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1. Recommendations on data sharing in HIV drug resistance research.

Author

Avila-Rios, Santiago, Ayitewala, Alisen, Bosch, Ronald, Calvez, Vincent, Ceccherini-Silberstein, Francesca, Charpentier, Charlotte, Descamps, Diane, Eshleman, Susan, Fokam, Joseph, Frenkel, Lisa, Gupta, Ravindra, Ioannidis, John, Kaleebu, Pontiano, Kantor, Rami, Kassaye, Seble, Kosakovsky Pond, Sergei, Kouamou, Vinie, Kouyos, Roger, Kuritzkes, Daniel, Lessells, Richard, Marcelin, Anne-Genevieve, Mbuagbaw, Lawrence, Inzaule, Seth, Siedner, Mark, Minalga, Brian, Ndembi, Nicaise, Neher, Richard, Paredes, Roger, Pillay, Deenan, Raizes, Elliot, Rhee, Soo-Yon, Ruxrungtham, Kiat, Sabeti, Pardis, Schapiro, Jonathan, Sirivichayakul, Sunee, Steegen, Kim, Sugiura, Wataru, van Zyl, Gert, Vandamme, Anne-Mieke, Wensing, Annemarie, Wertheim, Joel, Gunthard, Huldrych, Jordan, Michael, Shafer, Robert, Little, Susan, and Richman, Douglas

Abstract

• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens.  • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens.  • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines.  • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing.  • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions.  • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.

Published
2023

3. Regional variation in weight change after the transition to dolutegravir in Uganda and South Africa

Author

Migisha, Richard, Chen, Geoffrey, Muyindike, Winnie R., Aung, Taing Nandi, Nanfuka, Victoria, Komukama, Nimusiima, Chandiwana, Nomathemba, Shazi, Gugulethu, Tien, Dessie, Moosa, Mahomed-Yunus S., Gupta, Ravindra K., Pillay, Deenan, Marconi, Vincent C., Hedt-Gauthier, Bethany, Venter, Willem D.F., Siedner, Mark J., McCluskey, Suzanne M., and Manne-Goehler, Jennifer

Published
2024
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4. Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study

Author

Agyei, Yaw, Beyers, Nulda, Bock, Peter, Bond, Virginia, Bwalya, Justin, Cori, Anne, Deventer, Anneen, Dunbar, Rory, El-Sadr, Wafaa, Emel, Lynda, Floyd, Sian, Griffith, Sam, Hargreaves, James, Hauck, Katharina, Headen, Tanette, Hoddinott, Graeme, James, Anelet, Jennings, Karen, Kanema, Sarah, Kosloff, Barry, Kruger, James, Kumar, Ramya, Macleod, David, Makola, Nozizwe, Mandla, Nomtha, Miller, Eric, Moore, Ayana, Mwenge, Lawrence, Noble, Heather, Phiri, Mwelwa, Pickles, Michael, Sabapathy, Kalpana, Sakala, Ephraim, Sauter, Rafael, Shanaube, Kwame, Silumesi, Andrew, Sista, Nirupama, Skalland, Tim, Smith, Peter, Thomas, Ranjeeta, Vermund, Sten, White, Rhonda, Wilson, Ethan, Yang, Blia, Yuhas, Krista, Bowden, Rory, Calvez, Vincent, Essex, Max, Grabowski, Kate, Gupta, Ravindra, Herbeck, Joshua, Kagaayi, Joseph, Kaleebu, Pontiano, Lingappa, Jairam, Moyo, Sikhulile, Novitsky, Vladimir, Ndung’u, Thumbi, Pillay, Deenan, Quinn, Thomas, Rambaut, Andrew, Seeley, Janet, Ssemwanga, Deogratius, Tanser, Frank, Wawer, Maria, Hall, Matthew, Golubchik, Tanya, Bonsall, David, Abeler-Dörner, Lucie, Limbada, Mohammed, Schaap, Ab, de Cesare, Mariateresa, MacIntyre-Cockett, George, Otecko, Newton, Probert, William, Ratmann, Oliver, Bulas Cruz, Ana, Piwowar-Manning, Estelle, Burns, David N, Cohen, Myron S, Donnell, Deborah J, Eshleman, Susan H, Simwinga, Musonda, Fidler, Sarah, Hayes, Richard, Ayles, Helen, and Fraser, Christophe

Published
2024
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5. Lateral flow test engineering and lessons learned from COVID-19

Author

Budd, Jobie, Miller, Benjamin S., Weckman, Nicole E., Cherkaoui, Dounia, Huang, Da, Decruz, Alyssa Thomas, Fongwen, Noah, Han, Gyeo-Re, Broto, Marta, Estcourt, Claudia S., Gibbs, Jo, Pillay, Deenan, Sonnenberg, Pam, Meurant, Robyn, Thomas, Michael R., Keegan, Neil, Stevens, Molly M., Nastouli, Eleni, Topol, Eric J., Johnson, Anne M., Shahmanesh, Maryam, Ozcan, Aydogan, Collins, James J., Fernandez Suarez, Marta, Rodriguez, Bill, Peeling, Rosanna W., and McKendry, Rachel A.

Published
2023
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6. Go local: The key to controlling the COVID-19 pandemic in the post lockdown era

Author

Bennett, Isabel, Budd, Jobie, Manning, Erin M., Manley, Ed, Zhuang, Mengdie, Cox, Ingemar J., Short, Michael, Johnson, Anne M., Pillay, Deenan, and McKendry, Rachel A.

Subjects
Computer Science - Computers and Society
Abstract

The UK government announced its first wave of lockdown easing on 10 May 2020, two months after the non-pharmaceutical measures to reduce the spread of COVID-19 were first introduced on 23 March 2020. Analysis of reported case rate data from Public Health England and aggregated and anonymised crowd level mobility data shows variability across local authorities in the UK. A locality-based approach to lockdown easing is needed, enabling local public health and associated health and social care services to rapidly respond to emerging hotspots of infection. National level data will hide an increasing heterogeneity of COVID-19 infections and mobility, and new ways of real-time data presentation to the public are required. Data sources (including mobile) allow for faster visualisation than more traditional data sources, and are part of a wider trend towards near real-time analysis of outbreaks needed for timely, targeted local public health interventions. Real time data visualisation may give early warnings of unusual levels of activity which warrant further investigation by local public health authorities., Comment: 6 pages, 3 figures

Published
2020

7. Effective immunity and second waves: a dynamic causal modelling study

Author

Friston, Karl J., Parr, Thomas, Zeidman, Peter, Razi, Adeel, Flandin, Guillaume, Daunizeau, Jean, Hulme, Oliver J., Billig, Alexander J., Litvak, Vladimir, Price, Cathy J., Moran, Rosalyn J., Costello, Anthony, Pillay, Deenan, and Lambert, Christian

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Quantitative Methods, q-bio.QM
Abstract

This technical report addresses a pressing issue in the trajectory of the coronavirus outbreak; namely, the rate at which effective immunity is lost following the first wave of the pandemic. This is a crucial epidemiological parameter that speaks to both the consequences of relaxing lockdown and the propensity for a second wave of infections. Using a dynamic causal model of reported cases and deaths from multiple countries, we evaluated the evidence models of progressively longer periods of immunity. The results speak to an effective population immunity of about three months that, under the model, defers any second wave for approximately six months in most countries. This may have implications for the window of opportunity for tracking and tracing, as well as for developing vaccination programmes, and other therapeutic interventions., Comment: 20 pages, 8 figures, 3 tables (technical report)

Published
2020

8. The met and unmet health needs for HIV, hypertension, and diabetes in rural KwaZulu-Natal, South Africa: analysis of a cross-sectional multimorbidity survey

