Table_1_The Diversity and Spatiotemporally Evolutionary Dynamic of Atypical Porcine Pestivirus in China.XLSX

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 × 10−3 (8.54 × 10−4-1.60 × 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.

由猪非典型瘟病毒（atypical porcine pestivirus, APPV）引发的A-II型新生仔猪先天性震颤（congenital tremor, CT）自2016年以来一直是学界关注的焦点。然而，目前学界对中国境内APPV的传染源、进化历史及传播模式仍知之甚少。本研究基于全球遗传多样性背景下已公开的完整E2基因序列，结合2016至2020年间在中国新测得的98条E2基因序列，开展了系统发育分析（phylogenetic analyses）。系统发育结果显示APPV可分为4个独立的进化支；值得注意的是，中国境内可检测到全部4个进化支，且遗传多样性最为丰富。贝叶斯系统发育分析（Bayesian phylogenetic analyses）结果表明，E2基因的平均进化速率为1.22×10⁻³（95%置信区间：8.54×10⁻⁴~1.60×10⁻³）替换位点/年（substitutions/site/year）。APPV的最近共同祖先可追溯至公元1886年（95%置信区间：1837~1924年），早于有记录的A型-II先天性震颤首次出现时间（1922年）。系统地理学分析（phylogeographic analyses）显示，APPV种群可能起源于畜牧业发达的荷兰，并于1837~2010年间传入中国。广东作为主要源种群（seeding population），与中国中部、西南地区构成的流行病传播纽带（epidemic linkers）共同推动了APPV在中国境内的扩散。“中国支系”（进化支3与进化支4）的传播模式呈现“由南向北”的移动趋势，这一现象可能与中国2000年以来实施的严格环境政策相关。种群历史重建结果显示，APPV的种群规模经历了多次波动，这与中国过去数十年间生猪存栏量的动态变化高度吻合。此外，正选择压力（positive selected pressure）与地理驱动的适应性演化被认为是APPV进化支多样化的关键驱动因素。本研究结果为中国境内APPV的遗传多样性及时空动态（spatiotemporal dynamic）提供了全面的认知。