant city of China. Virus Evol 2021; 7:veab094. [PMID: 35299786 PMCID: PMC8923236 DOI: 10.1093/ve/veab094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Abstract
Shenzhen, a city with >12 million migrant population, may play a key role in the spread of human immunodeficiency virus (HIV)-1 in China. The transmission dynamics of CRF01_AE, a predominant subtype in Shenzhen, is a good model to characterize the impact of human mobility on HIV-1 epidemic locally and nationally. We used phylodynamic and phylogeographic methods to estimate the viral transmission dynamics and migration trajectory of variable lineages based on 1,423 CRF01_AE sequences in Shenzhen sampled between 2006 and 2015. Eleven lineages of CRF01_AE were detected in Shenzhen. Of those, four main lineages originated during the 1990s. Their basic viral reproduction number (R0) ranged 1.96–3.92. The effective viral reproduction number (Re) of two lineages prevalent among heterosexuals/people who inject drugs had reduced <1 at the end of sampling, and the main sources were the intra-provincial immigrants (72 per cent) for one and local residents of Shenzhen (91 per cent) for another. Within two lineages among men who have sex with men (MSM), Re had been above or close to 1 at the end of sampling, and the immigrants from Jiangxi/Shaanxi and Hubei as sources accounted for 93 per cent and 68 per cent of all viral migration events, respectively. Moreover, no obvious recipients were found throughout the viral migration history for any lineage. Our findings demonstrate that HIV epidemic is declining in Shenzhen, which coincided with the initiation of the interventions during the 2000s. However, the obvious differences of the epidemic patterns between lineages emphasize the importance of further targeting interventions and continued molecular tracing, focusing on high-risk transmission sources among MSM.
Collapse
Affiliation(s)
- Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
- Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Hao Li
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Zhengrong Yang
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Yongxia Gan
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
- Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
- Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
| |
Collapse
|
6
|
Marini S, Mavian C, Riva A, Prosperi M, Salemi M, Rife Magalis B. Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinformatics 2021; 38:856-860. [PMID: 34672334 PMCID: PMC8756195 DOI: 10.1093/bioinformatics/btab725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/10/2021] [Accepted: 10/18/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY TARDiS is a novel phylogenetic tool for optimal genetic subsampling. It optimizes both genetic diversity and temporal distribution through a genetic algorithm. AVAILABILITY AND IMPLEMENTATION TARDiS, along with example datasets and a user manual, is available at https://github.com/smarini/tardis-phylogenetics.
Collapse
Affiliation(s)
- Simone Marini
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA,Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA,Department of Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA
| | | | | |
Collapse
|
7
|
Nduva GM, Nazziwa J, Hassan AS, Sanders EJ, Esbjörnsson J. The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review. Viruses 2021; 13:1174. [PMID: 34205246 PMCID: PMC8235305 DOI: 10.3390/v13061174] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.
Collapse
Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Eduard J. Sanders
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| |
Collapse
|
8
|
Molecular network-based intervention brings us closer to ending the HIV pandemic. Front Med 2020; 14:136-148. [PMID: 32206964 DOI: 10.1007/s11684-020-0756-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/13/2020] [Indexed: 01/08/2023]
Abstract
Precise identification of HIV transmission among populations is a key step in public health responses. However, the HIV transmission network is usually difficult to determine. HIV molecular networks can be determined by phylogenetic approach, genetic distance-based approach, and a combination of both approaches. These approaches are increasingly used to identify transmission networks among populations, reconstruct the history of HIV spread, monitor the dynamics of HIV transmission, guide targeted intervention on key subpopulations, and assess the effects of interventions. Simulation and retrospective studies have demonstrated that these molecular network-based interventions are more cost-effective than random or traditional interventions. However, we still need to address several challenges to improve the practice of molecular network-guided targeting interventions to finally end the HIV epidemic. The data remain limited or difficult to obtain, and more automatic real-time tools are required. In addition, molecular and social networks must be combined, and technical parameters and ethnic issues warrant further studies.
Collapse
|
9
|
Theys K, Lemey P, Vandamme AM, Baele G. Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases. Front Public Health 2019; 7:208. [PMID: 31428595 PMCID: PMC6688121 DOI: 10.3389/fpubh.2019.00208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 07/12/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution assist in drawing conclusions from phylogenetic estimates and may even have potential to better inform public health and treatment decisions, but the design (and choice of what analyses are shown) is hindered by the complexity of information embedded within current phylogenetic models and the integration of available meta-data. In this review, we discuss visualization challenges for the interpretation and exploration of reconstructed histories of viral epidemics that arose from increasing volumes of sequence data and the wealth of additional data layers that can be integrated. We focus on solutions that address joint temporal and spatial visualization but also consider what the future may bring in terms of visualization and how this may become of value for the coming era of real-time digital pathogen surveillance, where actionable results and adequate intervention strategies need to be obtained within days.
Collapse
Affiliation(s)
- Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| |
Collapse
|