Scientific Publications

Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression
Aguiar VRC, Castelli EC, Single RM, Bashirova A, Ramsuran V, Kulkarni S, Augusto DG, Martin MP, Gutierrez-Arcelus M, Carrington M, Meyer D.
Immunogenetics

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Ancestral Origin and Dissemination Dynamics of Reemerging Toxigenic Vibrio cholerae, Haiti
Mavian CN, Tagliamonte MS, Alam MT, Sakib SN, Cash MN, Moir M, Jimenez JP, Riva A, Nelson EJ, Cato ET, Ajayakumar J, Louis R, Curtis A, De Rochars VMB, Rouzier V, Pape JW, de Oliveira T, Morris JG Jr, Salemi M, Ali A
Emerging Infectious Diseases

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Prevalence and incidence of sexually transmitted infections among South African women initiating injectable and long-acting contraceptives
Harryparsad R, Meyer B, Taku O, Serrano M, Chen PL, Gao X, Williamson AL, Mehou-Loko C, d'Hellencourt FL, Smit J, Strauss J, Nanda K, Ahmed K, Beksinska M, Buck G, Morrison C, Deese J, Masson L
PLoS One

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Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population
Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ
Journal of Virology

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The association of host genes with specific sexually transmitted infections
Bovungana Q, Arumugam T, Ramsuran V
Frontiers in Reproductive Health

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HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d'Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos RD
Lancet HIV

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Ratios from full blood count as markers for TB diagnosis, treatment, prognosis: a systematic review
Fritschi N, Vaezipour N, Buettcher M, Portevin D, Naranbhai V, Ritz N
he International Journal of Tuberculosis and Lung Disease

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Doxycycline post-exposure prophylaxis for sexually transmitted infections in South Africa
Peters RPH, McIntyre JA, Garrett N, Brink AJ, Celum CL, Bekker LG
Southern African Journal of HIV Medicine

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Adherence to daily, oral TDF/FTC PrEP during periconception among HIV-exposed South African women
Hurwitz KE, Isehunwa OO, Hendrickson KR, Jaggernath M, Kriel Y, Smith PM, Mathenjwa M, Bennett K, Psaros C, Baeten JM, Bangsberg DR, Haberer JE, Smit JA, Matthews LT
Frontiers in Reproductive Health

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Bayesian spatial modelling of intimate partner violence and associated factors among adult women and men: evidence from 2019/2020 Rwanda Demographic and Health Survey
Maposa I, Twabi HS, Matsena-Zingoni Z, Batidzirai JM, Singini G, Mohammed M, Bere A, Kgarosi K, Mchunu N, Nevhungoni P, Moyo-Chilufya M, Ojifinni O, Musekiwa A
BMC Public Health

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Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol
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
Global Public Health

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Broadening access to tenofovir alafenamide for the treatment and prevention of HIV-1 infection.
Osuala EC, Naidoo A, Dooley KE, Naidoo K, Perumal R
Expert Review of Clinical Pharmacology

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Despite delayed kinetics, people living with HIV achieve equivalent antibody function after SARS-CoV-2 infection or vaccination
Motsoeneng BM, Manamela NP, Kaldine H, Kgagudi P, Hermanus T, Ayres F, Makhado Z, Moyo-Gwete T, van der Mescht MA, Abdullah F, Boswell MT, Ueckermann V, Rossouw TM, Madhi SA, Moore PL, Richardson SI
Frontiers in Immunology

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Diagnostic accuracy of a point-of-care urine tenofovir assay, and associations with HIV viraemia and drug resistance among people receiving dolutegravir and efavirenz-based antiretroviral therapy
Dorward J, Lessells R, Govender K, Moodley P, Samsunder N, Sookrajh Y, Turner P, Butler CC, Hayward G, Gandhi M, Drain PK, Garrett N
Journal of the International AIDS Society

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Clinical outcomes after extended 12-month antiretroviral therapy prescriptions in a community-based differentiated HIV service delivery programme in South Africa: a retrospective cohort study
Lewis L, Sookrajh Y, van der Molen J, Khubone T, Sosibo P, Maraj M, van Heerden R, Little F, Kassanjee R, Garrett N, Dorward J
Journal of the International AIDS Society

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Comparison of Antiretroviral Therapies in Pregnant Women Living With Human Immunodeficiency Virus and Hepatitis B Virus: A Randomized Controlled Trial
Bhattacharya D, Tierney C, Butler K, Kiweewa FM, Moodley D, Govender V, Vhembo T, Mohtashemi N, Ship H, Dula D, George K, Chaktoura N, Fowler MG, Peters MG, Currier JS
Obstetrics & Gynecology

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The met and unmet health needs for HIV, hypertension, and diabetes in rural KwaZulu-Natal, South Africa: analysis of a cross-sectional multimorbidity survey
Singh U, Olivier S, Cuadros D, Castle A, Moosa Y, Zulu T, Edwards JA, Kim HY, Gunda R, Koole O, Surujdeen A, Gareta D, Munatsi D, Modise TH, Dreyer J, Nxumalo S, Smit TK, Ordering-Jespersen G, Mpofana IB, Khan K, Sikhosana ZEL, Moodley S, Shen YJ, Khoza T, Mhlongo N, Bucibo S, Nyamande K, Baisley KJ, Grant AD, Herbst K, Seeley J, Pillay D, Hanekom W, Ndung'u T, Siedner MJ, Tanser F, Wong EB; Vukuzazi team
Lancet Global Health

