1
|
Mulenga LB, Hines JZ, Stafford KA, Dzekedzeke K, Sivile S, Lindsay B, Chola M, Ussery F, Patel HK, Abimiku A, Birhanu S, Minchella PA, Stevens T, Hanunka B, Chisenga T, Shibemba A, Fwoloshi S, Siame M, Mutukwa J, Chirwa L, Siwingwa M, Mulundu G, Agbakwuru C, Mapondera P, Detorio M, Agolory SG, Monze M, Bronson M, Charurat ME. Comparison of HIV prevalence, incidence, and viral load suppression in Zambia population-based HIV impact assessments from 2016 and 2021. AIDS 2024; 38:895-905. [PMID: 38227572 DOI: 10.1097/qad.0000000000003834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
BACKGROUND The Zambian government has implemented a public health response to control the HIV epidemic in the country. Zambia conducted a population-based HIV impact assessment (ZAMPHIA) survey in 2021 to assess the status of the HIV epidemic to guide its public health programs. METHODS ZAMPHIA 2021 was a cross-sectional two-stage cluster sample household survey among persons aged ≥15 years conducted in Zambia across all 10 provinces. Consenting participants were administered a standardized questionnaire and whole blood was tested for HIV according to national guidelines. HIV-1 viral load (VL), recent HIV infection, and antiretroviral medications were tested for in HIV-seropositive samples. Viral load suppression (VLS) was defined as <1000 copies/ml. ZAMPHIA 2021 results were compared to ZAMPHIA 2016 for persons aged 15-59 years (i.e., the overlapping age ranges). All estimates were weighted to account for nonresponse and survey design. RESULTS During ZAMPHIA 2021, of 25 483 eligible persons aged ≥15 years, 18 804 (73.8%) were interviewed and tested for HIV. HIV prevalence was 11.0% and VLS prevalence was 86.2% overall, but was <80% among people living with HIV aged 15-24 years and in certain provinces. Among persons aged 15-59 years, from 2016 to 2021, HIV incidence declined from 0.6% to 0.3% ( P -value: 0.07) and VLS prevalence increased from 59.2% to 85.7% ( P -value: <0.01). DISCUSSION Zambia has made substantial progress toward controlling the HIV epidemic from 2016 to 2021. Continued implementation of a test-and-treat strategy, with attention to groups with lower VLS in the ZAMPHIA 2021, could support reductions in HIV incidence and improve overall VLS in Zambia.
Collapse
Affiliation(s)
- Lloyd B Mulenga
- Ministry of Health
- University Teaching Hospital
- University of Zambia, School of Medicine
| | - Jonas Z Hines
- U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Kristen A Stafford
- Center for International Health, Education, and Biosecurity, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kumbutso Dzekedzeke
- Center for International Health, Education, and Biosecurity, Maryland Global Initiatives Corporation-an affiliate of the University of Maryland, Baltimore, Lusaka, Zambia
| | | | - Brianna Lindsay
- Center for International Health, Education, and Biosecurity, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mumbi Chola
- Center for International Health, Education, and Biosecurity, Maryland Global Initiatives Corporation-an affiliate of the University of Maryland, Baltimore, Lusaka, Zambia
| | - Faith Ussery
- U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Hetal K Patel
- U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Alash'le Abimiku
- Center for International Health, Education, and Biosecurity, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sehin Birhanu
- U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Thomas Stevens
- U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Brave Hanunka
- U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | | | | | | | | | | | | | - Mpanji Siwingwa
- University Teaching Hospital
- University of Zambia, School of Medicine
| | - Gina Mulundu
- University Teaching Hospital
- University of Zambia, School of Medicine
| | - Chinedu Agbakwuru
- Center for International Health, Education, and Biosecurity, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Prichard Mapondera
- Center for International Health, Education, and Biosecurity, Maryland Global Initiatives Corporation-an affiliate of the University of Maryland, Baltimore, Lusaka, Zambia
| | - Mervi Detorio
- U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Simon G Agolory
- U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Mwaka Monze
- Ministry of Health
- University Teaching Hospital
| | - Megan Bronson
- U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Man E Charurat
- Center for International Health, Education, and Biosecurity, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
2
|
Fiorentino M, Yanwou N, Gravier-Dumonceau Mazelier R, Eubanks A, Roux P, Laurent C, Spire B. Sexual behaviours and risk with women in MSM in sub-Saharan Africa. AIDS 2024; 38:273-287. [PMID: 38300157 PMCID: PMC10842665 DOI: 10.1097/qad.0000000000003787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/09/2023] [Indexed: 02/02/2024]
Abstract
In sub-Saharan Africa (SSA), MSM - a high HIV prevalence group - experience strong social stigma and pressure to have female partners. Accordingly, they could constitute a bridging group for HIV transmission to cisgender women. We developed a multilevel summary of MSM sexual behaviors and risk with women in various SSA regions. Following PRISMA guidelines, we conducted a mixed-method systematic review of data of sex with women in MSM in SSA. We performed meta-analyses on quantitative data (i.e. percent of recent sex and condomless sex with women) for each SSA region (when proportions reported in ≥4 studies). Pooled proportions were calculated using random-effects models. Qualitative data were analyzed using the three-step thematic synthesis methodology. The pooled proportion of MSM who had sex with women was 58% (33-83%) in East Africa (in the previous 3 months), and 27% (13-48%) in Southern Africa and 50% (95% CI 39-62%) in West Africa (in the previous 6 months); 23% (16-32%) of MSM in West Africa had condomless sex with a woman (during the most recent encounter). Approximately one quarter of MSM had recent multiple female partners. MSM reported having sex with women because of heteronormative pressure, erotic/romantic attraction, or financial needs leading to transactional sex. MSM may act as a bridging population to women in SSA, as they commonly practice sex with women and risky sexual behaviors with them. HIV programmes and community-based support for MSM should be adapted to this population to reduce this risk.
