Community based studies of major bacterial and viral pathogens are undertaken to support epidemiological research of the Department.  Interest focuses on Streptococcus pneumonia (Spn) and respiratory syncytial virus (RSV). The aim of this work is to describe the natural history of infection, the patterns of transmission, and who acquires infection from whom,  to improve understanding of the mechanisms of persistence of these pathogens in the host population, for example the interaction of infection and host immunity. Antigenic variation of the organism is a complicating factor for both Spn and RSV. 

Our work is undertaken both in the absence or following intervention introduction, producing the essential empirical base for studies of vaccine programme design and evaluation (eg PCVIS – pneumococcal conjugate vaccine impact study), and in support of vaccine trials across the Programme (Vaccines). Recent work investigated the prevalence and duration of Spn carriage to estimate rates of serotype specific infection and recovery, used to investigate serotype dynamics and competition. Follow up prevalence studies of nasophayngeal carriage look at the impact of recent vaccine introduction on serotype replacement and compared to predictions based on the earlier serotype infection dynamics work. 

Community studies of RSV and other respiratory viruses investigate transmission in households to enquire ‘who acquires infection from whom’, and in particular who infects the vulnerable infant.  The question of ‘who contacts whom’ which underlies transmission chains is investigated using contact diary and electronic tracking methods. A birth cohort study addressed issues of RSV natural history and immunity to reinfection in relation to RSV genetic and antigen diversity. 

Future research 
Within the household setting the question of WAIFW has identified the need to carry out whole genome deep sequencing to resolve chains of transmission. We are collaborating with WT Sanger Institute in developing a WGS method for RSV. Pilot studies using radio frequency ID tags in the community have shown the feasibility of electronic methods to identify networks of contact and this is an area for continued development. 

A major study is beginning which aims to identify the pathways of transmission of respiratory viruses at a range of organization levels  within the Kenya population from individual to countrywide to ultimately inform on innovative control methods.  The work will combine temporal, spatial, genetic sequence and age-related infection data, linked to data on contact networks, to gain a better understanding of the spread of infection within the population.