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Post-trial access to and use of pre-exposure prophylaxis in Durban, South Africa
Beesham I, Milford C, Smit J, Joseph Davey DL, Baeten JM, Heffron R, Beksinska M, Mansoor LE
BMC Public Health

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Pharmacokinetic serum concentrations of VRC01 correlate with prevention of HIV-1 acquisition
Seaton KE, Huang Y, Karuna S, Heptinstall JR, Brackett C, Chiong K, Zhang L, Yates NL, Sampson M, Rudnicki E, Juraska M, deCamp AC, Edlefsen PT, Mullins JI, Williamson C, Rossenkhan R, Giorgi EE, Kenny A, Angier H, Randhawa A, Weiner JA, Rojas M, Sarzotti-Kelsoe M, Zhang L, Sawant S, Ackerman ME, McDermott AB, Mascola JR, Hural J, McElrath MJ, Andrew P, Hidalgo JA, Clark J, Laher F, Orrell C, Frank I, Gonzales P, Edupuganti S, Mgodi N, Corey L, Morris L, Montefiori D, Cohen MS, Gilbert PB, Tomaras GD
EBioMedicine

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Managing and assembling population-scale data streams, tools and workflows to plan for future pandemics within the INFORM-Africa Consortium
Poongavanan J, Xavier J, Dunaiski M, Tegally H, Oladejo SO, Ayorinde O, Wilkinson E, Baxter C, Oliveira TD
South African Journal of Science

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Long-acting antiretrovirals: research and implementation considerations in Africa
Norcross C, Ombajo LA, Kassim S, Garrett N, Cresswell FV, Ruzagira E
Lancet HIV

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Revealing human mobility trends during the SARS-CoV-2 pandemic in Nigeria via a data-driven approach
Luo W, Xiong C, Wan J, Feng Z, Ayorinde O, Blanco N, Charurat M, Naranbhai V, Riley C, Winters A, Murtala-Ibrahim F
South African Journal of Science

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Setting up data science research in Africa and engagement of stakeholders.
Murtala-Ibrahim F, Jumare J, Charurat M, Xiong C, Naranbhai V, Dakum P, Collie S, Jassat W, Aliyu G, Ifedayo A, Abimiku AL
South African Journal of Science

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Disclosure of HIV-serodiscordant relationships and association with viral suppression: results from the Positive Plus One study
Mendelsohn JB, Calzavara L, Bullock S, Iveniuk J, Tan DHS, Burchell AN, Bourne A, Lebouché B, Daftary A, Moravan V, Loutfy M, Conway B; Positive Plus One Study Team
AIDS Care

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High prevalence of vaccine-preventable anal human papillomavirus infections is associated with HIV infection among gay, bisexual, and men who have sex with men in Nairobi, Kenya
Oo MM, Moore S, Gibbons S, Adhiambo W, Muthoga P, Siele N, Akolo M, Gebrebrhan H, Sivro A, Ball BT, Lorway RR, Severini A, Kimani J, McKinnon LR
Cancer Medicine

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Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection
Ahuja SK, Manoharan MS, Lee GC, McKinnon LR, Meunier JA, Steri M, Harper N, Fiorillo E, Smith AM, Restrepo MI, Branum AP, Bottomley MJ, Orrù V, Jimenez F, Carrillo A, Pandranki L, Winter CA, Winter LA, Gaitan AA, Moreira AG, Walter EA, Silvestri G, King CL, Zheng YT, Zheng HY, Kimani J, Blake Ball T, Plummer FA, Fowke KR, Harden PN, Wood KJ, Ferris MT, Lund JM, Heise MT, Garrett N, Canady KR, Abdool Karim SS, Little SJ, Gianella S, Smith DM, Letendre S, Richman DD, Cucca F, Trinh H, Sanchez-Reilly S, Hecht JM, Cadena Zuluaga JA, Anzueto A, Pugh JA; South Texas Veterans Health Care System COVID-19 team; Agan BK, Root-Bernstein R, Clark RA, Okulicz JF, He W
Nature Communications

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Vaccine access, equity and justice: COVID-19 vaccines and vaccination
Privor-Dumm L, Excler JL, Gilbert S, Karim SS, Hotez PJ, Thompson D, Kim JH
BMJ Global Health

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Monocyte, Lymphocyte and Neutrophil Ratios - Easy-to-Use Biomarkers for the Diagnosis of Pediatric Tuberculosis
Kissling M, Fritschi N, Baumann P, Buettcher M, Bonhoeffer J, Naranbhai V, Ritz N; ProPAED and CITRUS study team
The Pediatric Infectious Disease Journal

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Delivery of Community-based Antiretroviral Therapy to Maintain Viral Suppression and Retention in Care in South Africa
Wang M, Violette LR, Dorward J, Ngobese H, Sookrajh Y, Bulo E, Quame-Amaglo J, Thomas KK, Garrett N, Drain PK
Journal of Acquired Immune Deficiency Syndromes

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Effect of the relationship between anaemia and systemic inflammation on the risk of incident tuberculosis and death in people with advanced HIV: a sub-analysis of the REMEMBER trial
Araújo-Pereira M, Krishnan S, Salgame P, Manabe YC, Hosseinipour MC, Bisson G, Severe DP, Rouzier V, Leong S, Mave V, Sawe FK, Siika AM, Kanyama C, Dadabhai SS, Lama JR, Valencia-Huamani J, Badal-Faesen S, Lalloo UG, Naidoo K, Mohapi L, Kityo C, Andrade BB and Gupta A
eClinicalMedicine

