The Diversity and Spatiotemporally Evolutionary Dynamic of Atypical Porcine Pestivirus in China

The presence of congenital tremor (CT) type A-II in newborn piglets, caused by atypical porcine pestivirus (APPV), has been a focus since 2016. However, the source, evolutionary history, and transmission pattern of APPV in China remain poorly understood. In this study, we undertook phylogenetic analyses based on available complete E2 gene sequences along with 98 newly sequenced E2 genes between 2016 and 2020 in China within the context of global genetic diversity. The phylogenies revealed four distinct lineages of APPV, and interestingly, all lineages could be detected in China with the greatest diversity. Bayesian phylogenetic analyses showed that the E2 gene evolves at a mean rate of 1.22 x 10(-3) (8.54 x 10(-4)-1.60 x 10(-3)) substitutions/site/year. The most recent common ancestor for APPVs is dated to 1886 (1837-1924) CE, somewhat earlier than the documented emergence of CT (1922 CE). Our phylogeographic analyses suggested that the APPV population possibly originated in the Netherlands, a country with developed livestock husbandry, and was introduced into China during the period 1837-2010. Guangdong, as a primary seeding population together with Central and Southwest China as epidemic linkers, was responsible for the dispersal of APPVs in China. The transmission pattern of China lineages (lineage 3 and lineage 4) presented a south to north movement tendency, which was likely associated with the implementation of strict environmental policy in China since 2000. Reconstruction of demographic history showed that APPV population size experienced multiple changes, which correlated well with the dynamic of the number of pigs in the past decades in China. Besides, positively selected pressure and geography-driven adaptation were supposed to be key factors for the diversification of APPV lineages. Our findings provide comprehensive insights into the diversity and spatiotemporal dynamic of APPV in China.

Automated summary

This study investigates the source, evolutionary history, and transmission pattern of atypical porcine pestivirus (APPV) in China. Phylogenetic analyses reveal four distinct lineages of APPV in China, with the greatest diversity observed in this country. Bayesian analyses suggest that the E2 gene of APPV evolves at a mean rate of 1.22 x 10(-3) substitutions/site/year. The most recent common ancestor of APPV is estimated to have existed in 1886, earlier than the emergence of congenital tremor (CT) in 1922. The study also finds that APPV possibly originated in the Netherlands and was introduced into China between 1837 and 2010. Guangdong, together with central and southwest China, played a significant role in the dispersal of APPV within China. The transmission pattern of China lineages shows a south to north movement tendency, possibly influenced by strict environmental policies implemented in China since 2000. The findings also suggest that the diversification of APPV lineages is driven by positively selected pressure and geographic adaptations.