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KEMRI Research Papers: Recent submissions

  • HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data 
    Tanya Golubchik, Lucie Abeler-Dörner , Matthew Hall Chris Wymant , David Bonsall , George Macintyre-Cockett , Laura Thomson , Jared M Baeten Connie L Celum , Ronald M Galiwango , Barry Kosloff Mohammed Limbada , Andrew Mujugira , Nelly R Mugo , Astrid Gall , François Blanquart , Margreet Bakker , Daniela Bezemer , Swee Hoe Ong , Jan Albert Norbert Bannert Jacques Fellay , Barbara Gunsenheimer-Bartmeyer , Huldrych F Günthard Pia Kivelä Roger D Kouyos Laurence Meyer , Kholoud Porter , Ard van Sighem , Mark van der Valk , Ben Berkhout , Paul Kellam , Marion Cornelissen , Peter Reiss , Helen Ayles David N Burns , Sarah Fidler Mary Kate Grabowski , Richard Hayes , Joshua T Herbeck , Joseph Kagaayi , Pontiano Kaleebu , Jairam R Lingappa Deogratius Ssemwanga , Susan H Eshleman , Myron S Cohen , Oliver Ratmann , Oliver Laeyendecker Christophe Fraser (BMC Bioinformatic s, 2025-08)
    Background: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as ...
  • HIV Knowledge, Information Sources, and Perceived Risk among Reproductive-Aged Individuals in Kisumu, Kenya: A Latent Profile Analysis 
    Talia A Loeb, K Willis , M A E Roach , V Sing'oei , J Otieno , R Oyugi , J Opany , C S Polyak , T A Crowell , J Owuoth , S Baral , K Rucinski ; RV393 Study Group (AIDS and Behaviou, 2025-09)
    Information, education, and communication programs to improve HIV knowledge and communication skills are critical to HIV responses. It is unclear if improved HIV knowledge translates to decreased HIV acquisition risks. We ...
  • Heterozygous pathogenic variants in the splicing factor SF1 lead to a large spectrum of neurodevelopmental disorders 
    Johnny Bou-Rouphael Auriane Cospain 1 Thomas Courtin Boris Keren Corentine Marie Marion Lesieur-Sebellin, Delphine Heron Jean-Madeleine de Sainte Agathe , Solveig Heide , Elodie Lejeune Chloe Quelin , François Lecoquierre , Mathilde Nizon , Bertrand Isidor , Thomas Besnard Benjamin Cogne , Xenia Latypova , Jonathan Levy , Pascal Joset Katharina Steindl Maria Palomares-Bralo , Fernando Santos-Simarro Mary Ann Thomas , Amina Abubakar Sally Ann Lynch , Amelie J Müller Tobias B Haack Martin Zenker Michael Parker , Emma Clossick Michael Spiller Renarta Crookes Muriel Holder-Espinasse , Allan Bayat , Rikke S Møller , Tomasz Stanislaw Mieszczanek , Pierre de la Grange , Julien Buratti , Pierre Marijon , Sabir Ataf , Ryan Gavin Carlos Parras Bassem A Hassan , Cyril Mignot Laïla El Khattabi (American Journal of Human Genetics, 2025-09)
    Alternative splicing is highly prevalent in the brain where it orchestrates key processes such as neurogenesis and synaptogenesis, both essential for the nervous system's complexity and plasticity. Dysregulation of splicing ...
  • Global Trends in CD4 Measurement and Immunosuppression at ART Initiation Among Children With HIV 
    Gabriela Patten, Karen Malateste , Carolyn Bolton Moore , Nosisa Sipambo Limpho Mokone , Nanina Anderegg , Kara Wools-Kaloustian , Denna Michael Francesca Odhiambo Charles Kasozi , Sophie Desmonde Madeleine Amorissani-Folquet Valériane Leroy , Dewi Kumara Wati , Revathy Nallusamy Aarti Kinikar Du Tuan Quy , Marcel Yotebieng , Peter Vanes Ebasone , Patricia Lelo Jorge Pinto , Vanessa Rouzier Daisy Maria Machado , Nel Jason Haw , Nathan Ford; International epidemiology Databases to Evaluate AIDS collaboratio (The Peadiatric Infectious Disease Journal, 2025-08)
    Eligibility for antiretroviral therapy is no longer based on immune criteria. In a global cohort of 97,453 children, between 2005 and 2021, we observed large declines in CD4 measurement, from 51% to 12% among <5 seconds, ...