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The attributable fraction of respiratory syncytial virus among patients of different ages with influenza-like illness and severe acute respiratory illness in a high HIV prevalence setting, South Africa, 2012-2016
Moyes J, Tempia S, Walaza S, McMorrow ML, Cohen AL, Treurnicht F, Hellferscee O, Wolter N, Von Gottberg A, Dawood H, Variava E, Kahn K, Madhi SA, Cohen C
International Journal of Infectious Diseases

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Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer
Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF
Nature Genetics

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Antibody-dependent cellular cytotoxicity against SARS-CoV-2 Omicron sub-lineages is reduced in convalescent sera regardless of infecting variant
Richardson SI, Kgagudi P, Manamela NP, Kaldine H, Venter EM, Pillay T, Lambson BE, van der Mescht MA, Hermanus T, Balla SR, de Beer Z, de Villiers TR, Bodenstein A, van den Berg G, du Pisanie M, Burgers WA, Ntusi NAB, Abdullah F, Ueckermann V, Rossouw TM, Boswell MT, Moore PL
Cell Reports Medicine

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COVID-19 vaccine acceptability amongst South African pharmacists
Dhindayal S, Letsoalo MP, Gengiah TN
South African Pharmaceutical Journal

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Implementation and outcomes of dolutegravir-based first-line antiretroviral therapy for people with HIV in South Africa: a retrospective cohort study
Dorward J, Sookrajh Y, Khubone T, van der Molen J, Govender R, Phakathi S, Lewis L, Bottomley C, Maraj M, Lessells RJ, Naidoo K, Butler CC, Van Heerden R, Garrett N
Lancet HIV

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Incidence, recurrence, and prevalence of bacterial vaginosis from acute to chronic HIV infection in a prospective cohort of women in South Africa
Asare K, Ngcapu S, Osman F, Vandormael A, Mindel A, Naicker N, Khanyile M, S Abdool Karim S, Tomita A, Garrett N
Annals of Epidemiology

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SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants
Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP
Stem Cell Reports

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HIV acquisition prior to entry into formal sex work: inference from next-generation viral sequencing
Neufeld B, Cholette F, Sandstrom P, Musyoki H, Ma H, Kaosa S, Kioko J, Isac S, Bhattacharjee P, Cheuk E, Pickles M, Mwatelah R, Capiña R, Daniuk C, Mckinnon LR, Blanchard J, Mishra S, Becker M; Transitions Study Team
AIDS

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Long COVID: a review and proposed visualization of the complexity of long COVID
Perumal R, Shunmugam L, Naidoo K, Abdool Karim SS, Wilkins D, Garzino-Demo A, Brechot C, Parthasarathy S, Vahlne A, Nikolich JŽ
Frontiers in Immunology

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Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing
Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, Oliveira de T, Giandhari G.
Plos One

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Impact of Point-of-Care Testing on the Management of Sexually Transmitted Infections in South Africa: Evidence from the HVTN702 Human Immunodeficiency Virus Vaccine Trial.
Asare K, Andine T, Naicker N, Dorward J, Singh N, Spooner E, Andriesen J, Osman F, Ngcapu S, Vandormael A, Mindel A, Abdool Karim SS, Bekker LG, Gray G, Corey L, Tomita A, Garrett N.
Clinical Infectious Diseases

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A systematic review of risk factors for mortality among tuberculosis patients in South Africa
Nicholson TJ, Hoddinott G, Seddon JA, Claassens MM, van der Zalm MM, Lopez E, Bock P, Caldwell J, Da Costa D, de Vaal C, Dunbar R, Du Preez K, Hesseling AC, Joseph K, Kriel E, Loveday M, Marx FM, Meehan SA, Purchase S, Naidoo K, Naidoo L, Solomon-Da Costa F, Sloot R, Osman M.
Systematic Reviews

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Correlates of Dapivirine Vaginal Ring Acceptance among Women Participating in an Open Label Extension Trial
Mirembe BG, Cabrera MV, van der Straten A, Nakalega R, Cobbing M, Mgodi NM, Palanee-Phillips T, Mayo AJ, Dadabhai S, Mansoor LE, Siva S, Nair G, Chinula L, Akello CA, Nakabiito C, Soto-Torres LE, Baeten JM, Brown ER
AIDS and Behavior

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Slow progression of pediatric HIV associates with early CD8+ T cell PD-1 expression and a stem-like phenotype.
Vieira V, Lim N, Singh A, Leitman E, Dsouza R, Adland E, Muenchhoff M, Roider J, Marin Lopez M, Carabelli J, Giandhari J, Groll A, Jooste P, Prado JG, Thobakgale C, Dong K, Kiepiela P, Prendergast AJ, Tudor-Williams G, Frater J, Walker BD, Ndung'u T, Ramsuran V, Leslie A, Kløverpris HN, Goulder P.
JCI Insight.