Collapse
Affiliation(s)
- Marion Fiorentino
- Aix Marseille Univ, IRD, Inserm, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM
| | - Nathan Yanwou
- Aix Marseille Univ, IRD, Inserm, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM
- ORS PACA, Observatoire régional de la santé Provence-Alpes-Côte d’Azur, Marseille
| | | | - August Eubanks
- Aix Marseille Univ, IRD, Inserm, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM
| | - Perrine Roux
- Aix Marseille Univ, IRD, Inserm, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM
| | | | - Bruno Spire
- Aix Marseille Univ, IRD, Inserm, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM
| |
Collapse
|
3
|
Nduva GM, Otieno F, Kimani J, Sein Y, Arimide DA, Mckinnon LR, Cholette F, Lawrence MK, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Medstrand P, Sanders EJ, Esbjörnsson J, Hassan AS. Temporal trends and transmission dynamics of pre-treatment HIV-1 drug resistance within and between risk groups in Kenya, 1986-2020. J Antimicrob Chemother 2024; 79:287-296. [PMID: 38091580 PMCID: PMC10832587 DOI: 10.1093/jac/dkad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Evidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) among risk groups is limited in Africa. We assessed the prevalence, trends and transmission dynamics of pre-treatment HIVDR within and between MSM, people who inject drugs (PWID), female sex workers (FSWs), heterosexuals (HETs) and perinatally infected children in Kenya. METHODS HIV-1 partial pol sequences from antiretroviral-naive individuals collected from multiple sources between 1986 and 2020 were used. Pre-treatment reverse transcriptase inhibitor (RTI), PI and integrase inhibitor (INSTI) mutations were assessed using the Stanford HIVDR database. Phylogenetic methods were used to determine and date transmission clusters. RESULTS Of 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSWs (15.1%) and HETs (13.9%). Overall, pre-treatment HIVDR increased consistently, from 6.9% (before 2005) to 24.2% (2016-20). Among HETs, pre-treatment HIVDR increased from 6.6% (before 2005) to 20.2% (2011-15), but dropped to 6.5% (2016-20). Additionally, 32 clusters with shared pre-treatment HIVDR mutations were identified. The majority of clusters had R0 ≥ 1.0, indicating ongoing transmissions. The largest was a K103N cluster involving 16 MSM sequences sampled between 2010 and 2017, with an estimated time to the most recent common ancestor (tMRCA) of 2005 [95% higher posterior density (HPD), 2000-08], indicating propagation over 12 years. CONCLUSIONS Compared to HETs, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2017 may have abrogated the increase in pre-treatment RTI mutations, albeit in the HET population only. Taken together, our findings underscore the need for targeted efforts towards equitable access to ART for children and key populations in Kenya.
