0709 203000 - Nairobi 0709 983000 - Kilifi
0709 203000 - NRB 0709 983000 - Kilifi
0709 203000 - NRB | 0709 983000 - Kilifi

Epidemiology & Demography

Bio

I am a molecular epidemiologist interested in the epidemiology and evolutionary dynamics of respiratory and gastrointestinal viruses in low-income settings. I trained as a Biochemist (University of Nairobi), and later earned an MSc, then PhD, in Virus Molecular Epidemiology (Open University). In 2022, I was awarded a Wellcome Career Development Award to study rates, determinants and transmissibility of respiratory virus reinfections. Currently, I head the Pathogen Epidemiology and Omics (PEO) research group within the KEMRI-Wellcome Trust Research Programme. The PEO team  conducts field studies, wholesome/systems laboratory (diagnostics, genomic and immunologic) characterisation for a range of infectious agents and downstream bioinformatic, statistical and modelling studies to elucidate host-pathogen interactions, infectious agent dispersal and predict intervention impact. Previous research roles: 1)Co-lead COVID-19 diagnostics  and genomic surveillance at KEMRI-Wellcome Trust Research Programme, 2) A Mid-Career Research Fellow supported by the Initiative to Develop African Research Leaders (IDeAL) studying the genomics of viral diarrhoea in Kenya prior to and following the introduction of the rotavirus vaccine, 3) Postdoctoral Scientist/Lead Bioinformatician for the SPReD studies (Studying the Pathways of Respiratory Virus Diseases).

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Current Work

An investigation into the rates, determinants, and transmission of respiratory virus reinfections (ResViRe) funded through the Wellcome Career Development Award Discovery Scheme

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Research Groups

ResViRe Water sequencing Adenovirus sequencing and antigenic characterisation

Recent publications

Assessing the Impact of SARS-CoV-2 Spike Mutations on Antibody Binding: A Comparative Assessment of the Wuhan and JN.1 Variants' Full-Length Spikes in a Multiplex Luminex Assay.
Waweru, G., Nyakundi, R., Kutima, B., Owuor, S., Konyino, G., Gitonga, J., Lugano, D., Maina, A., Musyoki, J., Ochola, L., Omondi, M., Kariuki, C. K., Ogongo, P., Mwachari, C., Shee, F., Agoti, C., Sande, C., Uyoga, S., Kagucia, E., Agweyu, A., Bejon, P., Scott, J. A. G., Warimwe, G. M., Ochola-Oyier, L. I., Nyagwange, J.
Viruses, (2025). 17:

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). 3:80

Cryptosporidium parvum virus 1 genome sequences from pediatric diarrhea cases in coastal Kenya.
Agoti, C. N., Njeru, R., Mwanga, M., Mutunga, M., Shah, S. P., Chu, T. Y., Nokes, D. J., Cotten, M., Phan, M. V. T.
Microbiol Resour Announc, (2025). :e0034925

Epidemiological dynamics of influenza B virus across multiple seasons in Kenya and Uganda inferred from sequence data, 2010-2021.
Nyarango, B. K., Owuor, D. C., Isoe, E., Mutunga, M., Cheruiyot, R., Katama, E. N., Makori, T., Lambisia, A., Nyiro, J., Githinji, G., Kiguli, S., Olupot-Olupot, P., Maitland, K., Agoti, C. N.
BMC Infect Dis, (2025). 25:1080

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.
J Infect Dis, (2025). :