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Clinical outcomes after extended 12-month antiretroviral therapy prescriptions in a community-based differentiated HIV service delivery programme in South Africa: a retrospective cohort study
Lewis L, Sookrajh Y, van der Molen J, Khubone T, Sosibo P, Maraj M, van Heerden R, Little F, Kassanjee R, Garrett N, Dorward J.
Journal of the International AIDS Society

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Threatening the Global AIDS Response-Obstacles to PEPFAR's Reauthorization.
Abdool Karim SS, Barre-Sinoussi F, Varmus HE, Serwadda D, Bukusi E, M'boup S, Kamarulzaman A, Swaminathan S, Pape JW.
New England Journal of Medicine

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High prevalence of vaccine-preventable anal human papillomavirus infections is associated with HIV infection among gay, bisexual, and men who have sex with men in Nairobi, Kenya.
Oo MM, Moore S, Gibbons S, Adhiambo W, Muthoga P, Siele N, Akolo M, Gebrebrhan H, Sivro A, Ball BT, Lorway RR, Severini A, Kimani J, McKinnon LR.
Cancer Medicine

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Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection
Ahuja SK, Manoharan MS, Lee GC, McKinnon LR, Meunier JA, Steri M, Harper N, Fiorillo E, Smith AM, Restrepo MI, Branum AP, Bottomley MJ, Orrù V, Jimenez F, Carrillo A, Pandranki L, Winter CA, Winter LA, Gaitan AA, Moreira AG, Walter EA, Silvestri G, King CL, Zheng YT, Zheng HY, Kimani J, Blake Ball T, Plummer FA, Fowke KR, Harden PN, Wood KJ, Ferris MT, Lund JM, Heise MT, Garrett N, Canady KR, Abdool Karim SS, Little SJ, Gianella S, Smith DM, Letendre S, Richman DD, Cucca F, Trinh H, Sanchez-Reilly S, Hecht JM, Cadena Zuluaga JA, Anzueto A, Pugh JA; South Texas Veterans Health Care System COVID-19 team; Agan BK, Root-Bernstein R, Clark RA, Okulicz JF, He W
Nature Communications

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Metformin Increases Cell Viability and Regulates Pro-Inflammatory Response to Mtb. Infect Drug Resist
Naicker N, Rodel H, Perumal R, Ganga Y, Bernstein M, Benede N, Abdool Karim S, Padayatchi N, Sigal A, Naidoo K.
Infectious Drig Resistance

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Nonoptimal bacteria species induce neutrophil-driven inflammation and barrier disruption in the female genital tract.
Costa-Fujishima M, Yazdanpanah A, Horne S, Lamont A, Lopez P, Farr Zuend C, Birse K, Taverner M, Greenslade R, Abou M, Noel-Romas L, Abrenica B, Ajibola O, Ikeogu N, Su RC, McKinnon LR, Pymar H, Poliquin V, Berard AR, Burgener AD, Murooka TT.
Mucosal Immunology

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Blood monocyte and dendritic cell profiles among people living with HIV with Mycobacterium tuberculosis co-infection
Rambaran S, Maseko TG, Lewis L, Hassan-Moosa R, Archary D, Ngcapu S, Garrett N, McKinnon LR, Padayatchi N, Naidoo K, Sivro A
BMC Immunology

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Performance of rapid antigen tests in identifying Omicron BA.4 and BA.5 infections in South Africa
Samsunder N, Lustig G, de Vos M, Ngcapu S, Giandhari J, Tshiabuila D, San EJ, Lewis L, Kharsany AB, Cawood C, de Oliveira T, Abdool Karim Q, Abdool Karim S, Escadafal C, Naidoo K, Sivro A.
Journal of Clinical Virology.2023

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Field evaluations of four SARS-CoV-2 rapid antigen tests during SARS-CoV-2 Delta variant wave in South Africa.
Samsunder N, Lustig G, Ngubane S, Maseko TG, Rambaran S, Ngcapu S, Magini SN, Lewis L, Cawood C, Kharsany ABM, Abdool Karim Q, Abdool Karim S, Naidoo K, Sivro A.
Diagnostic and Prognostic Research.20237(1):14.doi:10.1186/s41512-023-00151-3.

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Biological mechanisms underpinning the development of long COVID
Perumal R, Shunmugam L, Naidoo K, Wilkins D, Garzino-Demo A, Brechot C, Vahlne A, Nikolich J
iScience. 2023;26(6):106935. doi: 10.1016/j.isci.2023.106935

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Perceptions of women enrolled in a cardiovascular disease screening and prevention in HIV study
Hanley S, Ndlazi GJ, Maddocks ST, Chetty V
South African Family Practice (2004). 2023;65(1):e1-e9.

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Long COVID: a review and proposed visualization of the complexity of long COVID
Perumal R, Shunmugam L, Naidoo K, Abdool Karim SS, Wilkins D, Garzino-Demo A, Brechot C, Parthasarathy S, Vahlne A, Nikolich JŽ.
Frontiers in Immunology. 2023;14:1117464.