Collapse
Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Yiakon Sein
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | - Dawit A Arimide
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Lyle R Mckinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Morris K Lawrence
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Moses Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Gaudensia Mutua
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Susan M Graham
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Department of Medicine, Global Health and Epidemiology, University of Washington, Seattle, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Matt A Price
- IAVI, NewYork, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology & Biostatistics, University of Illinois at Chicago, Chicago, IL, USA
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Eduard J Sanders
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| |
Collapse
|
4
|
Jamrozik E, Munung NS, Abeler-Dorner L, Parker M. Public health use of HIV phylogenetic data in sub-Saharan Africa: ethical issues. BMJ Glob Health 2023; 8:e011884. [PMID: 37407228 DOI: 10.1136/bmjgh-2023-011884] [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: 02/15/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
Phylogenetic analyses of HIV are an increasingly accurate method of clarifying population-level patterns of transmission and linking individuals or groups with transmission events. Viral genetic data may be used by public health agencies to guide policy interventions focused on clusters of transmission or segments of the population in which transmission is concentrated. Analyses of HIV phylogenetics in high-income countries have often found that clusters of transmission play a significant role in HIV epidemics. In sub-Saharan Africa, HIV phylogenetic analyses to date suggest that clusters of transmission play a relatively minor role in local epidemics. Such analyses could nevertheless be used to guide priority setting and HIV public health programme design in Africa for sub-populations in which transmission events are more concentrated. Phylogenetic analysis raises ethical issues, in part due to the range of potential benefits and potential harms (ie, risks). Potential benefits include (1) improving knowledge of transmission patterns, (2) informing the design of focused public health interventions for subpopulations in which transmission is concentrated, (3) identifying and responding to clusters of transmission, (4) reducing stigma (in some cases) and (5) informing estimates of the (cost-)effectiveness of HIV treatment programmes. Potential harms include (1) privacy infringements, (2) increasing stigma (in some cases), (3) reducing trust in public health programmes, and (4) increased prosecution of legal cases where HIV transmission, homosexuality or sex work is criminalised. This paper provides analysis of relevant issues with a focus on sub-Saharan Africa in order to inform consultations regarding ethical best practice for HIV phylogenetics.
Collapse
Affiliation(s)
- Euzebiusz Jamrozik
- Ethox and the Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
- Royal Melbourne Hospital Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
- Monash Bioethics Centre, Monash University, Melbourne, Victoria, Australia
| | | | | | - Michael Parker
- Ethox and the Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
| |
Collapse
|
5
|
Cholette F, Lazarus L, Macharia P, Thompson LH, Githaiga S, Mathenge J, Walimbwa J, Kuria I, Okoth S, Wambua S, Albert H, Mwangi P, Adhiambo J, Kasiba R, Juma E, Battacharjee P, Kimani J, Sandstrom P, Meyers AFA, Joy JB, Thomann M, McLaren PJ, Shaw S, Mishra S, Becker ML, McKinnon L, Lorway R. Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol. Glob Public Health 2023; 18:2269435. [PMID: 37851872 DOI: 10.1080/17441692.2023.2269435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Inferring HIV transmission networks from HIV sequences is gaining popularity in the field of HIV molecular epidemiology. However, HIV sequences are often analyzed at distance from those affected by HIV epidemics, namely without the involvement of communities most affected by HIV. These remote analyses often mean that knowledge is generated in absence of lived experiences and socio-economic realities that could inform the ethical application of network-derived information in 'real world' programmes. Procedures to engage communities are noticeably absent from the HIV molecular epidemiology literature. Here we present our team's protocol for engaging community activists living in Nairobi, Kenya in a knowledge exchange process - The CIPHR Project (Community Insights in Phylogenetic HIV Research). Drawing upon a community-based participatory approach, our team will (1) explore the possibilities and limitations of HIV molecular epidemiology for key population programmes, (2) pilot a community-based HIV molecular study, and (3) co-develop policy guidelines on conducting ethically safe HIV molecular epidemiology. Critical dialogue with activist communities will offer insight into the potential uses and abuses of using such information to sharpen HIV prevention programmes. The outcome of this process holds importance to the development of policy frameworks that will guide the next generation of the global response.