Author

Wong, Emily B., Olivier, Stephen, Gunda, Resign, Koole, Olivier, Surujdeen, Ashmika, Gareta, Dickman, Munatsi, Day, Modise, Tswaraganang H., Dreyer, Jaco, Nxumalo, Siyabonga, Smit, Theresa K., Ording-Jespersen, Greg, Mpofana, Innocentia B., Khan, Khadija, Sikhosana, Zizile E.L., Moodley, Sashen, Shen, Yen-Ju, Khoza, Thandeka, Mhlongo, Ngcebo, Bucibo, Sana, Nyamande, Kennedy, Baisley, Kathy J., Cuadros, Diego, Tanser, Frank, Grant, Alison D., Herbst, Kobus, Seeley, Janet, Hanekom, Willem A., Ndung'u, Thumbi, Siedner, Mark J., Pillay, Deenan, Suleman, Mosa, Kalideen, Jaikrishna, Jackpersad, Ramesh, Moropane, Kgaugelo, Mfolo, Boitsholo, Malomane, Khabonina, Khumalo, Hlolisile, Buthelezi, Nompilo, Mbonambi, Nozipho, Ngubane, Hloniphile, Simelane, Thokozani, Buthelezi, Khanyisani, Ntuli, Sphiwe, Zondi, Nombuyiselo, Nene, Siboniso, Ndlovu, Bongumenzi, Ntimbane, Talente, Mbuyisa, Mbali, Mkhize, Xolani, Sibiya, Melusi, Ntombela, Ntombiyenkosi, Dlamini, Mandisi, Chonco, Hlobisile, Dlamini, Hlengiwe, Mlambo, Doctar, Mzimela, Nonhlahla, Buthelezi, Zinhle, Mthembu, Zinhle, Bhengu, Thokozani, Mtehmbu, Sandile, Mthethwa, Phumelele, Mbatha, Zamashandu, Mthembu, Welcome Petros, Mkhwanazi, Anele, Sikhali, Mandlakayise, Mkhwanazi, Phakamani, Mkhwanazi, Ntombiyenhlahla, Myeni, Rose, Mfeka, Fezeka, Gumede, Hlobisile, Mfeka, Nonceba, Zungu, Ayanda, Mfekayi, Nonhlahla, Zulu, Smangaliso, Buthelezi, Mzamo, Mkhwanazi, Senzeni, Dube, Mlungisi, Matthews, Philippa, Dlamini, Siphephelo, Kambonde, Hosea, Mthembu, Lindani, Mchunu, Seneme, Gumbi, Sibahle, Madolo, Tumi, Nkosi, Thengokwakhe, Mkhwanazi, Sibusiso, Nsibande, Simbusio, Steto, Mpumelelo, Mhlongo, Sibusiso, Vellem, Velile, Tshivase, Pfarelo, Kwinda, Jabu, Magwaza, Bongani, Nsibande, Siyabonga, Mthombeni, Skhumbuzo, Mthembu, Sphiwe Clement, Rapulana, Antony, Cousins, Jade, Zondi, Thabile, Padayachi, Nagavelli, Mabetlela, Freddy, Ntshangase, Simphiwe, Luthuli, Nomfundo, Ngcobo, Sithembile, Brien, Kayleen, Ndlela, Sizwe, Ngema, Nomfundo, Ntshakala, Nokukhanya, Singh, Anupa, Singh, Rochelle, Pillay, Logan, Chetty, Kandaseelan, Govender, Asthentha, Ramkalawon, Pamela, Mabaso, Nondumiso, Perumal, Kimeshree, Makhari, Senamile, Khuluse, Nondumiso, Zitha, Nondumiso, Khati, Hlengiwe, Mofokeng, Mbuti, Majozi, Nomathamsanqa, Gqaleni, Nceba, Keal, Hannah, Ngcobo, Phumla, Criticos, Costa, Zondo, Raynold, Kalyan, Dilip, Mavimbela, Clive, Ramnanan, Anand, Harilall, Sashin, Singh, Urisha, Castle, Alison, Moosa, Yumna, Zulu, Thando, Edwards, Jonathan Alex, Kim, Hae-Young, Modise, Tshwaraganang H, Smit, Theresa K, Ordering-Jespersen, Greg, Mpofana, Innocentia B, Sikhosana, Zinzile E L, Bucibo, Sanah, Baisley, Kathy J, Grant, Alison D, Hanekom, Willem, Ndung’u, Thumbi, Siedner, Mark J, and Wong, Emily B

Published
2023
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9. A national initiative in data science for health: an evaluation of the UK Farr Institute

Author

Hemingway, H, Lyons, R, Li, Q, Buchan, I, Ainsworth, J, Pell, J, Morris, A, Barnes, Michael R, Bedford, Helen, Bennie, Marion, Blandford, Ann, Briggs, Andy, Brocklehurst, Peter, Brophy, Sinead, Brown, Gavin, Burton, Paul, Butler, Christopher, Capewell, Simon, Carpenter, James, Carroll, John, Cassell, Jackie A, Castillo, Fortunato, Catchpole, Mike, Caulfield, Mark, Colhoun, Helen, Coveney, Peter, Cunningham-Burley, Sarah, Custovic, Adnan, Deanfield, John, Denaxas, Spiros, Dennis, Michael, Dezateux, Carol, Dibben, Chris, Diggle, Peter, Dixon, Will, Dunn, Graham, Emam, Khaled El, Fone, David, Ford, David, Ford, Ian, Frank, John, Freemantle, Nick, Gabbe, Belinda, Gallacher, John, Gibson, Martin, Gilbert, Ruth, Gissler, Mika, Goble, Carol, Goldberg, Andy, Gravenor, Mike, Gunnell, David, Hannaford, Phil, Hayward, Andrew, Hickman, Matthew, Hingorani, Aroon, Holm, Soren, Holman, Cashel, John, Gareth, John, Ann, Jones, Kerina, Kalra, Dipak, Laurie, Graeme, Lewis, Shon, Lloyd, Keith, Lowe, Sarah, McCowan, Colin, Macleod, John, Martin, Richard M, Moore, Anthony, Moore, Laurence, Nazareth, Irwin, Nenadic, Goran, Paranjothy, Shantini, Parmar, Max, Pebody, Richard, Petersen, Steffen, Petersen, Irene, Pillay, Deenan, Preen, David, Pickett, Kate, Pritchard-Jones, Kathy, Przulj, Natasa, Renehan, Andrew, Roberts, Stephen, Robson, John, Rodgers, Sarah, Rossor, Martin, Russell, Ian, Shawe-Taylor, John, Sheikh, Aziz, Siebert, Stefan, Snooks, Helen, Sperrin, Matthew, Stephenson, Judith, Sullivan, Frank, Taylor, Chris, Taylor, Paul, Timmis, Adam, and Ward, Hester JT

Subjects
Information and Computing Sciences, Library and Information Studies, Health Sciences, Generic health relevance, Health sciences, Human society, Information and computing sciences
Abstract

ObjectiveTo evaluate the extent to which the inter-institutional, inter-disciplinary mobilisation of data and skills in the Farr Institute contributed to establishing the emerging field of data science for health in the UK.Design and outcome measuresWe evaluated evidence of six domains characterising a new field of science:defining central scientific challenges,demonstrating how the central challenges might be solved,creating novel interactions among groups of scientists,training new types of experts,re-organising universities,demonstrating impacts in society.We carried out citation, network and time trend analyses of publications, and a narrative review of infrastructure, methods and tools.SettingFour UK centres in London, North England, Scotland and Wales (23 university partners), 2013-2018.Results1. The Farr Institute helped define a central scientific challenge publishing a research corpus, demonstrating insights from electronic health record (EHR) and administrative data at each stage of the translational cycle in 593 papers with at least one Farr Institute author affiliation on PubMed. 2. The Farr Institute offered some demonstrations of how these scientific challenges might be solved: it established the first four ISO27001 certified trusted research environments in the UK, and approved more than 1000 research users, published on 102 unique EHR and administrative data sources, although there was no clear evidence of an increase in novel, sustained record linkages. The Farr Institute established open platforms for the EHR phenotyping algorithms and validations (>70 diseases, CALIBER). Sample sizes showed some evidence of increase but remained less than 10% of the UK population in primary care-hospital care linked studies. 3.The Farr Institute created novel interactions among researchers: the co-author publication network expanded from 944 unique co-authors (based on 67 publications in the first 30 months) to 3839 unique co-authors (545 papers in the final 30 months). 4. Training expanded substantially with 3 new masters courses, training >400 people at masters, short-course and leadership level and 48 PhD students. 5. Universities reorganised with 4/5 Centres established 27 new faculty (tenured) positions, 3 new university institutes. 6. Emerging evidence of impacts included: > 3200 citations for the 10 most cited papers and Farr research informed eight practice-changing clinical guidelines and policies relevant to the health of millions of UK citizens.ConclusionThe Farr Institute played a major role in establishing and growing the field of data science for health in the UK, with some initial evidence of benefits for health and healthcare. The Farr Institute has now expanded into Health Data Research (HDR) UK but key challenges remain including, how to network such activities internationally.

Published
2020

10. Disability for HIV and Disincentives for Health: The Impact of South Africa's Disability Grant on HIV/AIDS Recovery

Author

Haber, Noah, Bärnighausen, Till, Bor, Jacob, Cohen, Jessica, Tanser, Frank, Pillay, Deenan, and Fink, Günther

Subjects
Economics - General Economics
Abstract

South Africa's disability grants program is tied to its HIV/AIDS recovery program, such that individuals who are ill enough may qualify. Qualification is historically tied to a CD4 count of 200 cells/mm3, which improve when a person adheres to antiretroviral therapy. This creates a potential unintended consequence where poor individuals, faced with potential loss of their income, may choose to limit their recovery through non-adherence. To test for manipulation caused by grant rules, we identify differences in disability grant recipients and non-recipients' rate of CD4 recovery around the qualification threshold, implemented as a fixed-effects difference-in-difference around the threshold. We use data from the Africa Health Research Institute Demographic and Health Surveillance System (AHRI DSS) in rural KwaZulu-Natal, South Africa, utilizing DG status and laboratory CD4 count records for 8,497 individuals to test whether there are any systematic differences in CD4 recover rates among eligible patients. We find that disability grant threshold rules caused recipients to have a relatively slower CD4 recovery rate of about 20-30 cells/mm3/year, or a 20% reduction in the speed of recovery around the threshold.