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Impact of Point-of-Care Testing on the Management of Sexually Transmitted Infections in South Africa: Evidence from the HVTN702 Human Immunodeficiency Virus Vaccine Trial
Asare K, Andine T, Naicker N, Dorward J, Singh N, Spooner E, Andriesen J, Osman F, Ngcapu S, Vandormael A, Mindel A, Abdool Karim SS, Bekker LG, Gray G, Corey L, Tomita A, Garrett N
Clinical Infectious Diseases. 2023 4;76(5):881-889

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Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry?
Khan A, Pillay M, Chimukangara B, Gounder L, Manyana S, Francois KL, Chipango K
Journal of Clinical Virology Plus 2023 3(2): 100141

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Mycobacterium tuberculosis Intra-Host Evolution Among Drug-Resistant Tuberculosis Patients Failing Treatment
Perumal R, Khan A, Naidoo K, Ngema SL, Nandlal L, Padayatchi N, Dookie N
Infection and Drug Resistance. 2023;16:2849-2859

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The burden of RSV-associated illness in children aged < 5 years, South Africa, 2011 to 2016
Moyes J, Tempia S, Walaza S, McMorrow ML, Treurnicht F, Wolter N, von Gottberg A, Kahn K, Cohen AL, Dawood H, Variava E, Cohen C
BMC Medicine. 2023;21(1):139. doi: 10.1186/s12916-023-02853-3.

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Vascular thrombosis after single dose Ad26.COV2.S vaccine in healthcare workers in South Africa: open label, single arm, phase 3B study (Sisonke study)
Jacobson BF, Schapkaitz E, Takalani A, Rowji PF, Louw V, Opie J, Bekker LG, Garrett N, Goga A, Reddy T, Zuma NY, Sanne I, Seocharan I, Peter J, Robinson M, Collie S, Khan A, Takuva S, Gray G
BMJ Med. 2023;2(1):e000302. doi: 10.1136/ bmjmed-2022-000302.

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Intimate Partner Violence and Engagement in the HIV Care Continuum among Women in Sub-Saharan Africa: A Prospective Cohort Study
Roberts ST, van der Straten A, Rael CT, Gorbach PM, Palanee-Phillips T, Reddy K, Naidoo K, Dadabhai S, Chinula L, Gaffoor Z, Levy L, Balkus JE, Riddler SA
AIDS and Behavior 2023; 27(3):984-989.

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COVID-19 vaccines and the pandemic: lessons learnt for other neglected diseases and future threats
Hotez PJ, Gilbert S, Saville M, Privor-Dumm L, Abdool-Karim S, Thompson D, Excler JL, Kim JH
BMJ Global Health. 2023;8(6):e011883.

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Commit to the Global South
Abdool Karim Q
Science. 2023;380(6650):1091. doi: 10.1126/ science.adj1621.

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Nonoptimal bacteria species induce neutrophil-driven inflammation and barrier disruption in the female genital tract
Costa-Fujishima M, Yazdanpanah A, Horne S, Lamont A, Lopez P, Farr Zuend C, Birse K, Taverner M, Greenslade R, Abou M, Noel-Romas L, Abrenica B, Ajibola O, Ikeogu N, Su RC, McKinnon LR, et al.
Mucosal Immunol. 2023;16(3):341-356.

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Factors, enablers and challenges for COVID-19 vaccine development
Excler JL, Saville M, Privor-Dumm L, Gilbert S, Hotez PJ, Thompson D, Abdool-Karim S, Kim JH
BMJ Global Health. 2023;8(6):e011879.

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COVID-19 vaccines and the pandemic: lessons learnt for other neglected diseases and future threats
Hotez PJ, Gilbert S, Saville M, Privor-Dumm L, Abdool-Karim S, Thompson D, Excler JL, Kim JH
BMJ Global Health. 2023 Jun 1;8(6):e011883.

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Vaccine access, equity and justice: COVID-19 vaccines and vaccination
Privor-Dumm L, Excler JL, Gilbert S, Karim SS, Hotez PJ, Thompson D, Kim JH
BMJ Global Health. 2023;8(6):e011881.

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Delivery of Community-based Antiretroviral Therapy to Maintain Viral Suppression and Retention in Care in South Africa
Wang M, Violette LR, Dorward J, Ngobese H, Sookrajh Y, Bulo E, Quame-Amaglo J, Thomas KK, Garrett N, Drain PK
JAIDS Journal of Acquired Immune Deficiency Syndromes. 2023;93(2): 126-133

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Effect of the relationship between anaemia and systemic inflammation on the risk of incident tuberculosis and death in people with advanced HIV: a sub-analysis of the REMEMBER trial
Araújo-Pereira M, Krishnan S, Salgame P, Manabe YC, Hosseinipour MC, Bisson G, Severe DP, Rouzier V, Leong S, Mave V, Sawe FK, Siika AM, Kanyama C, Dadabhai SS, Lama JR, Valencia-Huamani J, Badal-Faesen S, Lalloo UG, Naidoo K, Mohapi L, Kityo C, Andrade BB and Gupta A
eClinicalMedicine. 2023;60:102030

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Dolutegravir once daily with rifampicin for HIV and tuberculosis
Naidoo A, Dooley KE
Lancet HIV. 2023:S2352-3018(23)00115-7

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Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer
Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, et al.
Nature Genetics. 2023;55(5):807-819.

