PUBLICATIONS SPOTLIGHT

PUBLICATIONS

Genomic Analysis of Pseudomonas aeruginosa Recovered From Surgical Site Infections From a Referral Hospital in Western Kenya Reveals Dominance of High?Risk Subtypes

Kindiki S, Kiprono S, Reva O, Nyongesa P, Mogoi N, Welch M, Sifuna A, International Journal of Microbiology (2026), 2026:3640494

Whole genome sequencing precision medicine strategy to shorten treatment for rifampicin-resistant tuberculosis (SMARTT): a pragmatic, randomised, single-blind phase 4 trial

Van Rie A, Conceição E, Ndebele F, Wells F, Paulse A, Mekonnen E, Ngarega M, Trang T, Bohlela S, Sibeko Z, Segwaba P, Verboven L, Heupink T, Fuertes M, Rennie V, Dippenaar A, Rigouts L, Setlhare L, Ogunbayo A, VanderSpoel Van Dyk A, Conradie F, Maartens G, Potgieter S, Black J, Fanampe B, Abrams S, Churchyard G, Warren R, Charalambous S, The Lancet Respiratory Medicine (2026), 14:521-532

Modernizing mageu fermentation through the use of defined Lactobacillaceae starter cultures with potential functional applications

Hartzenberg-Aeroe K, Kullin B, Passmore J, Happel A, Gamieldien H, Fagan-Endres M, Journal of Ethnic Foods (2026), 13:

Evaluation and estimation of epidemic trajectories for SARS-CoV-2 from clinical and wastewater data in Gauteng Province, South Africa

Mthombothi Z, Lison A, Els F, van Schalkwyk C, Danon L, Maree G, Bingham J, Gwala S, Mabasa V, Singh N, Phalane E, Macheke M, Rachida S, Ndlovu N, Sankar C, Maposa S, Yousif M, McCarthy K, O’Reilly K, PLOS Global Public Health (2026), 6:e0006424

Genotyping of Mycobacterium leprae in humans and six-banded armadillos suggests lack of inter-species transmission in Rio Grande do Norte, northeast Brazil

Ferreira J, Conceição E, Antunes J, Fontes A, Vasconcellos S, Souza e Guimarães R, Lisboa Nobre M, Glauce I, McIntosh D, Suffys P, Acta Tropica (2026), 280:108186

Andes Virus on a Cruise Ship, what it Tells us About the Global Pandemic Preparedness Agenda

Koopmans M, Brechot C, Bruzzone R, Diagne M, Drosten C, Eckerle I, Gallo R, Hayman D, Horby P, Hotez P, de Jong M, Krammer F, Manuguerra J, Palacios G, Palmarini M, Schreijer A, Tischler N, de Oliveira T, Oude Munnink B, Peiris M, Thomson E, Vapalahti O, Venter M, Weyer J, Yazdanpanah Y, Karlsson E, The Lancet Regional Health - Europe (2026), 66:101755

Cervicovaginal inflammation and HIV target cell activation in adolescent girls and young women with Chlamydia trachomatis infections

Dabee S, Barnabas S, Kullin B, Versteeg B, Mkhize N, Muller E, Maseko V, Lewis D, Dietrich J, Gray G, Gill K, Bekker L, Sinkala M, Martin D, Bruisten S, Jaspan H, Passmore J, Sexually Transmitted Infections (2026), :sextrans-2025-056900

One Health Genomic Surveillance at Human–Animal Interfaces in Rural Ghana Reveals Underreported Viruses of Zoonotic and Economic Concern

Paoli J, Trovão N, Odoom T, Mohktar Q, Buabeng K, Adu B, Tasiame W, Anderson B, Tawiah-Yingar D, Subramaniam K, von Fricken M, Mensah G, Mietzsch M, McKenna R, Johnson S, Mavian C, Viruses (2026), 18:644

Draft genome sequence of Legionella pneumophila strains isolated from engineered water systems in Brazil

de Melo Ferrari D, Machado E, Conceição E, Sharma A, Lima S, Lima K, Teixeira R, Magdinier Gomes H, Suffys P, Microbiology Resource Announcements (2026), 15:e0133225

Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing

Conceicao E, Haffejee M, Wells F, Mann B, Heupink T, Paulse A, Williams J, Dippenaar A, Ghebrekristos Y, Burger M, Rennie V, de Diego Fuertes M, Al-Talib I, Ismail N, Grobbelaar M, Streicher E, de Oliveira T, Van der Spuy G, Van Rie A, Warren R, BMC Genomics (2026), :

Ebola outbreak caused by Bundibugyo virus: challenges and priorities for epidemic preparedness and response

Nachega J, Mbala-Kingebeni P, Mulangu S, Ndembi N, Preiser W, Skinner D, Sam-Agudu N, Ntoumi F, Tegally H, Baxter C, de Oliveira T, Bosa H, Kaleebu P, Kallay O, Uthman O, Mills E, Rosenthal P, Zumla A, Muyembe-Tamfum J, The Lancet (2026), :

Targeted and whole-genome sequencing for drug resistance and genetic relatedness inference of rifampicin-resistant Mycobacterium tuberculosis: an in-depth comparison

de Diego Fuertes M, Costa Conceição E, Wells F, Rennie V, Heupink T, Churchyard G, Ndebele F, Van der Spoel Van Dijk A, Fanampe B, Charalombous S, Ayodeji Ogunbayo E, Quispe Rojas W, Warren R, Van Rie A, Dippenaar A, ERJ Open Research (2026), 12:00630-2025

Dynamics and ecology of a multistage expansion of Oropouche virus in Brazil

Tegally H, Dellicour S, Poongavanan J, Mavian C, Dor G, Fonseca V, Tagliamonte M, Dunaiski M, Moir M, Wilkinson E, Campelo de Albuquerque C, Frutuoso L, Holmes E, Baxter C, Lessells R, Kraemer M, Lourenço J, Alcantara L, de Oliveira T, Giovanetti M on behalf of CLIMADE, Nature Ecology & Evolution (2026), :

Antibiotic dispensing practices and antimicrobial stewardship gaps in community pharmacies in Kakamega County, Kenya

Turnbull-Jones E, Langtree S, Mogoi N, Sifuna A, Gadaffi L, Jewell T, (2026), :

Evolutionary dynamics and molecular adaptation of Rift Valley fever virus across human and non-human outbreaks in Africa

Omara I, Juma J, Tshiabuila D, Dor G, Wilkinson E, Baxter C, Tegally H, Moir M, Oyola S, de Oliveira T, Neurosurgical focus: Video (2026), 2:V1

Approaches to the Management of Virologic Failure on Dolutegravir-Based Antiretroviral Therapy in the 50 Countries With the Highest Adult HIV Prevalence

Nutt C, Lessells R, Muyindike W, Johnson L, Kouyos R, Loosli T, Ombajo L, Brijkumar J, Hyle E, Moosa M, Gandhi M, Vitoria M, Jordan M, Siedner M, McCluskey S, Clinical Infectious Diseases (2026), 82:265-273

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Hunt M, Hinrichs A, Anderson D, Karim L, Dearlove B, Knaggs J, Constantinides B, Fowler P, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego L, Amuzu D, Avaro M, Awandare G, Ayivor-Djanie R, Barkham T, Bashton M, Batty E, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers S, Campos J, Carr R, Chen Y, Cuba F, Dattero M, Dejnirattisai W, Dilthey A, Duedu K, Endler L, Engelmann I, Francisco N, Fuchs J, Gnimpieba E, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao N, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki K, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige G, Mashe T, Mongkolsapaya J, Montes B, Mora J, Morang’a C, Mvula B, Nagarajan N, Nelson A, Ngoi J, da Paixão J, Panning M, Poklepovich T, Quashie P, Ranasinghe D, Russo M, San J, Sanderson N, Scaria V, Screaton G, Sessions O, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson R, Williamson C, Zair X, Biere B, Dürrwald R, Mache C, Oh D, Schulze J, Wedde M, Wolff T, Fuchs S, Semmler T, Paraskevopoulou S, Kerber R, Kröger S, Haas W, Bode K, Corman V, Erren M, Finzer P, Grosser R, Haffner M, Hermann B, Kiel C, Krumbholz A, Lorentz T, Meinck K, Nitsche A, Petzold M, Schwanz T, Szabados F, Tewald F, Tiemann C, de Oliveira T, Peto T, Crook D, Corbett-Detig R, Iqbal Z, Nature Methods (2026), 23:653-662