Published
2018

11. Recommendations on data sharing in HIV drug resistance research

Author

Inzaule, Seth C., Siedner, Mark J., Little, Susan J., Avila-Rios, Santiago, Ayitewala, Alisen, Bosch, Ronald J., Calvez, Vincent, Ceccherini-Silberstein, Francesca, Charpentier, Charlotte, Descamps, Diane, Eshleman, Susan H., Fokam, Joseph, Frenkel, Lisa M., Gupta, Ravindra K., Ioannidis, John P.A., Kaleebu, Pontiano, Kantor, Rami, Kassaye, Seble G., Kosakovsky Pond, Sergei L., Kouamou, Vinie, Kouyos, Roger D., Kuritzkes, Daniel R., Lessells, Richard, Marcelin, Anne-Genevieve, Mbuagbaw, Lawrence, Minalga, Brian, Ndembi, Nicaise, Neher, Richard A., Paredes, Roger, Pillay, Deenan, Raizes, Elliot G., Rhee, Soo-Yon, Richman, Douglas D., Ruxrungtham, Kiat, Sabeti, Pardis C., Schapiro, Jonathan M., Sirivichayakul, Sunee, Steegen, Kim, Sugiura, Wataru, van Zyl, Gert U., Vandamme, Anne-Mieke, Wensing, Annemarie M.J., Wertheim, Joel O., Gunthard, Huldrych F., Jordan, Michael R., and Shafer, Robert W.

Subjects
United States. Centers for Disease Control and Prevention, United States. National Institutes of Health, Merck & Company Inc., Gilead Sciences Inc., Biological products industry, HIV (Viruses) -- Drug therapy, Rilpivirine, Drug resistance -- Drug therapy, Pharmaceutical industry, Biological sciences, World Health Organization
Abstract

Author(s): Seth C. Inzaule 1, Mark J. Siedner 2, Susan J. Little 3, Santiago Avila-Rios 4, Alisen Ayitewala 5, Ronald J. Bosch 6, Vincent Calvez 7, Francesca Ceccherini-Silberstein 8, Charlotte [...]

Published
2023
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12. Population Effectiveness of Dolutegravir Implementation in Uganda - A Prospective Observational Cohort Study (DISCO): 48-week Results

Author

McCluskey, Suzanne M, primary, Muyindike, Winnie R, additional, Nanfuka, Victoria, additional, Omoding, Daniel, additional, Komukama, Nimusiima, additional, Barigye, Ian T, additional, Kansiime, Lydia, additional, Tumusiime, Justus, additional, Aung, Taing N, additional, Stuckwisch, Ashley, additional, Hedt-Gauthier, Bethany, additional, Marconi, Vincent C, additional, Moosa, Mahomed-Yunus S, additional, Pillay, Deenan, additional, Giandhari, Jennifer, additional, Lessells, Richard, additional, Gupta, Ravindra K, additional, and Siedner, Mark J, additional

Published
2024
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13. Reply to Ambrosioni et al.

Author

Günthard, Huldrych F, Calvez, Vincent, Paredes, Roger, Pillay, Deenan, Shafer, Robert W, Wensing, Annemarie M, Jacobsen, Donna M, and Richman, Douglas D

Subjects
Antiviral Agents, Drug Resistance, HIV, HIV Infections, Humans, Societies, Biological Sciences, Medical and Health Sciences, Microbiology
Published
2019

14. Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

Author

Ratmann, Oliver, Grabowski, M Kate, Hall, Matthew, Golubchik, Tanya, Wymant, Chris, Abeler-Dörner, Lucie, Bonsall, David, Hoppe, Anne, Brown, Andrew Leigh, de Oliveira, Tulio, Gall, Astrid, Kellam, Paul, Pillay, Deenan, Kagaayi, Joseph, Kigozi, Godfrey, Quinn, Thomas C, Wawer, Maria J, Laeyendecker, Oliver, Serwadda, David, Gray, Ronald H, Fraser, Christophe, and PANGEA Consortium and Rakai Health Sciences Program

Subjects
PANGEA Consortium and Rakai Health Sciences Program, Humans, HIV-1, HIV Infections, Phylogeny, Base Sequence, Adolescent, Adult, Middle Aged, Africa, Young Adult, Epidemics, High-Throughput Nucleotide Sequencing
Abstract

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.

Published
2019

15. Risks and benefits of dolutegravir-based antiretroviral drug regimens in sub-Saharan Africa: a modelling study

Author

Phillips, Andrew N, Venter, Francois, Havlir, Diane, Pozniak, Anton, Kuritzkes, Daniel, Wensing, Annemarie, Lundgren, Jens D, De Luca, Andrea, Pillay, Deenan, Mellors, John, Cambiano, Valentina, Bansi-Matharu, Loveleen, Nakagawa, Fumiyo, Kalua, Thokozani, Jahn, Andreas, Apollo, Tsitsi, Mugurungi, Owen, Clayden, Polly, Gupta, Ravindra K, Barnabas, Ruanne, Revill, Paul, Cohn, Jennifer, Bertagnolio, Silvia, and Calmy, Alexandra

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Prevention, HIV/AIDS, Pediatric, Aetiology, Evaluation of treatments and therapeutic interventions, 2.2 Factors relating to the physical environment, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Adolescent, Adult, Africa South of the Sahara, Antiretroviral Therapy, Highly Active, Developmental Disabilities, Drug Resistance, Viral, Female, HIV Infections, HIV Integrase Inhibitors, Heterocyclic Compounds, 3-Ring, Humans, Male, Middle Aged, Oxazines, Piperazines, Pregnancy, Pyridones, Risk Assessment, Sustained Virologic Response, Treatment Outcome, Viral Load, Young Adult, Medical and Health Sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundThe integrase inhibitor dolutegravir could have a major role in future antiretroviral therapy (ART) regimens in sub-Saharan Africa because of its high potency and barrier to resistance, good tolerability, and low cost, but there is uncertainty over appropriate policies for use relating to the potential for drug resistance spread and a possible increased risk of neural tube defects in infants if used in women at the time of conception. We used an existing individual-based model of HIV transmission, progression, and the effect of ART with the aim of informing policy makers on approaches to the use of dolutegravir that are likely to lead to the highest population health gains.MethodsWe used an existing individual-based model of HIV transmission and progression in adults, which takes into account the effects of drug resistance and differential drug potency in determining viral suppression and clinical outcomes to compare predicted outcomes of alternative ART regimen policies. We calculated disability adjusted life-years (DALYs) for each policy, assuming that a woman having a child with a neural tube defect incurs an extra DALY per year for the remainder of the time horizon and accounting for mother-to-child transmission. We used a 20 year time horizon, a 3% discount rate, and a cost-effectiveness threshold of US$500 per DALY averted.FindingsThe greatest number of DALYs is predicted to be averted with use of a policy in which tenofovir, lamivudine, and dolutegravir is used in all people on ART, including switching to tenofovir, lamivudine, and dolutegravir in those currently on ART, regardless of current viral load suppression and intention to have (more) children. This result was consistent in several sensitivity analyses. We predict that this policy would be cost-saving.InterpretationUsing a standard DALY framework to compare health outcomes from a public health perspective, the benefits of transition to tenofovir, lamivudine, and dolutegravir for all substantially outweighed the risks.FundingBill & Melinda Gates Foundation.

Published
2019

16. Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society–USA Panel

Author

Günthard, Huldrych F, Calvez, Vincent, Paredes, Roger, Pillay, Deenan, Shafer, Robert W, Wensing, Annemarie M, Jacobsen, Donna M, and Richman, Douglas D

Subjects
Clinical Research, Antimicrobial Resistance, HIV/AIDS, Infectious Diseases, Evaluation of treatments and therapeutic interventions, Development of treatments and therapeutic interventions, 6.1 Pharmaceuticals, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Anti-HIV Agents, Developing Countries, Drug Resistance, Viral, HIV Infections, HIV-1, Humans, Internationality, Societies, Scientific, United States, HIV, antiretroviral therapy, drug resistance, therapeutic failure, resource-rich, low and middle income countries, HIV-1 subtype, genotypic drug resistance, sanger sequencing, next generation sequencing, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

BackgroundContemporary antiretroviral therapies (ART) and management strategies have diminished both human immunodeficiency virus (HIV) treatment failure and the acquired resistance to drugs in resource-rich regions, but transmission of drug-resistant viruses has not similarly decreased. In low- and middle-income regions, ART roll-out has improved outcomes, but has resulted in increasing acquired and transmitted resistances. Our objective was to review resistance to ART drugs and methods to detect it, and to provide updated recommendations for testing and monitoring for drug resistance in HIV-infected individuals.MethodsA volunteer panel of experts appointed by the International Antiviral (formerly AIDS) Society-USA reviewed relevant peer-reviewed data that were published or presented at scientific conferences. Recommendations were rated according to the strength of the recommendation and quality of the evidence, and reached by full panel consensus.ResultsResistance testing remains a cornerstone of ART. It is recommended in newly-diagnosed individuals and in patients in whom ART has failed. Testing for transmitted integrase strand-transfer inhibitor resistance is currently not recommended, but this may change as more resistance emerges with widespread use. Sanger-based and next-generation sequencing approaches are each suited for genotypic testing. Testing for minority variants harboring drug resistance may only be considered if treatments depend on a first-generation nonnucleoside analogue reverse transcriptase inhibitor. Different HIV-1 subtypes do not need special considerations regarding resistance testing.ConclusionsTesting for HIV drug resistance in drug-naive individuals and in patients in whom antiretroviral drugs are failing, and the appreciation of the role of testing, are crucial to the prevention and management of failure of ART.