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Antibody-dependent cellular cytotoxicity against SARS-CoV-2 Omicron sub-lineages is reduced in convalescent sera regardless of infecting variant
Richardson SI, Kgagudi P, Manamela NP, Kaldine H, Venter EM, Pillay T, Lambson BE, van der Mescht MA, Hermanus T, Balla SR, de Beer Z, de Villiers TR, Bodenstein A, van den Berg G, du Pisanie M, Burgers WA, Ntusi NAB, Abdullah F, Ueckermann V, Rossouw TM, Boswell MT, Moore PL
Cell Reports Medicine. 2023;4(1):100910

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COVID-19 vaccine acceptability amongst South African pharmacists
Dhindayal S, Letsoalo MP, Gengiah TN
South African Pharmaceutical Journal. 2023. 90(2):20-25

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Incidence, recurrence, and prevalence of bacterial vaginosis from acute to chronic HIV infection in a prospective cohort of women in South Africa
Asare K, Ngcapu S, Osman F, Vandormael A, Mindel A, Naicker N, Khanyile M, S Abdool Karim S, Tomita A, Garrett N
Annals of Epidemiology 2023;82:33-39

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HIV acquisition prior to entry into formal sex work: inference from next-generation viral sequencing
Neufeld B, Cholette F, Sandstrom P, Musyoki H, Ma H, Kaosa S, Kioko J, Isac S, Bhattacharjee P, Cheuk E, Pickles M, Mwatelah R, Capiña R, Daniuk C, Mckinnon LR, Blanchard J, Mishra S, Becker M; Transitions Study Team
AIDS. 2023;37(6):987-992

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Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression
Aguiar VRC, Castelli EC, Single RM, Bashirova A, Ramsuran V, Kulkarni S, Augusto DG, Martin MP, Gutierrez-Arcelus M, Carrington M, Meyer D
Immunogenetics. 2023;75(3):249-262.

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Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing
Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, Oliveira de T, Giandhari G
PloS One. 2023;18(4):e0283219.

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Therapeutic Failure and Acquired Bedaquiline and Delamanid Resistance in Treatment of Drug-Resistant TB
Millard J, Rimmer S, Nimmo C, O’Donnell M
Emerging Infectious Diseases. 2023;29(5):1081

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PEPFAR at 20 - A Game-Changing Impact on HIV in Africa
Nachega JB, Serwadda D, Abimiku A, Sikazwe I, Abdool Karim Q
NEJM, 2023 DOI: 10.1056/NEJMp2304600

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Nonoptimal bacteria species induce neutrophil-driven inflammation and barrier disruption in the female genital tract.
Costa-Fujishima M, Yazdanpanah A, Horne S, Lamont A, Lopez P, Farr Zuend C, Birse K, Taverner M, Greenslade R, Abou M, Noel-Romas L, Abrenica B, Ajibola O, Ikeogu N, Su RC, McKinnon LR, Pymar H, Poliquin V, Berard AR, Burgener AD, Murooka TT.
Mucosal Immunology

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Nonoptimal bacteria species induce neutrophil-driven inflammation and barrier disruption in the female genital tract.
Costa-Fujishima M, Yazdanpanah A, Horne S, Lamont A, Lopez P, Farr Zuend C, Birse K, Taverner M, Greenslade R, Abou M, Noel-Romas L, Abrenica B, Ajibola O, Ikeogu N, Su RC, McKinnon LR, Pymar H, Poliquin V, Berard AR, Burgener AD, Murooka TT
Mucosal Immunology

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HIV acquisition prior to entry into formal sex work: inference from next-generation viral sequencing
Neufeld B, Cholette F, Sandstrom P, Musyoki H, Ma H, Kaosa S, Kioko J, Isac S, Bhattacharjee P, Cheuk E, Pickles M, Mwatelah R, Capiña R, Daniuk C, Mckinnon LR, Blanchard J, Mishra S, Becker M; Transitions Study Team
AIDS

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Heterogeneity in COVID-19 infection among older persons in South Africa: Evidence from national surveillance data
Abdelatif N, Naidoo I, Dunn S, Mazinu M, Essack Z, Groenewald C, Maharaj P, Msomi N, Reddy T, Roberts B, Zuma K.
Front Public Health. 2023;11:1009309.

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Cervicovaginal Human Papillomavirus Genomes, Microbiota Composition and Cytokine Concentrations in South African Adolescents
Happel AU, Balle C, Havyarimana E, Brown B, Maust BS, Feng C, Yi BH, Gill K, Bekker LG, Passmore JS, Jaspan HB, Varsani A
Viruses. 2023 ;15(3):758

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Consequences of rpoB mutations missed by the GenoType MTBDRplus assay in a programmatic setting in South Africa
Mvelase NR, Cele LP, Singh R, Naidoo Y, Giandhari J, Wilkinson E, de Oliveira T, Swe-Han KS, Mlisana KP
Afr J Lab Med. 2023;12(1):1975.

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Integrating gender-based violence screening and support into the research clinic setting: experiences from an HIV prevention open-label extension trial in Sub-Saharan Africa
Garcia M, Roberts ST, Mayo AJ, Scheckter R, Mansoor LE, Palanee-Phillips T, Reddy K, Naidoo Y, Akello CA, Gaffoor Z, Siva S
AIDS and Behaviour. 2023 ;27(4):1277-86.

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Trends in Cases, Hospitalizations, and Mortality Related to the Omicron BA.4/BA.5 Subvariants in South Africa
Jassat W, Abdool Karim SS, Ozougwu L, Welch R, Mudara C, Masha M, Rousseau P, Wolmarans M, Selikow A, Govender N, Walaza S, von Gottberg A, Wolter N, Terrence Pisa P, Sanne I, Govender S, Blumberg L, Cohen C, Groome MJ; DATCOV Author Group
Clinical Infectious Diseases. 2023 ;76(8):1468-1475

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Whole-Genome Sequencing to Predict Antimicrobial Susceptibility Profiles in Neisseria gonorrhoeae
Bristow CC, Mortimer TD, Morris S, Grad YH, Soge OO, Wakatake E, Pascual R, Murphy SM, Fryling KE, Adamson PC, Dillon JA, Parmar NR, Le HHL, Van Le H, Ovalles Ureña RM, Mitchev N, Mlisana K, Wi T, Dickson SP, Klausner JD
J InfectiousDiseases. 2023 12;227(7):917-925.

