The classification, origin and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia

Abstract

Objectives The classification of the severe fever with thrombocytopenia syndrome virus (SFTSV) lacked consistency due to limited virus sequences used across previous studies, and the origin and transmission dynamics of the SFTSV remains not fully understood. In this study, we analyzed the diversity and phylodynamics of SFTSV using the most comprehensive and largest dataset publicly available for a better understanding of SFTSV classification and transmission. Methods 1,267 L segments, 1,289 M segments, and 1,438 S segments collected from China, South Korea, and Japan were included in this study. Maximum likelihood trees were reconstructed to classify the lineages. Discrete phylogeographic analysis was conducted to infer the phylodynamics of SFTSV. Results We found that the L, M, and S segments were highly conserved, with mean pairwise nucleotide distances of 2.80%, 3.36%, and 3.35% and could be separated into 16, 13, and 15 lineages, respectively. The evolutionary rate for L, M and the S segment was 0.61×10-4 (95% HPD: 0.48–0.73×10-4), 1.31×10-4 (95% HPD: 0.77–1.77×10-4) and 1.27×10-4 (95% HPD: 0.65–1.85×10-4) subs/site/year. The SFTSV most likely originated from South Korea around the year of 1617.6 (95% HPD: 1513.1–1724.3), 1700.4 (95% HPD: 1493.7–1814.0) and 1790.1 (95% HPD: 1605.4–1887.2) for L, M and S segments, respectively. Hubei Province in China played a critical role in the geographical expansion of the SFTSV. The effective population size of SFTSV peaked around 2010 to 2013. We also identified several codons under positive selection in the RdRp, Gn-Gc and NS genes. Conclusions By leveraging the largest dataset of SFTSV, our analysis could provide new insights into the evolution and dispersal of SFTSV, which may be beneficial for the control and prevention of severe fever with thrombocytopenia syndrome.