Published
2019

17. Ethical considerations in global HIV phylogenetic research

Author

Coltart, Cordelia EM, Hoppe, Anne, Parker, Michael, Dawson, Liza, Amon, Joseph J, Simwinga, Musonda, Geller, Gail, Henderson, Gail, Laeyendecker, Oliver, Tucker, Joseph D, Eba, Patrick, Novitsky, Vladimir, Vandamme, Anne-Mieke, Seeley, Janet, Dallabetta, Gina, Harling, Guy, Grabowski, M Kate, Godfrey-Faussett, Peter, Fraser, Christophe, Cohen, Myron S, Pillay, Deenan, Group, Ethics in HIV Phylogenetics Working, Baggaley, Rachel, Bernard, Edwin J, Burns, David, Coltart, Cordelia C, Dedes, Nikos, Delpech, Valerie, Eba, Patrick M, German, Danielle, Grabowksi, M Kate, Hall, Irene, Kozlakidis, Zisis, Mwanza, Felix, Reis, Andreas, Simwanga, Musonda, Wertheim, Joel O, and Zimmerman, Rick

Subjects
Biomedical and Clinical Sciences, Public Health, Health Sciences, HIV/AIDS, Infectious Diseases, Genetics, 8.3 Policy, ethics, and research governance, Health and social care services research, 8.1 Organisation and delivery of services, Infection, Good Health and Well Being, Biomedical Research, Guidelines as Topic, HIV, HIV Infections, Human Rights, Humans, Phylogeny, Research Design, Risk Assessment, Ethics in HIV Phylogenetics Working Group, Medical and Health Sciences, Biomedical and clinical sciences, Health sciences
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.

Published
2018

19. Isisekelo Sempilo study protocol for the effectiveness of HIV prevention embedded in sexual health with or without peer navigator support (Thetha Nami) to reduce prevalence of transmissible HIV amongst adolescents and young adults in rural KwaZulu-Natal: a 2 × 2 factorial randomised controlled trial

Author

Chidumwa, Glory, Chimbindi, Natsayi, Herbst, Carina, Okeselo, Nonhlanhla, Dreyer, Jaco, Zuma, Thembelihle, Smith, Theresa, Molina, Jean-Michel, Khoza, Thandeka, McGrath, Nuala, Seeley, Janet, Pillay, Deenan, Tanser, Frank, Harling, Guy, Sherr, Lorraine, Copas, Andrew, Baisley, Kathy, and Shahmanesh, Maryam

Published
2022
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21. Cost-effectiveness of public-health policy options in the presence of pretreatment NNRTI drug resistance in sub-Saharan Africa: a modelling study

Author

Phillips, Andrew N, Cambiano, Valentina, Nakagawa, Fumiyo, Revill, Paul, Jordan, Michael R, Hallett, Timothy B, Doherty, Meg, De Luca, Andrea, Lundgren, Jens D, Mhangara, Mutsa, Apollo, Tsitsi, Mellors, John, Nichols, Brooke, Parikh, Urvi, Pillay, Deenan, de Wit, Tobias Rinke, Sigaloff, Kim, Havlir, Diane, Kuritzkes, Daniel R, Pozniak, Anton, van de Vijver, David, Vitoria, Marco, Wainberg, Mark A, Raizes, Elliot, Bertagnolio, Silvia, and Africa, Working Group on Modelling Potential Responses to High Levels of Pre-ART Drug Resistance in Sub-Saharan

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Public Health, Health Sciences, Antimicrobial Resistance, HIV/AIDS, Infectious Diseases, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Adolescent, Adult, Africa South of the Sahara, Cost-Benefit Analysis, HIV Infections, HIV Integrase Inhibitors, Health Policy, Heterocyclic Compounds, 3-Ring, Humans, Middle Aged, Models, Economic, Oxazines, Piperazines, Pyridones, Treatment Outcome, Young Adult, Working Group on Modelling Potential Responses to High Levels of Pre-ART Drug Resistance in Sub-Saharan Africa, Medical and Health Sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundThere is concern over increasing prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) resistance in people initiating antiretroviral therapy (ART) in low-income and middle-income countries. We assessed the effectiveness and cost-effectiveness of alternative public health responses in countries in sub-Saharan Africa where the prevalence of pretreatment drug resistance to NNRTIs is high.MethodsThe HIV Synthesis Model is an individual-based simulation model of sexual HIV transmission, progression, and the effect of ART in adults, which is based on extensive published data sources and considers specific drugs and resistance mutations. We used this model to generate multiple setting scenarios mimicking those in sub-Saharan Africa and considered the prevalence of pretreatment NNRTI drug resistance in 2017. We then compared effectiveness and cost-effectiveness of alternative policy options. We took a 20 year time horizon, used a cost effectiveness threshold of US$500 per DALY averted, and discounted DALYs and costs at 3% per year.FindingsA transition to use of a dolutegravir as a first-line regimen in all new ART initiators is the option predicted to produce the most health benefits, resulting in a reduction of about 1 death per year per 100 people on ART over the next 20 years in a situation in which more than 10% of ART initiators have NNRTI resistance. The negative effect on population health of postponing the transition to dolutegravir increases substantially with higher prevalence of HIV drug resistance to NNRTI in ART initiators. Because of the reduced risk of resistance acquisition with dolutegravir-based regimens and reduced use of expensive second-line boosted protease inhibitor regimens, this policy option is also predicted to lead to a reduction of overall programme cost.InterpretationA future transition from first-line regimens containing efavirenz to regimens containing dolutegravir formulations in adult ART initiators is predicted to be effective and cost-effective in low-income settings in sub-Saharan Africa at any prevalence of pre-ART NNRTI resistance. The urgency of the transition will depend largely on the country-specific prevalence of NNRTI resistance.FundingBill & Melinda Gates Foundation, World Health Organization.

Published
2018

22. Comparative assessment of five trials of universal HIV testing and treatment in sub‐Saharan Africa

Author

Perriat, Delphine, Balzer, Laura, Hayes, Richard, Lockman, Shahin, Walsh, Fiona, Ayles, Helen, Floyd, Sian, Havlir, Diane, Kamya, Moses, Lebelonyane, Refeletswe, Mills, Lisa A, Okello, Velephi, Petersen, Maya, Pillay, Deenan, Sabapathy, Kalpana, Wirth, Kathleen, Orne‐Gliemann, Joanna, Dabis, François, and Consortium, the Universal Test and Treat Trials

Subjects
Public Health, Health Sciences, Clinical Trials and Supportive Activities, Behavioral and Social Science, Clinical Research, Health Services, Infectious Diseases, HIV/AIDS, Comparative Effectiveness Research, Prevention, Generic health relevance, Infection, Good Health and Well Being, Adult, Africa South of the Sahara, Clinical Trials as Topic, Epidemics, Female, HIV Infections, Humans, Male, Research Design, HIV, universal test and treat, randomized trials, comparative assessment, protocols, sub-Saharan Africa, Universal Test and Treat Trials Consortium, HIV, Clinical Sciences, Public Health and Health Services, Other Medical and Health Sciences, Clinical sciences, Epidemiology, Public health
Abstract

DesignUniversal voluntary HIV counselling and testing followed by prompt initiation of antiretroviral therapy (ART) for all those diagnosed HIV-infected (universal test and treat, UTT) is now a global health standard. However, its population-level impact, feasibility and cost remain unknown. Five community-based trials have been implemented in sub-Saharan Africa to measure the effects of various UTT strategies at population level: BCPP/YaTsie in Botswana, MaxART in Swaziland, HPTN 071 (PopART) in South Africa and Zambia, SEARCH in Uganda and Kenya and ANRS 12249 TasP in South Africa. This report describes and contrasts the contexts, research methodologies, intervention packages, themes explored, evolution of study designs and interventions related to each of these five UTT trials.MethodsWe conducted a comparative assessment of the five trials using data extracted from study protocols and collected during baseline studies, with additional input from study investigators. We organized differences and commonalities across the trials in five categories: trial contexts, research designs, intervention packages, trial themes and adaptations.ResultsAll performed in the context of generalized HIV epidemics, the trials highly differ in their social, demographic, economic, political and health systems settings. They share the common aim of assessing the impact of UTT on the HIV epidemic but differ in methodological aspects such as study design and eligibility criteria for trial populations. In addition to universal ART initiation, the trials deliver a wide range of biomedical, behavioural and structural interventions as part of their UTT strategies. The five studies explore common issues, including the uptake rates of the trial services and individual health outcomes. All trials have adapted since their initiation to the evolving political, economic and public health contexts, including adopting the successive national recommendations for ART initiation.ConclusionsWe found substantial commonalities but also differences between the five UTT trials in their design, conduct and multidisciplinary outputs. As empirical literature on how UTT may improve efficiency and quality of HIV care at population level is still scarce, this article provides a foundation for more collaborative research on UTT and supports evidence-based decision making for HIV care in country and internationally.

