Prof. James Nokes


Prof. James Nokes

Principal Investigator

Research group:


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. 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.



  • Matt Keeling, University of Warwick, UK 
  • Graham Medley, LSHTM, UK 
  • Matt Cotten, UVRI Uganda; LSHTM, UK 
  • My Phan, UVRI Uganda, LSHTM, UK 

Other roles 

  • Professor of Infectious Disease Epidemiology, School of Life Sciences (Faculty Member) and Zeeman Institute (SBIDER), University of Warwick, Coventry UK 
  • Director, NIHR Global Health Research Group, on the Application of Genomics and Modelling to the Control of Virus Pathogens (GeMVi) in East Africa  
  • Member, Scientific Advisory Board, ASPIRE Afrique ONE 
  • Member, Kanya National COVID-19 Modelling Technical Advisory Committee 


Wellcome Trust, NIHR, FCDO, BMGF, PATH 


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  • Brand SPC, Ojal J, Aziza R, Were V, Okiro EA, Kombe IK, Mburu C, Ogero M, Agweyu A, Warimwe GM, Nyagwange J, Karanja H, Gitonga JN, Mugo D, Uyoga S, Adetifa IMO, Scott JAG, Otieno E, Murunga N, Otiende M, Ochola-Oyier LI, Agoti CN, Githinji G, Kasera K, Amoth P, Mwangangi M, Aman R, Ng'ang'a W, Tsofa B, Bejon P, Keeling MJ, Nokes DJ, Barasa E. COVID-19 transmission dynamics underlying epidemic waves in Kenya. Science. 2021 Nov 19;374(6570):989-994. doi: 10.1126/science.abk0414. Epub 2021 Oct 7.  
  • Abidha CA, Nyiro J, Kamau E, Abdullahi O, Nokes DJ, Agoti CN. Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-16. Virus Evol. 2020 June 2;6(1):veaa031. doi: 10.1093/ve/veaa031.  
  • Brand SP, Munywoki P, Walumbe D, Keeling MJ, Nokes DJ. Reducing respiratory syncytial virus (RSV) hospitalization in a lower-income country by vaccinating mothers-to-be and their households. Elife. 2020 Mar 27;9:e47003. doi:10.7554/eLife.47003. 
  • Otieno GP, Bottomley C, Khagayi S, Adetifa I, Ngama M, Omore R, Ogwel B, Owor BE, Bigogo G, Ochieng JB, Onyango C, Juma J, Mwenda J, Tabu C, Tate JE, Addo Y, Britton T, Parashar UD, Breiman RF, Verani JR, Nokes DJ. Impact of the Introduction of Rotavirus Vaccine on Hospital Admissions for Diarrhea Among Children in Kenya: A Controlled Interrupted Time-Series Analysis. Clin Infect Dis. 2020 May 23;70(11):2306-2313. doi: 10.1093/cid/ciz912.  
  • Agoti CN, Phan MVT, Munywoki PK, Githinji G, Medley GF, Cane PA, Kellam P, Cotten M, Nokes DJ. Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant. Sci Rep. 2019 Jul 11;9(1):10076. doi: 10.1038/s41598-019-46509-w.  
  • Kombe IK, Munywoki PK, Baguelin M, Nokes DJ, Medley GF. Model-based estimates of transmission of respiratory syncytial virus within households. Epidemics. 2019 Jun;27:1-11. doi: 10.1016/j.epidem.2018.12.001. 
  • Kamau E, Onyango CO, Otieno GP, Kiyuka PK, Agoti CN, Medley GF, Cane PA, Nokes DJ, Munywoki PK. An Intensive, Active Surveillance Reveals Continuous Invasion and High Diversity of Rhinovirus in Households. J Infect Dis. 2019 Mar 15;219(7):1049-1057. doi: 10.1093/infdis/jiy621. 
  • Nyiro JU, Munywoki P, Kamau E, Agoti C, Gichuki A, Etyang T, Otieno G, Nokes DJ. Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya: baseline epidemiological observations. Wellcome Open Res. 2018 Jul 25;3:89. doi: 10.12688/wellcomeopenres.14662.1. 
  • Kiti MC, Tizzoni M, Kinyanjui TM, Koech DC, Munywoki PK, Meriac M, Cappa L, Panisson A, Barrat A, Cattuto C, Nokes DJ. Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors. EPJ Data Sci. 2016;5:21. doi: 10.1140/epjds/s13688-016-0084-2.  
  • Munywoki PK, Koech DC, Agoti CN, Lewa C, Cane PA, Medley GF, Nokes DJ. The source of respiratory syncytial virus infection in infants: a household cohort study in rural Kenya. J Infect Dis. 2014 Jun 1;209(11):1685-92. doi: 10.1093/infdis/jit828. 
  • Ohuma EO, Okiro EA, Ochola R, Sande CJ, Cane PA, Medley GF, Bottomley C, Nokes DJ. The natural history of respiratory syncytial virus in a birth cohort: the influence of age and previous infection on reinfection and disease. Am J Epidemiol. 2012 Nov 1;176(9):794-802. doi: 10.1093/aje/kws257. 
  • Charles Nyaigoti 
  • Charles Sande 
  • George Githinji 
  • Joyce Nyiro 
  • Cameline Orlendo 
  • Ivy Kombe (Oxford) 
  • Sam Brand (Warwick) 
  • Joe Hilton (Warwick) 
  • Andrea Parisi (Warwick)