Evolution of respiratory syncytial virus (RSV) over space and time in rural Filipino children

Very little is known about how spatial distance influences viral evolution or what local spatio-temporal patterns of evolution look like. In this study, we use data from a randomized controlled efficacy trial of an 11-valent pneumococcal vaccine (PCV) undertaken in the Bohol province of the Philippines from July 2000 to December 2004. Viral culture and multiplex PCR were done on nasal wash specimens, collected from a sample of infants visiting the regional hospital or outpatient clinics during the vaccine trial. We performed a nested phylogeographic analysis of respiratory syncytial virus (RSV) positive samples and classified virus samples into distinct subgroups. The geographic coordinates of household of residence were obtained for study participants using GPS and used to link phylogenetic results to the geographic location of each patient. We then performed a retrospective space-time scan statistic to identify the spatial location and temporal extent of clusters of each subgroup and visualized geographic patterns using GIS. The spatio-temporal scan statistic identified several unique space-time clusters of RSV-A and RSV-B subgroups. The results show that RSV subgroups evolve in distinct localized areas at different points in time, suggesting that spatial distance a population factors play an important role in viral evolution. Spatial analysis and geovisualization is the first step in exploring the effects of distance on viral evolution and potential ecological pressures that contribute to evolutionary pressures.