Published
2018

23. HIV treatment is associated with a two-fold higher probability of raised triglycerides: Pooled Analyses in 21 023 individuals in sub-Saharan Africa.

Author

Ekoru, Kenneth, Young, Elizabeth H, Dillon, David G, Gurdasani, Deepti, Stehouwer, Nathan, Faurholt-Jepsen, Daniel, Levitt, Naomi S, Crowther, Nigel J, Nyirenda, Moffat, Njelekela, Marina A, Ramaiya, Kaushik, Nyan, Ousman, Adewole, Olanisun O, Anastos, Kathryn, Compostella, Caterina, Dave, Joel A, Fourie, Carla M, Friis, Henrik, Kruger, Iolanthe M, Longenecker, Chris T, Maher, Dermot P, Mutimura, Eugene, Ndhlovu, Chiratidzo E, Praygod, George, Pefura Yone, Eric W, Pujades-Rodriguez, Mar, Range, Nyagosya, Sani, Mahmoud U, Sanusi, Muhammad, Schutte, Aletta E, Sliwa, Karen, Tien, Phyllis C, Vorster, Este H, Walsh, Corinna, Gareta, Dickman, Mashili, Fredirick, Sobngwi, Eugene, Adebamowo, Clement, Kamali, Anatoli, Seeley, Janet, Smeeth, Liam, Pillay, Deenan, Motala, Ayesha A, Kaleebu, Pontiano, and Sandhu, Manjinder S

Subjects
Antiretroviral therapy, Cardiovascular disease, HIV, Lipids, Sub-Saharan Africa, Triglycerides
Abstract

BackgroundAnti-retroviral therapy (ART) regimes for HIV are associated with raised levels of circulating triglycerides (TG) in western populations. However, there are limited data on the impact of ART on cardiometabolic risk in sub-Saharan African (SSA) populations.MethodsPooled analyses of 14 studies comprising 21 023 individuals, on whom relevant cardiometabolic risk factors (including TG), HIV and ART status were assessed between 2003 and 2014, in SSA. The association between ART and raised TG (>2.3 mmol/L) was analysed using regression models.FindingsAmong 10 615 individuals, ART was associated with a two-fold higher probability of raised TG (RR 2.05, 95% CI 1.51-2.77, I2=45.2%). The associations between ART and raised blood pressure, glucose, HbA1c, and other lipids were inconsistent across studies.InterpretationEvidence from this study confirms the association of ART with raised TG in SSA populations. Given the possible causal effect of raised TG on cardiovascular disease (CVD), the evidence highlights the need for prospective studies to clarify the impact of long term ART on CVD outcomes in SSA.

Published
2018

24. HIV treatment is associated with a twofold higher probability of raised triglycerides: pooled analyses in 21 023 individuals in sub-Saharan Africa

Author

Ekoru, Kenneth, Young, Elizabeth H, Dillon, David G, Gurdasani, Deepti, Stehouwer, Nathan, Faurholt-Jepsen, Daniel, Levitt, Naomi S, Crowther, Nigel J, Nyirenda, Moffat, Njelekela, Marina A, Ramaiya, Kaushik, Nyan, Ousman, Adewole, Olanisun O, Anastos, Kathryn, Compostella, Caterina, Dave, Joel A, Fourie, Carla M, Friis, Henrik, Kruger, Iolanthe M, Longenecker, Chris T, Maher, Dermot P, Mutimura, Eugene, Ndhlovu, Chiratidzo E, Praygod, George, Pefura Yone, Eric W, Pujades-Rodriguez, Mar, Range, Nyagosya, Sani, Mahmoud U, Sanusi, Muhammad, Schutte, Aletta E, Sliwa, Karen, Tien, Phyllis C, Vorster, Este H, Walsh, Corinna, Gareta, Dickman, Mashili, Fredirick, Sobngwi, Eugene, Adebamowo, Clement, Kamali, Anatoli, Seeley, Janet, Smeeth, Liam, Pillay, Deenan, Motala, Ayesha A, Kaleebu, Pontiano, and Sandhu, Manjinder S

Subjects
Public Health, Health Sciences, Prevention, Cardiovascular, Heart Disease, HIV/AIDS, Mental Health, Infectious Diseases, Good Health and Well Being, Antiretroviral therapy, cardiovascular disease, HIV, lipids, sub-Saharan Africa, triglycerides, Cardiovascular disease, Lipids, Sub-Saharan Africa, Triglycerides, Genetics, Epidemiology, Public health
Abstract

Anti-retroviral therapy (ART) regimes for HIV are associated with raised levels of circulating triglycerides (TG) in western populations. However, there are limited data on the impact of ART on cardiometabolic risk in sub-Saharan African (SSA) populations. Pooled analyses of 14 studies comprising 21 023 individuals, on whom relevant cardiometabolic risk factors (including TG), HIV and ART status were assessed between 2003 and 2014, in SSA. The association between ART and raised TG (>2.3 mmol/L) was analysed using regression models. Among 10 615 individuals, ART was associated with a two-fold higher probability of raised TG (RR 2.05, 95% CI 1.51-2.77, I2=45.2%). The associations between ART and raised blood pressure, glucose, HbA1c, and other lipids were inconsistent across studies. Evidence from this study confirms the association of ART with raised TG in SSA populations. Given the possible causal effect of raised TG on cardiovascular disease (CVD), the evidence highlights the need for prospective studies to clarify the impact of long term ART on CVD outcomes in SSA.

Published
2018

25. Association of pregnancy with engagement in HIV care among women with HIV in the UK: a cohort study

Author

Ainsworth, Jonathan, Allan, Sris, Anderson, Jane, Apoola, Ade, Chadwick, David, Churchill, Duncan, Delpech, Valerie, Dunn, David, Fairley, Ian, Fox, Ashini, Gilson, Richard, Gompels, Mark, Hay, Phillip, Hembrom, Rajesh, Hill, Teresa, Johnson, Margaret, Jose, Sophie, Kegg, Stephen, Leen, Clifford, Mital, Dushyant, Nelson, Mark, Okhai, Hajra, Orkin, Chloe, Palfreeman, Adrian, Phillips, Andrew, Pillay, Deenan, Price, Ashley, Post, Frank, Pritchard, Jillian, Sabin, Caroline, Schwenk, Achim, Tariq, Anjum, Trevelion, Roy, Ustianowski, Andy, Walsh, John, Tariq, Shema, Burns, Fiona, Gilleece, Yvonne, Dhairyawan, Rageshri, Peters, Helen, Thorne, Claire, and Sabin, Caroline A

Published
2021
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26. Regional variation in weight change after the transition to dolutegravir: a prospective cohort study in Uganda and South Africa

Author

Migisha, Richard, primary, Chen, Geoffrey, additional, Muyindike, Winnie R., additional, Aung, Taing Nandi, additional, Nanfuka, Victoria, additional, Komukama, Nimusiima, additional, Chandiwana, Nomathemba, additional, Shazi, Gugulethu, additional, Tien, Dessie, additional, Moosa, Mahomed-Yunus S., additional, Gupta, Ravindra K., additional, Pillay, Deenan, additional, Marconi, Vincent C., additional, Hedt-Gauthier, Bethany, additional, Venter, Willem D.F., additional, Siedner, Mark J., additional, McCluskey, Suzanne M., additional, and Manne-Goehler, Jennifer, additional

Published
2024
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27. Rapid roll out of SARS-CoV-2 antibody testing—a concern

Author

Andersson, Monique, Low, Nicola, French, Neil, Greenhalgh, Trisha, Jeffery, Katie, Brent, Andrew, Ball, Jonathan, Pollock, Allyson, McCoy, David, Iturriza-Gomara, Miren, Buchan, Iain, Salisbury, Helen, Pillay, Deenan, and Irving, Will

Published
2020

28. Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study

Author

Frampton, Dan, Rampling, Tommy, Cross, Aidan, Bailey, Heather, Heaney, Judith, Byott, Matthew, Scott, Rebecca, Sconza, Rebecca, Price, Joseph, Margaritis, Marios, Bergstrom, Malin, Spyer, Moira J, Miralhes, Patricia B, Grant, Paul, Kirk, Stuart, Valerio, Chris, Mangera, Zaheer, Prabhahar, Thaventhran, Moreno-Cuesta, Jeronimo, Arulkumaran, Nish, Singer, Mervyn, Shin, Gee Yen, Sanchez, Emilie, Paraskevopoulou, Stavroula M, Pillay, Deenan, McKendry, Rachel A, Mirfenderesky, Mariyam, Houlihan, Catherine F, and Nastouli, Eleni