  • Getting back on track to meet global anaemia reduction targets: a Lancet Haematology Commission 
    Sarah H Atkinson Parminder S Suchdev Michael Bode, Bianca Carducci Carla Cerami Martin N Mwangi Sorrel Namaste , Pattanee Winichagoon , Sumie Leung , Agnes M Mutua , Kelvin Mokaya Abuga , Imelda Angeles-Agdeppa , Robin Blythe , Natalie Carvalho , Ana Cepeda-Lopez James H Cross Saskia de Pee Erica Di Ruggiero, Jessica Fanzo, Ugo Gentilini , Wanjiku N Gichohi-Wainaina , Clare Glover-Wright , Filomena Gomes , Sonja Hess Jacinta Holloway-Brown Fatou Joof , Crystal Karakochuk Nicholas J Kassebaum , Leila Larson , Sachith Mettananda , John Muthii Muriuki , Martha Mwangome , Eric O Ohuma Victoria Oliver , Nandita Perumal , Kamija Phiri , Folake Samuel , Sheela Sinharoy Tinashe Tizifa , Giorgia Valleriani , Kesso Gabrielle van Zutphen-Küffer Florencia Vasta , Hans Verhoef Yingying Wang , Kapil Yadav Zhenyu Yang , Melissa Young , Michael B Zimmermann Sant-Rayn Pasricha (Lancet Haematology, 2025-08)
    Global Burden and Data Gaps: Many countries lack reliable data on anaemia prevalence, especially for populations beyond young children and women of reproductive age. Few national surveys measure both anaemia and its ...
  • Geostatistical modelling of soil-transmitted helminth prevalence in Kenya: Informing targeted interventions to accelerate elimination efforts 
    Nyamai Mutono, Brian Njuguna , Stella Kepha , Florence Wakesho , Wyckliff Omondi , Paul Kibati , Irene Chami , Alison Ower , Kevin McRae-McKee , Chitiavi Juma , Ivy Sempele , Vincent Ouma , Josphat Martin Muchangi , Maurice R. Odiere , S.M. Thumbi (Internation al Journal of Infectious Diseases,, 2025-07)
    Objectives This study estimates the prevalence of soil-transmitted helminths (STH) in Kenya, identifying high- and low-burden communities to optimize intervention strategies. Methods Using prevalence data from 146,668 ...
  • Genomic surveillance reveals geographical heterogeneity and differences in known and novel insecticide resistance mechanisms in Anopheles arabiensis across Kenya 
    Brian Polo, Kelly L. Bennett, Sonia Barasa, Jon Brenas, Silas Agumba, Joseph Mwangangi, Lucy Wachira, Stanley Kitur, Damaris Matoke-Muhia, David M. Mburu, Edith Ramaita, Elijah O. Juma, Charles Mbogo, Eric Ochomo, Chris S. Clarkson, Alistair Miles & Luna Kamau (BMC Genomics, 2025-07)
    Background Insecticide resistance in disease vectors poses a significant threat to the control of transmission globally. In Anopheles mosquitoes, resistance has jeopardized gains made in malaria control and led to the ...
  • Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022-2023 cholera outbreak in Kenya. 
