Bayesian Phylogeographic Inference Suggests Japan as the Center for the Origin and Dissemination of Rice Stripe Virus

Abstract

Rice stripe virus (RSV) is one of the most important viral pathogens of rice in East Asia. The origin and dispersal of RSV remain poorly understood, but an emerging hypothesis suggests that: (i) RSV originates from Yunnan, a southwest province of China; and (ii) some places of eastern China have acted as a center for the international dissemination of RSV. This hypothesis, however, has never been tested rigorously. Using a data set comprising more than 200 time-stamped coat protein gene sequences of RSV from Japan, China and South Korea, we reconstructed the phylogeographic history of RSV with Bayesian phylogeographic inference. Unexpectedly, the results did not support the abovementioned hypothesis. Instead, they suggested that RSV originates from Japan and Japan has been the major center for the dissemination of RSV in the past decades. Based on these data and the temporal dynamics of RSV reported recently by another group, we proposed a new hypothesis to explain the origin and dispersal of RSV. This new hypothesis may be valuable for further studies aiming to clarify the epidemiology of RSV. It may also be useful in designing management strategies against this devastating virus.

Bayesian phylodynamic analysis reveals the evolutionary history and the dispersal patterns of citrus tristeza virus in China based on the p25 gene

“…The molecular characteristics and pathogenesis of CTV as a worldwide disease has been extensively studied, but limited attention has been given to the evolutionary dynamics of this virus, especially regarding its evolutionary dynamics and dispersal patterns in China, studies of the evolutionary dynamics have been reported in rice stripe virus, tomato mosaic virus, infectious bursal disease viruses [ 15 – 17 ]. Silva et al [ 18 ] used the p25 gene to estimate the rate of evolution of CTV, and the substitution rate was 1.5 × 10 − 4 subs/site/year (95% credible interval: 1.73 × 10 − 4 subs/site/year − 3.16 × 10 − 4 subs/site/year), which proved that CTV was an exceptionally slowly evolving virus.…”