Published
2021
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29. Convergence of infectious and non-communicable disease epidemics in rural South Africa: a cross-sectional, population-based multimorbidity study

Author

Wong, Emily B., Olivier, Stephen, Gunda, Resign, Koole, Olivier, Surujdeen, Ashmika, Gareta, Dickman, Munatsi, Day, Modise, Tswaraganang H., Dreyer, Jaco, Nxumalo, Siyabonga, Smit, Theresa K., Ording-Jespersen, Greg, Mpofana, Innocentia B., Khan, Khadija, Sikhosana, Zizile E.L., Moodley, Sashen, Shen, Yen-Ju, Khoza, Thandeka, Mhlongo, Ngcebo, Bucibo, Sana, Nyamande, Kennedy, Baisley, Kathy J., Cuadros, Diego, Tanser, Frank, Grant, Alison D., Herbst, Kobus, Seeley, Janet, Hanekom, Willem A., Ndung'u, Thumbi, Siedner, Mark J., Pillay, Deenan, Suleman, Mosa, Kalideen, Jaikrishna, Jackpersad, Ramesh, Moropane, Kgaugelo, Mfolo, Boitsholo, Malomane, Khabonina, Khumalo, Hlolisile, Buthelezi, Nompilo, Mbonambi, Nozipho, Ngubane, Hloniphile, Simelane, Thokozani, Buthelezi, Khanyisani, Ntuli, Sphiwe, Zondi, Nombuyiselo, Nene, Siboniso, Ndlovu, Bongumenzi, Ntimbane, Talente, Mbuyisa, Mbali, Mkhize, Xolani, Sibiya, Melusi, Ntombela, Ntombiyenkosi, Dlamini, Mandisi, Chonco, Hlobisile, Dlamini, Hlengiwe, Mlambo, Doctar, Mzimela, Nonhlahla, Buthelezi, Zinhle, Mthembu, Zinhle, Bhengu, Thokozani, Mtehmbu, Sandile, Mthethwa, Phumelele, Mbatha, Zamashandu, Mthembu, Welcome Petros, Mkhwanazi, Anele, Sikhali, Mandlakayise, Mkhwanazi, Phakamani, Mkhwanazi, Ntombiyenhlahla, Myeni, Rose, Mfeka, Fezeka, Gumede, Hlobisile, Mfeka, Nonceba, Zungu, Ayanda, Mfekayi, Nonhlahla, Zulu, Smangaliso, Buthelezi, Mzamo, Mkhwanazi, Senzeni, Dube, Mlungisi, Matthews, Philippa, Dlamini, Siphephelo, Kambonde, Hosea, Mthembu, Lindani, Mchunu, Seneme, Gumbi, Sibahle, Madolo, Tumi, Nkosi, Thengokwakhe, Mkhwanazi, Sibusiso, Nsibande, Simbusio, Steto, Mpumelelo, Mhlongo, Sibusiso, Vellem, Velile, Tshivase, Pfarelo, Kwinda, Jabu, Magwaza, Bongani, Nsibande, Siyabonga, Mthombeni, Skhumbuzo, Mthembu, Sphiwe Clement, Rapulana, Antony, Cousins, Jade, Zondi, Thabile, Padayachi, Nagavelli, Mabetlela, Freddy, Ntshangase, Simphiwe, Luthuli, Nomfundo, Ngcobo, Sithembile, Brien, Kayleen, Ndlela, Sizwe, Ngema, Nomfundo, Ntshakala, Nokukhanya, Singh, Anupa, Singh, Rochelle, Pillay, Logan, Chetty, Kandaseelan, Govender, Asthentha, Ramkalawon, Pamela, Mabaso, Nondumiso, Perumal, Kimeshree, Makhari, Senamile, Khuluse, Nondumiso, Zitha, Nondumiso, Khati, Hlengiwe, Mofokeng, Mbuti, Majozi, Nomathamsanqa, Gqaleni, Nceba, Keal, Hannah, Ngcobo, Phumla, Criticos, Costa, Zondo, Raynold, Kalyan, Dilip, Mavimbela, Clive, Ramnanan, Anand, Harilall, Sashin, Wong, Emily B, Modise, Tshwaraganang H, Smit, Theresa K, Mpofana, Innocentia B, Sikhosana, Zizile E L, Bucibo, Sanah, Baisley, Kathy J, Grant, Alison D, Hanekom, Willem A, and Siedner, Mark J

Published
2021
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30. Deep learning of HIV field-based rapid tests

Author

Turbé, Valérian, Herbst, Carina, Mngomezulu, Thobeka, Meshkinfamfard, Sepehr, Dlamini, Nondumiso, Mhlongo, Thembani, Smit, Theresa, Cherepanova, Valeriia, Shimada, Koki, Budd, Jobie, Arsenov, Nestor, Gray, Steven, Pillay, Deenan, Herbst, Kobus, Shahmanesh, Maryam, and McKendry, Rachel A.

Published
2021
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31. 2017 Update of the Drug Resistance Mutations in HIV-1.

Author

Wensing, Annemarie M, Calvez, Vincent, Günthard, Huldrych F, Johnson, Victoria A, Paredes, Roger, Pillay, Deenan, Shafer, Robert W, and Richman, Douglas D

Subjects
Humans, HIV-1, Drug Resistance, Viral, Mutation, Societies, Scientific, United States, Drug Resistance, Viral, Societies, Scientific
Abstract

The 2017 edition of the IAS-USA drug resistance mutations list updates the figures last published in November 2015. The mutations listed are those that have been identified by specific criteria for evidence and drugs described. The figures are designed to assist practitioners in identifying key mutations associated with resistance to antiretroviral drugs and, therefore, in making clinical decisions regarding antiretroviral therapy.

Published
2016

32. Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buvé, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Hervé, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Kirtley, Shona, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2020
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33. Community-based antiretroviral therapy versus standard clinic-based services for HIV in South Africa and Uganda (DO ART): a randomised trial

Author

Barnabas, Ruanne V, Szpiro, Adam A, van Rooyen, Heidi, Asiimwe, Stephen, Pillay, Deenan, Ware, Norma C, Schaafsma, Torin T, Krows, Meighan L, van Heerden, Alastair, Joseph, Philip, Shahmanesh, Maryam, Wyatt, Monique A, Sausi, Kombi, Turyamureeba, Bosco, Sithole, Nsika, Morrison, Susan, Shapiro, Adrienne E, Roberts, D Allen, Thomas, Katherine K, Koole, Olivier, Bershteyn, Anna, Ehrenkranz, Peter, Baeten, Jared M, and Celum, Connie

Published
2020
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34. HIV transmission dynamics and populationwide drug resistance in rural South Africa.

Author

Kemp, Steven A., Kamelian, Kimia, Cuadros, Diego F., Cheng, Mark T. K., Okango, Elphas, Hanekom, Willem, Ndung’u, Thumbi, Pillay, Deenan, Bonsall, David, Wong, Emily B., Tanser, Frank, Siedner, Mark J., and Gupta, Ravindra K.

Abstract

Despite expanded antiretroviral therapy (ART) in South Africa, HIV-1 transmission persists. Integrase strand transfer inhibitors (INSTI) and long-acting injectables offer potential for superior viral suppression, but pre-existing drug resistance could threaten their effectiveness. In a community-based study in rural KwaZulu-Natal, prior to widespread INSTI usage, we enroled 18,025 individuals to characterise HIV-1 drug resistance and transmission networks to inform public health strategies. HIV testing and reflex viral load quantification were performed, with deep sequencing (20% variant threshold) used to detect resistance mutations. Phylogenetic and geospatial analyses characterised transmission clusters. One-third of participants were HIV-positive, with 21.7% having detectable viral loads; 62.1% of those with detectable viral loads were ART-naïve. Resistance to older reverse transcriptase (RT)-targeting drugs was found, but INSTI resistance remained low (<1%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, particularly to rilpivirine (RPV) even in ART-naïve individuals, was concerning. Twenty percent of sequenced individuals belonged to transmission clusters, with geographic analysis highlighting higher clustering in peripheral and rural areas. Our findings suggest promise for INSTI-based strategies in this setting but underscore the need for RPV resistance screening before implementing long-acting cabotegravir (CAB) + RPV. The significant clustering emphasises the importance of geographically targeted interventions to effectively curb HIV-1 transmission. [ABSTRACT FROM AUTHOR]

Published
2024
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37. Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Author

