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).

See more

Current Work

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

See more

Research Groups

ResViRe Water sequencing Adenovirus sequencing and antigenic characterisation

Recent publications

Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya.
Musundi, S., Mwanga, M., Lambisia, A., Morobe, J. M., Murunga, N., Moraa, E., Ndwiga, L., Cheruiyot, R., Musyoki, J., Mutunga, M., Guzman-Rincon, L. M., Sande, C., Mwangangi, J., Bejon, P., Ochola-Oyier, L. I., Nokes, D. J., Agoti, C. N., Nyiro, J., Githinji, G.
Virus Evol, (2025). 11:veaf035

The genome sequence of varicella-zoster virus (Varicellovirus humanalpha3) obtained by metagenomics from a patient presenting with an exanthem rash.
Musundi, S., Okanda, D., Lambisia, A., Morobe, J. M., Muthanje, E., Ochola-Oyier, L. I., Carter, D. P., Agoti, C. N., Kiiru, J., Githinji, G.
Microbiol Resour Announc, (2025). :e0024825

Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.
Lambisia, A. W., Mwita Morobe, J., Moraa, E., Mwarumba, S., Korir, F. K. N., Seif Athman, R., Kiptui, R., Mbee, M., Mugo, N., Amoth, P., Muange, P., Houldcroft, J. C., Barasa, E., Mwangangi, J., Githinji, G., Holmes, C. E., Ochola-Oyier, L. I., Agoti, C. N.
Wellcome Open Res, (2025). 10:28

Molecular Analysis of Human Respiratory Syncytial Virus Group B Strains Isolated in Kenya Before and During the Emergence of Pandemic Influenza A/H1N1.
Wangui, J., Gachara, G., Mobegi, V., Agoti, C., Otieno, J., Opanda, S., Opot, B., Ngeranwa, J. N., Njeru, R., Bulimo, W.
Influenza Other Respir Viruses, (2025). 19:e70082

Adenovirus-Specific T Cells in Adults Are Frequent, Cross-Reactive to Common Childhood Adenovirus Infections and Boosted by Adenovirus-Vectored Vaccines.
Mukhopadhyay, R., Lambisia, A. W., Hoang, J. P., Ravenhill, B. J., Agoti, C. N., Krishna, B. A., Houldcroft, C. J.
J Med Virol, (2025). 97:e70222