Epidemiology & Demography


James trained in Zoology (BSc), then a PhD in virus epidemiology (Imperial College), followed by post-docs at Imperial College, Oxford and Warwick. Although Warwick remains his home institution where he is a Professor of Infectious Disease Epidemiology, James has been seconded to KEMRI-Wellcome Trust Research Programme, Kilifi since 2001. His principal interest over the last two decades has been in the transmission dynamics and control of human viral pathogens, primarily respiratory syncytial virus (RSV). James leads the Virus Epidemiology and Control Research Group, which is inter-disciplinary using molecular, phylogenetic, immunological, mathematical, statistical and field approaches to address key questions relating to respiratory and enteric virus persistence, transmission, and intervention. He has been supported by Wellcome Trust Research Leave, Programme Grant and Senior Investigator Awards.

Current Work

Recent work has focused on the integration of epidemiological and genomic data to infer transmission pathways at different scales of interest from the household to countrywide. This has led to a NIHR Global Health Research Project GeMVi (on the application of genomics and modelling to the control of virus pathogens in East Africa). The COVID-19 pandemic led to redeployment of the diagnostics, genomics, modelling and community epidemiology platforms to SARS-CoV-2, with Emergency Funding from FCDO/Wellcome and NIHR.


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Project Research

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Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, during the COVID-19 pandemic, 2019-2022.
Lambisia, A. W., Murunga, N., Mutunga, M., Cheruiyot, R., Maina, G., Makori, T. O., Nokes, D. J., Agoti, C. N.
Gut Pathog, (2024). 16:2

Changes in the global hospitalisation burden of respiratory syncytial virus in young children during the COVID-19 pandemic: a systematic analysis.
Cong, B., Koç, U., Bandeira, T., Bassat, Q., Bont, L., Chakhunashvili, G., Cohen, C., Desnoyers, C., Hammitt, L. L., Heikkinen, T., Huang, Q. S., Markić, J., Mira-Iglesias, A., Moyes, J., Nokes, D. J., Ploin, D., Seo, E., Singleton, R., Wolter, N., Fu Yung, C., Zar, H. J., Feikin, D. R., Sparrow, E. G., Nair, H., Li, Y.
Lancet Infect Dis, (2023). S1473-3099:00630-8

Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons.
Owuor, D. C., de Laurent, Z. R., Nyawanda, B. O., Emukule, G. O., Kondor, R., Barnes, J. R., Nokes, D. J., Agoti, C. N., Chaves, S. S.
Sci Rep, (2023). 13:22342

Symptom prevalence and secondary attack rate of SARS-CoV-2 in rural Kenyan households: A prospective cohort study.
Gallagher, K. E., Nyiro, J., Agoti, C. N., Maitha, E., Nyagwange, J., Karani, A., Bottomley, C., Murunga, N., Githinji, G., Mutunga, M., Ochola-Oyier, L. I., Kombe, I., Nyaguara, A., Kagucia, E. W., Warimwe, G., Agweyu, A., Tsofa, B., Bejon, P., Scott, J. A. G., Nokes, D. J.
Influenza Other Respir Viruses, (2023). 17:e13185

New SARS-CoV-2 Omicron Variant with Spike Protein Mutation Y451H, Kilifi, Kenya, March-May 2023.
Mwanga, M. J., Lambisia, A. W., 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.
Emerg Infect Dis, (2023). 29: