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Professor D James Nokes

Research/Teaching Interests

The focus of the research of my team is to gain a better understanding of how viruses spread in human populations with the aim of developing improved intervention strategies, particularly in low and middle income countries (LMICs) such as Kenya.

Most of this work has been directed to the little known respiratory syncytial virus (RSV) which is, in fact, the major cause of childhood pneumonia globally and against which there is no licensed vaccine. More recently, attention has turned to COVID-19 transmission and control.

Our research involves community collection of samples (such as nasal swabs to detect virus and blood samples to detect antibodies specific to a virus), molecular diagnostics, whole genome sequencing and associated bioinformatic analysis, serological epidemiology (looking at virus specific antibodies) and modelling infection dynamics and simulating intervention strategies.

My team is principally based in Kenya at the KEMRI-Wellcome Trust Research Programme and linked to the School of Life Sciences and the Zeeman Institute at Warwick. The work has relevance to the design of interventions such as vaccination and we report to the Kenya Ministry of Health. An important element is capacity building through a range of professional development, including Diploma and Master’s project students and PhD training. .

Research: Technical Summary

The development of optimal control strategies for endemic and emerging pathogens is underpinned by detailed understanding of the epidemiology of the pathogen-host system. The research of my group based at KEMRI-Wellcome Trust Research Programme (KWTRP), Kilifi Kenya, focuses on describing the rates, patterns, and mechanisms of transmission of respiratory and enteric viruses of medical importance in low resource settings. Our key focus over the last 20 years has been on respiratory syncytial virus (RSV) as a major cause of lower respiratory tract disease in young children and of more recently work on SARS-CoV-2 during the pandemic.

We link national and health facility case surveillance, spatio-temporal seroprevalence and household-based cohort study data with laboratory molecular diagnostics, genomic sequencing and epidemiological analysis, immunoepidemiology and transmission dynamic modelling. The central objective is to improve understanding of the spread of pathogens through populations, in the context of community structure and social interactions and virus antigenic diversity and evolution, through which to develop optimal control programme design. This work is in close collaboration with members of the Zeeman Institute at Warwick (Director Matt Keeling).

We are involved in disease burden estimation and cost-effectiveness evaluation of vaccine interventions. KWTRP runs the largest Health and Demographic Surveillance System in Africa which, for example, we have used to evaluate the impact of the introduction of rotavirus vaccine into the infant immunization schedule and estimate disease burden of a range of respiratory viruses. Through collaboration with CDC-Kenya and London School of Hygiene and Tropical Medicine we have linked disease burden and cost data for RSV to assess the cost-effectiveness of a monoclonal antibody birth dose or maternal RSV vaccination. We have described the genomic epidemiology and transmission dynamics of SARS-CoV-2 in Kenya providing forecasts of the potential impact of changes to interventions, introduction of immune evading variants and of different vaccination strategies for reduction of COVID-19 disease. This work is relayed directly to the Ministry of Health, Government of Kenya through Policy Briefs.


For a full list of publications, see WRAP

  • Director, NIHR Global Health Research Project, Application of genomics and modelling to the control of virus pathogens in East Africa (GeMVi) 2018-22
  • Member, National COVID-19 Modelling Technical Committee, Kenya 2020-present
  • Honorary Research Fellow, Nuffield Department of Medicine, University of Oxford, 2016-19
  • Chairman of Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) 2012-15
  • Senior Research Scientist, KWTRP 2001-present
  • Professor, School of Life Sciences, University of Warwick 2009-present
  • Lecturer, Senior Lecturer, Reader, School of Life Sciences, University of Warwick 1999-2009
  • Royal Society University Research Fellow, Imperial/Oxford/Warwick 1990-99
  • PDRA Imperial College 1987-90
  • PhD Parasite Epidemiology Imperial College 1983-87
  • BSc Zoology Imperial College 1979-82