History of the Emergence and Spatiotemporal Spread of Tobacco Mosaic Virus in China

The ongoing spread of Tobacco mosaic virus (TMV) throughout China threatens and diminishes proceeds from production of tobacco and other crops. Determining how and when TMV first emerged in China, its current evolutionary rate, diffusion pathways, spatial and plant host distributions, can help minimize the risk associated with mosaic disease (MD). Here, 110 TMV Coat Protein (CP) gene sequences sampled from 12 distinct plant hosts between 1997 and 2015 from 18 geographical locations within China (14 Provinces, two Municipalities and two Autonomous regions) were used in a probabilistic Bayesian inferential framework implemented in BEAST v1.8.1 to reconstruct TMV's evolutionary history from emergence to spatiotemporal diffusion. This entailed estimating and inferring; (a) the time when and location where TMV's most recent common ancestor (MRCA) emerged, (b) the evolutionary rate, (c) diffusion pathways, (d) levels of genetic diversity and, (e) phylogenetic relationships amongst viruses. This study infers that TMV emerged around 1924 (95% HPD; 1860 to 1971) in Henan province. Its mean nucleotide substitution rate of 1.09 × 10-3 is marginally higher than previous TMV and Tobamovirus species rates. TMV's current wide spatial and plant host distribution across China is due largely to (i) utilization of 15 Bayes factor supported diffusion pathways, 60% of which were outward bound viral movements from Yunnan province to proximal and distant sampling locations and (ii) a growing shift toward cost-efficient tobacco crop substitution alternatives and adoption of a mixed-crop farming system. These analyses also suggest that Yunnan province is most probably both a source rather than a sink of TMV dispersal throughout China and a major thoroughfare of trans-China TMV movements. Finally, results also indicate that TMV populations exhibited both low effective population sizes and levels of genetic diversity, while individuals from distinct hosts were phylogenetically similar probably due to strong bottlenecks and purifying selection.