Collapse
Affiliation(s)
- François Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Lisa Lazarus
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Pascal Macharia
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - Laura H Thompson
- Sexually Transmitted and Blood-Borne Infections Surveillance Division, Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Canada
| | - Samuel Githaiga
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - John Mathenge
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | | | - Irene Kuria
- Key Population Consortium of Kenya, Nairobi, Kenya
| | - Silvia Okoth
- Bar Hostess Empowerment and Support Programme, Nairobi, Kenya
| | | | - Harrison Albert
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - Peninah Mwangi
- Bar Hostess Empowerment and Support Programme, Nairobi, Kenya
| | - Joyce Adhiambo
- Partners for Health Development in Africa (PHDA), Nairobi, Kenya
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
| | | | - Esther Juma
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
| | | | - Joshua Kimani
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Paul Sandstrom
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Adrienne F A Meyers
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS (BCCfE), St. Paul's Hospital, Vancouver, Canada
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, Canada
| | - Matthew Thomann
- Department of Anthropology, University of Maryland, College Park, MD, USA
| | - Paul J McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Souradet Shaw
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
| | - Marissa L Becker
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Lyle McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Robert Lorway
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| |
Collapse
|
6
|
Fan Q, Zhang J, Luo M, Feng Y, Ge R, Yan Y, Zhong P, Ding X, Xia Y, Guo Z, Pan X, Chai C. Molecular Genetics and Epidemiological Characteristics of HIV-1 Epidemic Strains in Various Sexual Risk Behaviour Groups in Developed Eastern China, 2017-2020. Emerg Microbes Infect 2022; 11:2326-2339. [PMID: 36032035 PMCID: PMC9542350 DOI: 10.1080/22221751.2022.2119167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Qin Fan
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Jiafeng Zhang
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Mingyu Luo
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Yi Feng
- 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, People’s Republic of China
| | - Rui Ge
- Division of AIDS/TB Prevention and Control, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, People’s Republic of China
| | - Yong Yan
- Division of AIDS/TB Prevention and Control, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, People’s Republic of China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200051, People’s Republic of China
| | - Xiaobei Ding
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Yan Xia
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Zhihong Guo
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Xiaohong Pan
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| | - Chengliang Chai
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, People’s Republic of China
| |
Collapse
|
7
|
Nduva GM, Otieno F, Kimani J, McKinnon LR, Cholette F, Sandstrom P, Graham SM, Price MA, Smith AD, Bailey RC, Hassan AS, Esbjörnsson J, Sanders EJ. Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya. Front Microbiol 2022; 13:843330. [PMID: 35356525 PMCID: PMC8959701 DOI: 10.3389/fmicb.2022.843330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006-2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2-20 sequences) were found-half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017-2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
Collapse
Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Lyle R. McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Susan M. Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Matt A. Price
- IAVI, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Adrian D. Smith
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Robert C. Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois Chicago, Chicago, IL, United States
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| |
Collapse
|
8
|
Nduva GM, Otieno F, Kimani J, Wahome E, McKinnon LR, Cholette F, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Baele G, Lemey P, Hassan AS, Sanders EJ, Esbjörnsson J. Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study. Virus Evol 2022; 8:veac016. [PMID: 35356640 PMCID: PMC8962731 DOI: 10.1093/ve/veac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.
Collapse
Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Frederick Otieno
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Elizabeth Wahome
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Lyle R McKinnon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Private Bag X7, Congella 4013, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Canada
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Center for Global Health Research, KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya
| | - Moses Masika
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Gaudensia Mutua
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Omu Anzala
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Susan M Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Office of the Chair, UW Box # 351619, Seattle, DC, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Matt A Price
- IAVI Global Headquarters, 125 Broad Street, 9th Floor, New York, NY 10004, USA
- Department of Epidemiology and Biostatistics, University of California, Mission Hall: Global Health & Clinical Sciences Building, 550 16th Street, 2nd Floor, San Francisco, CA 94158-2549, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, 1603 W Taylor St, Chicago, IL 60612, USA
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| |
Collapse
|
9
|
Phylogenetic Insights on Patterns of HIV-1 Spread and the Design of Epidemic Control Measures. Viruses 2022; 14:v14020332. [PMID: 35215925 PMCID: PMC8877004 DOI: 10.3390/v14020332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
|
10
|
Brenner BG, Ibanescu RI, Osman N, Cuadra-Foy E, Oliveira M, Chaillon A, Stephens D, Hardy I, Routy JP, Thomas R, Baril JG, Leblanc R, Tremblay C, Roger M. The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020). Viruses 2021; 13:1643. [PMID: 34452506 PMCID: PMC8402830 DOI: 10.3390/v13081643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/23/2023] Open
Abstract
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.
Collapse
Affiliation(s)
- Bluma G. Brenner
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Medicine (Surgery, Infectious Disease), McGill University, Montréal, QC H3A 2M7, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Nathan Osman
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Ernesto Cuadra-Foy
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Maureen Oliveira
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego, CA 93903, USA;
| | - David Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, QC H3A 0B9, Canada;
| | - Isabelle Hardy
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Jean-Pierre Routy
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC H3A 3J1, Canada;
| | - Réjean Thomas
- Clinique Médicale l’Actuel, Montréal, QC H2L 4P9, Canada;
| | - Jean-Guy Baril
- Clinique Médicale Urbaine du Quartier Latin, Montréal, QC H2L 4E9, Canada;
| | - Roger Leblanc
- Clinique Médicale OPUS, Montréal, QC H3A 1T1, Canada;
| | - Cecile Tremblay
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Michel Roger
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | | |
Collapse
|