Defining pathways of respiratory virus transmission leading to improved intervention strategies. (360G-Wellcome-102975_Z_13_Z)

The central question is whether sequence data for respiratory viruses sampled at a range of social organisational levels within a country can identify pathways of transmission that suggest particular intervention designs? Using an established framework across Kenya to sample for a variety of medically important respiratory viruses the following will be addressed: (A) Can transmission pathways be mapped across social organisation levels using whole genome sequence (WGS) data? i. How are p opulation groups linked by infection transmission? ii. Are schools hubs for the spread of infection to households in a community? iii. Who introduces infection and who infects whom in households? iv. Do transmission pathways differ for different viral pathogen types? v. Can social contact structures be defined that determine transmission patterns? vi. What recommendations for sampling design arise for future studies? (B) What new insight will knowledge of transmission structure provide for the design of intervention programmes? For example: i. Is community or nationwide control achievable through school-based delivery systems? ii. Who should be targeted for vaccination within the household? iii. What sections of the population should be targeted to most effectively prevent the spread of novel or emerging pathogens?