    Lydia M. Mageto Lydia M. Mageto Gabriel Oluga Aboge Gabriel Oluga Aboge Zelalem H. Mekuria Zelalem H. Mekuria Peter Gathura Peter Gathura John Juma John Juma Michael Mugo Michael Mugo Collins Kipkorir Kebenei Collins Kipkorir Kebenei D Diana Imoli Beatrice Atieno Ongadi Beatrice Atieno Ongadi Kelvin Kering Kelvin Kering Cecilia Kathure Mbae Cecilia Kathure Mbae See less Samuel Kariuki Samuel Kariuki (Frontiers in Microbiology, 2025-09)
    Background: Cholera remains a public health challenge in Kenya. To better understand its dynamics, we analyzed Vibrio cholerae genomes from clinical and environmental samples collected during the 2022–2023 outbreak. These ...
  • Genomic characterization of multidrug-resistant extended-spectrum β-lactamase-producing Vibrio cholerae O1 strains from 2022 cholera outbreak in Kenya. 
    Imoli D, Maingi JM, Mbae C, Kavai SM, Wairimu C, Mundalo S, Odityo G, Wairimu M, Mekuria Z, Gebreyes W, Kariuki S. (Journal of Antimicrobial Chemotherapy, 2025-09)
    Background In mid-2021, a global surge in cholera cases was reported. This study characterized Vibrio cholerae O1 isolates obtained from faecal samples of cholera-positive cases during the 2022 cholera outbreak in ...
  • Genomic and clinical epidemiology of SARS CoV-2 in coastal Kenya: insights into variant circulation, reinfection, and multiple lineage importations during a post-pandemic wave 
    Lambisia, A. W., Katama, E. N., Moraa, E., Mwita, J. M., Gallagher, K., Mutunga, M., Nyale, E., Omungala, J., Mwanga, M., Murunga, N., Nyiro, J., Nyagwange, J., Sande, C., Bejon, P., Githinji, G., Dellicour, S., Phan, M. V. T., Cotten, M., Ochola-Oyier, L. I., Holmes, E. C., Agoti, C. N. (BMC Glob Public Health, 2025-09)
    Background: Between November 2023 and March 2024, coastal Kenya experienced another wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections detected through our continued genomic surveillance. Herein, ...
  • Genes linked to schistosome resistanceidentified in a genome-wide association study of Africa snail vectors 
    Tom Pennance, Jacob A. Tennessen, Johannie M. Spaan,Tammie J. McQuistan, George Ogara, Fredrick Rawago , Kennedy Andiego,Boaz Mulonga, Meredith Odhiambo, MartinW. Mutuku, GeraldM. Mkoji,Eric S. Loker, Maurice R. Odiere & Michelle L. Steinauer (Nature Communications, 2025-07)
    Schistosomiasis, a neglected tropical disease, is transmitted by freshwater snails. Interruption of transmission will require novel vector-focused interventions. We performed a genome-wide association study of African ...
  • Forensic biobank; towards comprehensive forensic genetic frequency database for the Kenyan population. 
    Aluvaala Nambati EK, Muge E, Azzam B, Maritim D, Kirosh N, Kamau L, Mpoke S, Cheriro W, Karani L, Sang M, Gosar A, Makwaga O, Eyase L, Wandera HT, Ariga S, Nyabera J, Mwangi M, Kimani F, Bulimo W (Forensic Sci Int Synerg., 2025-07)
    Forensic genetic frequency databases (FGFD) are used in estimating the probability of a DNA match in forensic investigations. They provide reference population data that can be used for statistical estimation for the rarity ...
  • Faecal exposure in cholera hotspots: Sanipath exposure assessment in informal settlements of Nairobi, Kenya. 
    Mbae C, Kering K, Mugo M, Yakubu H, Wang Y, Kavai S, Ngetich R, Mundalo S, Imoli D, Kioko C, Kebenei C, Wakio Z, Ongadi B, Kibet E, Moe CL, Kariuki S. (2025-08)
    Urban informal settlements are characterized by poor sanitation infrastructure, and inadequate hygiene practices, exposing residents to infectious pathogens. We conducted a study involving environmental sampling and behaviour ...