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Key stakeholders’ perspectives on providing oral pre-exposure prophylaxis as HIV-prevention standard of care in clinical trials in South Africa
Beesham I, Milford C, Joseph Davey DL, Smit J, Mansoor LE, Beksinska M
African Journal of AIDS Research. 2023:1-9.

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Clinical impact of plasma concentrations of first-line antituberculosis drugs
Perumal R, Naidoo K, Naidoo A, Padayatchi N
SAMJ: South African Medical Journal. 2023;113(3):148-53.

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Safety and pharmacokinetics of escalating doses of neutralising monoclonal antibody CAP256V2LS administered with and without VRC07-523LS in HIV-negative women in South Africa (CAPRISA 012B): a phase 1, dose-escalation, randomised controlled trial
Mahomed S, Garrett N, Capparelli EV, Osman F, Mkhize NN, Harkoo I, Gengiah TN, Mansoor LE, Baxter C, Archary D, Yende-Zuma N, Samsunder N, Carlton K, Narpala S, McDermott AB, Doria-Rose NA, Moore PL, Morris L, Abdool Karim Q, Mascola JR, Abdool Karim SS
Lancet HIV. 2023;10(4):e230-e243.

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Advances in tuberculosis control during the past decade
Naidoo K, Perumal R
Lancent Respir Med 2023.doi:10.1016/S2213-2600(23)00090-5

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Implementation and outcomes of dolutegravir-based first-line antiretroviral therapy for people with HIV in South Africa: a retrospective cohort study
Dorward J, Sookrajh Y, Khubone T, van der Molen J, Govender R, Phakathi S, Lara Lewis L, Bottomley C, Maraj M, Lessells RJ, Naidoo K, Butler CC, Van Heerden R, Garrett N
Lancet HIV 2023; doi:10.1016/S2352-3018(23)00047-4

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Correlates of Dapivirine Vaginal Ring Acceptance among Women Participating in an Open Label Extension Trial
Mirembe BG, Cabrera MV, van der Straten A, Nakalega R, Cobbing M, Mgodi NM, Palanee-Phillips T, Mayo AJ, Dadabhai S, Mansoor LE, Siva S, Nair G, Chinula L, Akello CA, Nakabiito C, Soto-Torres LE, Baeten JM, Brown ER
AIDS and Behavior 2023;27(3):1030-1043

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Genome Sequences of Anelloviruses, a Genomovirus, Microviruses, Polyomaviruses, and an Unclassified Caudovirus Identified in Vaginal Secretions from South African Adolescents
Jimoh AO, Balle C, Brown B, Feng C, Havyarimana E, Konstantinus IN, Gill K, Bekker LG, Passmore JS, Jaspan HB, Varsani A, Happel AU
Microbiology Resource Announcements 2023; 12(1):e0114322.

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A systematic review of risk factors for mortality among tuberculosis patients in South Africa
Nicholson TJ, Hoddinott G, Seddon JA, Claassens MM, van der Zalm MM, Lopez E, Bock P, Caldwell J, Da Costa D, de Vaal C, Dunbar R, Du Preez K, Hesseling AC, Joseph K, Kriel E, Loveday M, Marx FM, Meehan SA, Purchase S, Naidoo K, Naidoo L, Solomon-Da Costa F, Sloot R, Osman M
Systematic Reviews. 2023;12(1):23

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Slow progression of pediatric HIV associates with early CD8+ T cell PD-1 expression and a stem-like phenotype
Vieira V, Lim N, Singh A, Leitman E, Dsouza R, Adland E, Muenchhoff M, Roider J, Marin Lopez M, Carabelli J, Giandhari J, Groll A, Jooste P, Prado JG, Thobakgale C, Dong K, Kiepiela P, Prendergast AJ, Tudor-Williams G, Frater J, Walker BD, Ndung'u T, Ramsuran V, Leslie A, Kløverpris HN, Goulder P
JCI Insight 2023; 8(3):e156049

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Durability of Vaccine-Induced and Natural Immunity Against COVID-19: A Narrative Review
Pooley N, Abdool Karim SS, Combadière B, Ooi EE, Harris RC, El Guerche Seblain C, Kisomi M, Shaikh N
Infectious Diseases and Therapy 2023; 12(2):367-387

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Shifting the power: scale-up of access to point-of-care and self-testing for sexually transmitted infections in low-income and middle-income settings
Khumalo F, Passmore JS, Manhanzva M, Meyer B, Duyver M, Lurie M, Tanko RF, Masson L
Current Opinion in Infectious Disease 2023; 36(1):49-56

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Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings
Manyana S, Pillay M, Gounder L, Khan A, Moodley P, Naidoo K, Chimukangara B
AIDS Research and Therapy 2023; 20(1):9

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Association between regular physical activity and the protective effect of vaccination against SARS-CoV-2 in a South African case-control study
Collie S, Saggers RT, Bandini R, Steenkamp L, Champion J, Gray G, Bekker LG, Goga A, Garrett N, Patricios J
British Journal of Sports Medicine 2023; 57(4):205-211