Ayles, Helen, Bowden, Rory, Calvez, Vincent, Cohen, Myron, Dennis, Anne, Essex, Max, Fidler, Sarah, Frampton, Dan, Hayes, Richard, Herbeck, Josh, Kaleebu, Pontiano, Kityo, Cissy, Lingappa, Jairam, Novitsky, Vladimir, Paton, Nick, Rambaut, Andrew, Seeley, Janet, Ssemwanga, Deogratius, Tanser, Frank, Lutalo, Tom, Galiwango, Ronald, Makumbi, Fred, Sewankambo, Nelson K., Nabukalu, Dorean, Ndyanabo, Anthony, Ssekasanvu, Joseph, Nakawooya, Hadijja, Nakukumba, Jessica, Kigozi, Grace N., Nantume, Betty S., Resty, Nampijja, Kambasu, Jedidah, Nalugemwa, Margaret, Nakabuye, Regina, Ssebanobe, Lawrence, Nankinga, Justine, Kayiira, Adrian, Nanfuka, Gorreth, Ahimbisibwe, Ruth, Tomusange, Stephen, Galiwango, Ronald M., Nakalanzi, Margaret, Otobi, Joseph O., Ankunda, Denis, Ssembatya, Joseph L., Ssemanda, John B., Kato, Emmanuel, Kairania, Robert, Kisakye, Alice, Batte, James, Ludigo, James, Nampijja, Abisagi, Watya, Steven, Nehemia, Kighoma, Anyokot, Sr. Margaret, Mwinike, Joshua, Kibumba, George, Ssebowa, Paschal, Mondo, George, Wasswa, Francis, Nantongo, Agnes, Kakembo, Rebecca, Galiwango, Josephine, Ssemango, Geoffrey, Redd, Andrew D., Santelli, John, Kennedy, Caitlin E., Wagman, Jennifer, Tobian, Aaron, Ratmann, Oliver, Kagaayi, Joseph, Hall, Matthew, Golubchick, Tanya, Kigozi, Godfrey, Xi, Xiaoyue, Wymant, Chris, Nakigozi, Gertrude, Abeler-Dörner, Lucie, Bonsall, David, Gall, Astrid, Hoppe, Anne, Kellam, Paul, Bazaale, Jeremiah, Kalibbala, Sarah, Laeyendecker, Oliver, Lessler, Justin, Nalugoda, Fred, Chang, Larry W, de Oliveira, Tulio, Pillay, Deenan, Quinn, Thomas C, Reynolds, Steven J, Spencer, Simon E F, Ssekubugu, Robert, Serwadda, David, Wawer, Maria J, Gray, Ronald H, Fraser, Christophe, and Grabowski, M Kate

Published
2020
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38. Updated assessment of risks and benefits of dolutegravir versus efavirenz in new antiretroviral treatment initiators in sub-Saharan Africa: modelling to inform treatment guidelines

Author

Phillips, Andrew N, Bansi-Matharu, Loveleen, Venter, Francois, Havlir, Diane, Pozniak, Anton, Kuritzkes, Daniel R, Wensing, Annemarie, Lundgren, Jens D, Pillay, Deenan, Mellors, John, Cambiano, Valentina, Jahn, Andreas, Apollo, Tsitsi, Mugurungi, Owen, Ripin, David, Da Silva, Juliana, Raizes, Elliot, Ford, Nathan, Siberry, George K, Gupta, Ravindra K, Barnabas, Ruanne, Revill, Paul, Cohn, Jennifer, Calmy, Alexandra, and Bertagnolio, Silvia

Published
2020
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39. Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study

Author

Hall, Matthew, primary, Golubchik, Tanya, additional, Bonsall, David, additional, Abeler-Dörner, Lucie, additional, Limbada, Mohammed, additional, Kosloff, Barry, additional, Schaap, Ab, additional, de Cesare, Mariateresa, additional, MacIntyre-Cockett, George, additional, Otecko, Newton, additional, Probert, William, additional, Ratmann, Oliver, additional, Bulas Cruz, Ana, additional, Piwowar-Manning, Estelle, additional, Burns, David N, additional, Cohen, Myron S, additional, Donnell, Deborah J, additional, Eshleman, Susan H, additional, Simwinga, Musonda, additional, Fidler, Sarah, additional, Hayes, Richard, additional, Ayles, Helen, additional, Fraser, Christophe, additional, Agyei, Yaw, additional, Beyers, Nulda, additional, Bock, Peter, additional, Bond, Virginia, additional, Bwalya, Justin, additional, Cori, Anne, additional, Deventer, Anneen, additional, Dunbar, Rory, additional, El-Sadr, Wafaa, additional, Emel, Lynda, additional, Floyd, Sian, additional, Griffith, Sam, additional, Hargreaves, James, additional, Hauck, Katharina, additional, Headen, Tanette, additional, Hoddinott, Graeme, additional, James, Anelet, additional, Jennings, Karen, additional, Kanema, Sarah, additional, Kruger, James, additional, Kumar, Ramya, additional, Macleod, David, additional, Makola, Nozizwe, additional, Mandla, Nomtha, additional, Miller, Eric, additional, Moore, Ayana, additional, Mwenge, Lawrence, additional, Noble, Heather, additional, Phiri, Mwelwa, additional, Pickles, Michael, additional, Sabapathy, Kalpana, additional, Sakala, Ephraim, additional, Sauter, Rafael, additional, Shanaube, Kwame, additional, Silumesi, Andrew, additional, Sista, Nirupama, additional, Skalland, Tim, additional, Smith, Peter, additional, Thomas, Ranjeeta, additional, Vermund, Sten, additional, White, Rhonda, additional, Wilson, Ethan, additional, Yang, Blia, additional, Yuhas, Krista, additional, Bowden, Rory, additional, Calvez, Vincent, additional, Essex, Max, additional, Grabowski, Kate, additional, Gupta, Ravindra, additional, Herbeck, Joshua, additional, Kagaayi, Joseph, additional, Kaleebu, Pontiano, additional, Lingappa, Jairam, additional, Moyo, Sikhulile, additional, Novitsky, Vladimir, additional, Ndung’u, Thumbi, additional, Pillay, Deenan, additional, Quinn, Thomas, additional, Rambaut, Andrew, additional, Seeley, Janet, additional, Ssemwanga, Deogratius, additional, Tanser, Frank, additional, and Wawer, Maria, additional

Published
2023
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40. HIV transmission dynamics and population-wide drug resistance in rural South Africa

Author

Gupta, Ravindra, primary, Kemp, Steven, additional, Kamelian, Kimia, additional, Cuadros, Diego, additional, Gupta, Ravindra, additional, Cheng, Mark, additional, Okango, Elphas, additional, Hanekom, Willem, additional, Ndung’u, Thumbi, additional, Pillay, Deenan, additional, Bonsall, David, additional, Wong, Emily, additional, Tanser, Frank, additional, and Siedner, Mark, additional

Published
2023
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41. 1498. Geographic differences in weight change on dolutegravir: a prospective cohort study

Author

Chen, Geoffrey, primary, Migisha, Richard, additional, Muyindike, Winnie R, additional, Aung, Taing N, additional, Nanfuka, Victoria, additional, Komukama, Nimusiima, additional, Chandiwana, Nomathemba, additional, Shazi, Gugulethu, additional, Moosa, Mahomed-Yunus S, additional, Gupta, Ravindra K, additional, Pillay, Deenan, additional, Marconi, Vincent, additional, Hedt-Gauthier, Bethany, additional, Francois Venter, W D, additional, Siedner, Mark J, additional, McCluskey, Suzanne M, additional, and Manne-Goehler, Jennifer, additional

Published
2023
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42. 2015 Update of the Drug Resistance Mutations in HIV-1.

Author

Wensing, Annemarie M, Calvez, Vincent, Günthard, Huldrych F, Johnson, Victoria A, Paredes, Roger, Pillay, Deenan, Shafer, Robert W, and Richman, Douglas D

Subjects
Humans, HIV-1, Anti-HIV Agents, Drug Resistance, Viral, Mutation, United States, Drug Resistance, Viral
Abstract

The 2015 edition of the IAS-USA drug resistance mutations list updates the figures last published in July 2014. The mutations listed are those that have been identified by specific criteria for evidence and drugs described. The figures are designed to assist practitioners in identifying key mutations associated with resistance to antiretroviral drugs and, therefore, in making clinical decisions regarding antiretroviral therapy.