  • Factors influencing birth preparedness and complication readiness during pregnancy in Turkana County, Kenya 
    Leila Chepkemboi Kibet, Anselimo Ouma Makokha, Joseph Kiplangat Muta (Pan African Medical Journal (PAMJ), 2025-07)
    Introduction pregnancy, childbirth, and the postnatal period involve risks that can lead to serious complications, but these can be reduced when mothers and families are aware of key obstetric danger signs and follow a ...
  • Factors for arboviral seropositivity in children in Teso South Sub County, Kenya 
    Mary Inziani, Jane Kilonzo, Marthaclaire Kerubo, Sylvia Mango, Mary Kavurani, Allan Ndirangu, Elizabeth Njeri, Diuniceous Oigara, Sylvester Ayoro, Shingo Inoue, Kouichi Morita, Matilu Mwau (medRxiv, 2025-08)
    Arboviruses like Yellow Fever Virus (YFV), Dengue Virus (DENV), Chikungunya Virus (CHIKV), and West Nile Virus (WNV) frequently cause outbreaks in sub-Saharan Africa. Identifying risk factors in children can improve ...
  • External validation of paediatric pneumonia and bronchiolitis risk scores to predict mortality in children hospitalised in Kenya: a retrospective cohort study 
    Gordon, B., Nyiro, J. U., Nair, H., Sheikh, Z., Katama, E., Agoti, C. N., Pei, R., Zar, H., Shi, T. (The Journal of Infectious Diseases, 2025-07)
    Background: Acute lower respiratory tract infections (ALRIs) are a leading cause of pediatric mortality in low- and middle-income countries. In recent years, substantial research has been done to enhance risk stratification ...
  • Experiences of mothers in the context of a staffing intervention in select newborn units in Kenyan public hospitals 
    Oluoch, D., Odinga, N., Waithira, C., Ngaiza,HIGH Q Hospital Group G., Maluni, J., Mutua, E., Maina, M., Karumba, K., Molyneux, S., Fuller, S., Were, F., English, M., Jones, C. (International journal of nursing studies, 2025-09)
    Background: Maternal involvement, effective communication and adequate support are widely recognised as promoting respectful care and better maternal experience of small and sick neonate care. Nurses play a critical role ...
  • Examining the prevalence, inequalities, and determinants of depression and anxiety in Kenya: A concentration index approach 
    Mokaya, P. O., István Ágoston , I., Galgalo, D. A., Maloba, G. O., Kazungu, J., Gabriella, H. F. (Acta Psychol (Amst), 2025-09)
    Background: Globally, mental disorders such as depression and anxiety are on the rise. While effective prevention and treatment interventions exist, access to these is influenced by, among other things, household socioeconomic ...
  • Evaluation of the PATHFAST TB LAM Ag assay as a treatment monitoring tool for pulmonary tuberculosis in Nairobi, Kenya 
    Fred Orina, Mayu Hikone, Nobuo Saito, Jane Ong’ang’o, Andrew Nyerere, Edinah Songoro and Helen Meme (Tropical Medicine and Health, 2025-07)
    Background: Treatment monitoring is important in pulmonary tuberculosis (PTB) management, since prolonged treatment necessitates regular assessments to prevent treatment failure and the emergence of drug-resistant strains. ...
  • Evaluating the effectiveness of a One-Stop PrEP Care model to enhance HIV prevention: a protocol for a cluster-randomised trial in Kisumu County, Kenya 
    Benn Kwach, Josephine B Odoyo, Amber R Lauff, Victor Omollo, Bernard Rono, Vallery Ogello, Victoria Mann, Zachary Kwena, Katherine Thomas, Monisha Sharma, Jennifer F Morton, Kenneth Ngure, Elizabeth Bukusi, Kenneth K Mugwanya, One-Stop PrEP Care Team (BMJ Open, 2025-09)
    Introduction: Oral HIV pre-exposure prophylaxis (PrEP) is a highly effective biomedical intervention for HIV prevention, but its access and utilisation are challenging, especially in high-burden settings such as Kenya. For ...

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