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Dapivirine ring HIV-1 prevention effectiveness for women engaged in vaginal and anal intercourse: insights from mathematical modeling
Peebles K, Brown ER, Hendrix CW, Palanee-Phillips T, van der Straten A, Harkoo I, Reddy K, Mirembe BG, Jeenarain N, Hillier SL, Baeten JM, Barnabas RV; MTN-020/ASPIRE study team
JAIDS 2023; 92(2):122-126

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Male partner opinions of the dapivirine vaginal ring used during an open-label extension HIV prevention trial in KwaZulu-Natal, South Africa
Morar NS, Mansoor LE, Naidoo K, Katz AW, Garcia M, Duma C, Precious Myeni NB, Tshbalala T, Naidoo S, Montgomery ET
JAIDS 2023; 92(2):127-133

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The impact of enteral feeding and therapeutic monitoring of rifampicin with dose-escalation in critically ill patients with tuberculosis
Perumal R, Naidoo K, Naidoo A, Letsoalo MP, Esmail A, Joubert I, Denti P, Wiesner L, Padayatchi N, Maartens G, Dheda K
International Journal of Infectious Diseases 2023; 126:174-180

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Gardnerella subgroup dominant microbiomes are associated with divergent cervicovaginal immune responses in a longitudinal cohort of Kenyan women
Shvartsman E, Perciani CT, Richmond MEI, Russell JNH, Tough RH, Vancuren SJ, Hill JE, Kavi-Icr, Jaoko W, McKinnon LR, Sandstrom PA, MacDonald KS
Frontiers in Immunology 2023;13:974195

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A cohort study of Post COVID-19 Condition across the Beta, Delta and Omicron waves in South Africa: 6-month follow up of hospitalised and non-hospitalised participants
Jassat W, Mudara C, Vika C, Welch R, Arendse T, Dryden M, Blumberg L, Mayet N, Tempia S, Parker A, Nel J, Perumal R, Groome MJ, Conradie F, Ndjeka N, Sigfrid L, Merson L, Cohen Ch.gov/pmc/articles/PMC9800016/
International Journal of Infectious Diseases 2023; 128:102-11116/

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Novavax NVX-COV2373 triggers neutralization of Omicron sub-lineages
Bhiman JN, Richardson SI, Lambson BE, Kgagudi P, Mzindle N, Kaldine H, Crowther C, Gray G, Bekker LG; Novavax trial clinical lead author group; Shinde V, Bennett C, Glenn GM, Madhi SA, Moore PL
Scientific Reports 2023;13(1):1222

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Association Between Human Immunodeficiency Virus Viremia and Compromised Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2 Beta Variant
Hwa SH, Snyman J, Bernstein M, Ganga Y, Cele S, Muema D, Tan CW, Khan K, Karim F, Hanekom W, Bernstein L, Kaufmann SHE, Wang LF, Ndung'u T, Sigal A
Journal of Infectious Diseases 2023; 227(2):211-220

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Efficacy and Action of the Dapivirine Vaginal Ring as Understood by Women Participating in an Open Label Extension Study
Naidoo K, Montgomery ET, Katz AW, Morgan G, Krishnaveni R, Lydia ST, Sarita N, Mansoor L
AIDS and Behavior 2023; 27(1):75-81

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Leveraging the HIV response to strengthen pandemic preparedness
Collins C, Isbell MT, Abdool Karim Q, Sohn AH, Beyrer C, Maleche A
PloS Global Public Health 2023; 3(1): e0001511

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Regimens for Drug-Resistant Tuberculosis
Perumal R, Nimmo C, O'Donnell M
New England Journal of Medicine 2023; 388(2):189

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Mechanistic model for booster doses effectiveness in healthy, cancer, and immunosuppressed patients infected with SARS-CoV-2
Voutouri C, Hardin CC, Naranbhai V, Nikmaneshi MR, Khandekar MJ, Gainor JF, Stylianopoulos T, Munn LL, Jain RK
PNAS 2023; 120(3):e2211132120.

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SARS-CoV-2 Africa dashboard for real-time COVID-19 information
Xavier JS, Moir M, Tegally H, Sitharam N, Abdool Karim W, San JE, Linhares J, Wilkinson E, Ascher DB, Baxter C, Pires DEV, de Oliveira T
Nature Microbiology 2023; 8(1):1-4

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Vaccine inequity and hesitancy persist-we must tackle both
Lazarus JV, Abdool Karim SS, Batista C, Rabin K, El-Mohandes A
BMJ 2023; 380:8

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Self-Reported Antiretroviral Adherence: Association with Maternal Viral Load Suppression in Postpartum Women Living with HIV-1 from Promoting Maternal and Infant Survival Everywhere (PROMISE), a Randomized Controlled Trial in Sub-Saharan Africa and India
Nevrekar N, Butler K, Shapiro DE, Atuhaire P, Taha TE, Makanani B, Chinula L, Owor M, Moodley D, Chipato T, McCarthy K, Flynn PM, Currier J, Fowler MG, Gupta A, Suryavanshi N
JAIDS 2023; 92(1):76-83.

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Diagnostic accuracy of the Alere Afinion AS100 point-of-care assay to screen for non-communicable diseases amongst people living with HIV
Bodley N, Dorward J, Naidoo J, Letsoalo M, Ramsaroop K, Sayed F, Sookrajh Y, Drain PK, Garrett N
JAIDS 2023; 92(1):e1-e3.

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