Unmet needs of young adults following first-episode psychosis in KwaZulu-Natal, South Africa: Baseline findings from a pilot randomised controlled trial of basic income support

Mlay J, Ntlantsana V, Gcabashe N, Jamieson L, Naidu T, Bhengu B, Thela L, Paruk S, Burns J, Chiliza B, Lessells R, Tomita A, South African Journal of Psychiatry (2026), 32:2455

The relationship between emotional dysregulation and, HIV acquisition risk behaviours and intimate partner violence perpetration among young men in rural areas and urban informal settlements in South Africa

Nyoni P, Gibbs A, Mkhwanazi S, Tomita A, Psychology, Health & Medicine (2026), :1-23

Peer network approaches for improving HIV testing, prevention and care utilisation among men in sub-Saharan Africa: a scoping review

Otambo W, Harling G, Inghels M, Otto M, Blose N, Tram K, Tanser F, Mee P, BMJ Open (2026), 16:e106124

Do men face greater barriers to accessing HIV testing services than women? Might HIV self-testing be the answer? Evidence from a longitudinal survey in east Zimbabwe (2018–2023)

Otambo W, Mandizvidza P, Moorhouse L, Inghels M, Moyo R, Okango E, Tsenesa B, Maswera R, Dzamatira F, Gregson S, Tanser F, Nyamukapa C, Mee P, PLOS Global Public Health (2026), 6:e0006125

Effect of enhanced peer PrEP referral with HIV self-testing delivery among young Kenyan women: A randomized controlled trial of peer networks

Ortblad K, Wairimu N, Culquichicon C, Njeru I, Malen R, Reedy A, Ekwunife O, McGowan M, Mwangi M, Muthoni A, Kiboi D, Njoroge S, Gao F, Baeten J, Ngure K, PLOS Medicine (2026), 23:e1005023

Disentangling Temporal Trends of Clade Ib Monkeypox Virus Transmission in Burundi

Jin S, Asakura T, Murayama H, Jung S, Niyukuri D, Nyandwi J, Nkengurutse L, Kamatari O, Lim J, Endo A, Dickens B, The Journal of Infectious Diseases (2026), 233:e140-e144

Retrospective cohort analysis of antiretroviral therapy initiation timelines and clinical outcomes in adults with HIV and TB disease in KwaZulu-Natal, South Africa

Jansen van Vuuren C, van der Molen J, Sookrajh Y, Ngwenya T, Khubone T, Mkhize S, Asare K, Naidoo K, Lessells R, Lewis L, Garrett N, Dorward J, International Journal of STD & AIDS (2026), 37:14-23

Enhancing SARS-CoV-2 response capacity in Africa and other centers for research in emerging infectious diseases centres through a collaborative training programme

Ahouidi A, Padane A, Gaye A, Sakuntabha A, Deme A, Cisse B, de Oliveira C, Weldon C, Diedhiou C, Ndiaye D, Gottlieb G, McOwen H, Dia I, Xavier J, Siddle K, Andersen K, Barrett L, Paye M, Diallo M, Tilles S, Weaver S, Wohl S, de Oliveira T, Junior Alcantara L, Van Voorhis W, Mboup S, Wilkinson E, Giovanetti M, Clinical Microbiology and Infection (2026), 32:192-195

A machine learning framework for predicting peptide inhibitors of insect voltage-gated sodium channels

da Silva Sousa J, Palmeira L, Barbosa F, Mercado H, Melo T, Azevedo V, Góes-Neto A, Xavier J, Andrade B, Journal of Molecular Graphics and Modelling (2026), 146:109398

Ethical design as a prerequisite for translational microbiome science

Passmore J, Nieves Delgado A, Happel A, Microbiome (2026), 14:

‘The not talking is actually what kills you’– young South African women’s communication barriers about sexual health

Hartley F, Trappler J, Gill K, Bekker L, MacKenny V, Knight L, Passmore J, Culture, Health & Sexuality (2026), :1-12

Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa

Dor G, Kekana D, Hisner R, Martin D, Korber B, Ernst T, Levy A, Speers D, Turville S, Sintchenko V, Basile K, Sullivan G, Rockett R, Kok J, Schoenmakers J, Gueli F, Lessels R, Baxter C, Wolter N, Gottberg A, Tegally H, de Oliveira T, Virus Evolution (2026), :

Human MERS-CoV cases are falling but pose an ongoing pandemic threat

Subissi L, Otieno J, Shah A, Abu-Raddad L, Agrawal A, Mehairi A, Albarraq A, Barakat A, Bashir I, Caly L, Chand M, Drosten C, Faria N, Fowotade A, von Gottberg A, Haagmans B, Huang B, Kindrachuk J, Koopmans M, Korber B, Leo Y, Mbala-Kingebeni P, Melhem N, Munster V, Ngere I, Njenga M, de Oliveira T, Palacios G, Peiris M, Rambaut A, Resende P, Saha S, Suzuki T, Yadav P, von Dobschuetz S, Azhar E, Van Kerkhove M, Nature Health (2026), :

Ranked by Impact Factor (top 20)

The tainted milk of human kindness. Lancet (2012), I.F.:47.831

Effect of the HIV epidemic on liver cancer in Africa. Lancet (2008), I.F.:47.831

Prevalence, incidence and mother-to-child transmission of HIV-1 in rural South Africa. Lancet (2002), I.F.:47.831

Microbial genome-wide association studies: lessons from human GWAS. Nature Reviews Genetics (2017), I.F.:40.282

Renewing Felsenstein's phylogenetic bootstrap in the era of big data. Nature (2018), I.F.:40.137

Public Database for HIV Drug Resistance in southern Africa. Nature (2010), I.F.:40.137

Libya should stop denying scientific evidence on HIV. Nature (2007), I.F.:40.137

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature (2006), I.F.:40.137

Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells. Science (2018), I.F.:37.205

Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science (2018), I.F.:37.205

High coverage of ART associated with decline in risk of HIV acquisition in rural KwaZulu-Natal, South Africa. Science (2013), I.F.:37.205

Scourge of a Continent: The BioAfrica Website. Science (2005), I.F.:37.205

HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis. Lancet ID (2018), I.F.:19.864

Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study. Lancet Infectious Diseases (2017), I.F.:19.864

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study. Lancet Infectious Diseases (2017), I.F.:19.864

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. Lancet Infect Dis. (2016), I.F.:19.864

PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect Dis. (2015), I.F.:19.864

HIV and hepatitis B co-infection in Africa. Lancet Infectious Diseases (2008), I.F.:19.864

Use of antiretroviral therapy in households and risk of HIV acquisition in rural KwaZulu-Natal, South Africa, 2004-12: a prospective cohort study. Lancet Global Health (2014), I.F.:17.686

Effect of population viral load on prospective HIV incidence in a hyperendemic rural African community. Science Translational Medicine (2017), I.F.:16.761

Ranked by Citation (top 20)

High coverage of ART associated with decline in risk of HIV acquisition in rural KwaZulu-Natal, South Africa. Science (2013), Citations:549

An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics (2005), Citations:439

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature (2006), Citations:151

Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus. J Virol (2000), Citations:142

A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS (2003), Citations:127

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009), Citations:117

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol (2007), Citations:109

Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infectious Genetics and Evolution (2013), Citations:107

Bypassing Osmotic Shock Dilemma in a Polystyrene Resin Using the Green Solvent Cyclopentyl methyl Ether (CPME): A Morphological Perspective.. Polymers (Basel) (2019), Citations:100

Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science (2018), Citations:100

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression. Gene (2020), Citations:100

Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004. Antivir Ther (2008), Citations:96

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J Virol (2005), Citations:93

Different epidemic potentials of the HIV-1B and C subtypes. J Mol Evol (2005), Citations:89

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies. J Virol (2003), Citations:85

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol (2007), Citations:81

Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. J Virol (2008), Citations:78

Sequential broadening of CTL responses in early HIV-1 infection is associated with viral escape. PLos One (2007), Citations:77

Variability at human immunodeficiency virus type 1 subtype C protease cleavage sites: an indication of viral fitness?. J Virol (2003), Citations:72

High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. PLoS One (2008), Citations:66