Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance

A comprehensive monitoring strategy is vital for tracking the spread of
mosquito-borne Japanese encephalitis virus (JEV), the leading cause of
viral encephalitis in Asia. Virus detection consists of passive
surveillance of primarily humans and swine, and/or active surveillance in
mosquitoes, which may be a valuable proxy in providing insights into
ecological processes underlying the spread and persistence of JEV.
However, it has not been well characterized whether passive surveillance
alone can capture the circulating genetic diversity to make reasonable
inferences. Here, we develop phylogenetic models to infer JEV host
changes, spatial diffusion patterns, and evolutionary dynamics from data
collected through active and passive surveillance. We evaluate the
feasibility of using JEV sequence data collected from mosquitoes to
estimate the migration histories of genotypes GI and GIII. We show that
divergence times estimated from this dataset were comparable to estimates
from all available data. Increasing the amount of data collected from
active surveillance improved time of most recent common ancestor estimates
and reduced uncertainty. Phylogenetic estimates using all available data
and only mosquito data from active surveillance produced similar results,
showing that GI epidemics were widespread and diffused significantly
faster between regions than GIII. In contrast, GIII outbreaks were highly
structured and unlinked suggesting localized, unsampled infectious
sources. Our results show that active surveillance of mosquitoes can
sufficiently capture circulating genetic diversity of JEV to confidently
estimate spatial and evolutionary patterns. While surveillance of other
hosts could contribute to more detailed disease tracking and evaluation,
comprehensive JEV surveillance programs should include systematic
surveillance in mosquitoes to infer the most complete patterns for
epidemiology, and risk assessment.