Published
2015

44. Temporal trends of population viral suppression in the context of Universal Test and Treat: the ANRS 12249 TasP trial in rural South Africa

Author

Larmarange, Joseph, Diallo, Mamadou H., Mcgrath, Nuala, Iwuji, Collins, Plazy, Melanie, Thiebaut, Rodolphe, Tanser, Frank, Barnighausen, Till, Orne-Gliemann, Joanna, Pillay, Deenan, and Dabis, Francois

Subjects
Highly active antiretroviral therapy -- Analysis, HIV -- Analysis, Antiretroviral agents -- Analysis, Health
Abstract

Introduction: The universal test-and-treat (UTT) strategy aims to maximize population viral suppression (PVS), that is, the proportion of all people living with HIV (PLHIV) on antiretroviral treatment (ART) and virally suppressed, with the goal of reducing HIV transmission at the population level. This article explores the extent to which temporal changes in PVS explain the observed lack of association between universal treatment and cumulative HIV incidence seen in the ANRS 12249 TasP trial conducted in rural South Africa. Methods: The TasP cluster-randomized trial (2012 to 2016) implemented six-monthly repeat home-based HIV counselling and testing (RHBCT) and referral of PLHIV to local HIV clinics in 2 x 11 clusters opened sequentially. ART was initiated according to national guidelines in control clusters and regardless of CD4 count in intervention clusters. We measured residency status, HIV status, and HIV care status for each participant on a daily basis. PVS was computed per cluster among all resident PLHIV ([greater than or equal to]16, including those not in care) at cluster opening and daily thereafter. We used a mixed linear model to explore time patterns in PVS, adjusting for sociodemographic changes at the cluster level. Results: 8563 PLHIV were followed. During the course of the trial, PVS increased significantly in both arms (23.5% to 46.2% in intervention, +22.8, p < 0.001; 26.0% to 44.6% in control, +18.6, p < 0.001). That increase was similar in both arms (p = 0.514). In the final adjusted model, PVS increase was most associated with increased RHBCT and the implementation of oca trial clinics (measured by time since cluster opening). Contextual changes (measured by calendar time) also contributed slightly. The effect of universal ART (trial arm) was positive but limited. Conclusions: PVS was improved significantly but similarly in both trial arms, explaining partly the null effect observed in terms of cumulative HIV incidence between arms. The PVS gains due to changes in ART-initiation guidelines alone are relatively small compared to gains obtained by strategies to maximize testing and linkage to care. The achievement of the 90-90-90 targets will not be met if the operational and implementational challenges limiting access to care and treatment, often context-specific, are not properly addressed. Clinical trial number: NCT01509508 (clinicalTrials.gov)/DOH-27-0512-3974 (South African National Clinical Trials Register). Keywords: HIV; antiretroviral therapy; sustained viral suppression; retention in care; population health; South Africa, 1 | INTRODUCTION Antiretroviral treatment (ART), when taken early has several benefits, both in terms of morbidity and mortality [1,2] and in terms of reduction in HIV sexual transmission [3]. [...]

Published
2019
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45. Digital technologies in the public-health response to COVID-19

Author

Budd, Jobie, Miller, Benjamin S., Manning, Erin M., Lampos, Vasileios, Zhuang, Mengdie, Edelstein, Michael, Rees, Geraint, Emery, Vincent C., Stevens, Molly M., Keegan, Neil, Short, Michael J., Pillay, Deenan, Manley, Ed, Cox, Ingemar J., Heymann, David, Johnson, Anne M., and McKendry, Rachel A.

Published
2020
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46. Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000–2016: A Pooled Sequence Analysis

Author

Chimukangara, Benjamin, Lessells, Richard J., Rhee, Soo-Yon, Giandhari, Jennifer, Kharsany, Ayesha B.M., Naidoo, Kogieleum, Lewis, Lara, Cawood, Cherie, Khanyile, David, Ayalew, Kassahun A., Diallo, Karidia, Samuel, Reshmi, Hunt, Gillian, Vandormael, Alain, Stray-Pedersen, Babill, Gordon, Michelle, Makadzange, Tariro, Kiepiela, Photini, Ramjee, Gita, Ledwaba, Johanna, Kalimashe, Monalisa, Morris, Lynn, Parikh, Urvi M., Mellors, John W., Shafer, Robert W., Katzenstein, David, Moodley, Pravi, Gupta, Ravindra K., Pillay, Deenan, Abdool Karim, Salim S., and de Oliveira, Tulio

Published
2019
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47. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2019
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48. Ethical considerations in global HIV phylogenetic research

Author

Amon, Joseph J., Baggaley, Rachel, Bernard, Edwin J., Burns, David, Cohen, Myron S., Coltart, Cordelia C., Dallabetta, Gina, Dawson, Liza, Dedes, Nikos, Delpech, Valerie, Eba, Patrick M., Fraser, Christophe, Geller, Gail, German, Danielle, Godfrey-Faussett, Peter, Grabowksi, M. Kate, Hall, Irene, Harling, Guy, Henderson, Gail, Hoppe, Anne, Kozlakidis, Zisis, Laeyendecker, Oliver, Mwanza, Felix, Novitsky, Vladimir, Parker, Michael, Pillay, Deenan, Reis, Andreas, Seeley, Janet, Simwanga, Musonda, Tucker, Joseph D., Vandamme, Anne-Mieke, Wertheim, Joel O., Zimmerman, Rick, Coltart, Cordelia E M, Amon, Joseph J, Simwinga, Musonda, Tucker, Joseph D, Eba, Patrick, Grabowski, M Kate, and Cohen, Myron S

Published
2018
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49. 2014 Update of the drug resistance mutations in HIV-1.

Author

Wensing, Annemarie M, Calvez, Vincent, Günthard, Huldrych F, Johnson, Victoria A, Paredes, Roger, Pillay, Deenan, Shafer, Robert W, and Richman, Douglas D

Subjects
Humans, HIV-1, HIV Infections, Anti-HIV Agents, Drug Resistance, Viral, Mutation, Missense, Point Mutation, Drug Resistance, Viral, Mutation, Missense
Abstract

This July 2014 edition of the IAS-USA drug resistance mutations list updates the figures last published in March 2013. The following mutations have been added to existing classes or drugs: K65E/N has been added to the bars for the nucleoside and nucleotide analogue reverse transcriptase inhibitors (nRTIs) abacavir, didanosine, emtricitabine, lamivudine, stavudine, and tenofovir; L100I has been added to the bar for the nonnucleoside analogue reverse transcriptase inhibitor (NNRTI) rilpivirine; and F121Y has been added to the bars for the integrase strand transfer inhibitors (InSTIs) dolutegravir, elvitegravir, and raltegravir. With regard to protease inhibitors (PIs), it cannot be excluded that drug resistance may be selected for outside the protease encoding region.

Published
2014

50. HIV, multimorbidity, and health-related quality of life in rural KwaZulu-Natal, South Africa: A population-based study.

Author

Stanton, Amelia M., Boyd, Ryan L., O'Cleirigh, Conall, Olivier, Stephen, Dolotina, Brett, Gunda, Resign, Koole, Olivier, Gareta, Dickman, Modise, Tshwaraganang H., Reynolds, Zahra, Khoza, Thandeka, Herbst, Kobus, Ndung'u, Thumbi, Hanekom, Willem A., Wong, Emily B., Pillay, Deenan, and Siedner, Mark J.

Subjects
QUALITY of life, MYCOBACTERIUM tuberculosis, COUNTRY life, RESOURCE-limited settings, COMORBIDITY, HIV, HYPERTENSION
Abstract

Health-related quality of life (HRQoL) assesses the perceived impact of health status across life domains. Although research has explored the relationship between specific conditions, including HIV, and HRQoL in low-resource settings, less attention has been paid to the association between multimorbidity and HRQoL. In a secondary analysis of cross-sectional data from the Vukuzazi ("Wake up and know ourselves" in isiZulu) study, which identified the prevalence and overlap of non-communicable and infectious diseases in the uMkhanyakunde district of KwaZulu-Natal, we (1) evaluated the impact of multimorbidity on HRQoL; (2) determined the relative associations among infectious diseases, non-communicable diseases (NCDs), and HRQoL; and (3) examined the effects of controlled versus non-controlled disease on HRQoL. HRQoL was measured using the EQ-5D-3L, which assesses overall perceived health, five specific domains (mobility, self-care, usual activities, pain/discomfort, and anxiety/depression), and three levels of problems (no problems, some problems, and extreme problems). Six diseases and disease states were included in this analysis: HIV, diabetes, stroke, heart attack, high blood pressure, and TB. After examining the degree to which number of conditions affects HRQoL, we estimated the effect of joint associations among combinations of diseases, each HRQoL domain, and overall health. Then, in one set of ridge regression models, we assessed the relative impact of HIV, diabetes, stroke, heart attack, high blood pressure, and tuberculosis on the HRQoL domains; in a second set of models, the contribution of treatment (controlled vs. uncontrolled disease) was added. A total of 14,008 individuals were included in this analysis. Having more conditions adversely affected perceived health (r = -0.060, p<0.001, 95% CI: -0.073 to -0.046) and all HRQoL domains. Infectious conditions were related to better perceived health (r = 0.051, p<0.001, 95% CI: 0.037 to 0.064) and better HRQoL, whereas non-communicable diseases (NCDs) were associated with worse perceived health (r = -0.124, p<0.001, -95% CI: 0.137 to -0.110) and lower HRQoL. Particular combinations of NCDs were detrimental to perceived health, whereas HIV, which was characterized by access to care and suppressed viral load in the large majority of those affected, was counterintuitively associated with better perceived health. With respect to disease control, unique combinations of uncontrolled NCDs were significantly related to worse perceived health, and controlled HIV was associated with better perceived health. The presence of controlled and uncontrolled NCDs was associated with poor perceived health and worse HRQoL, whereas the presence of controlled HIV was associated with improved HRQoL. HIV disease control may be critical for HRQoL among people with HIV, and incorporating NCD prevention and attention to multimorbidity into healthcare strategies may improve HRQoL. [ABSTRACT FROM AUTHOR]

Published
2024
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