Phylogeography and evolutionary dynamics of Nairobi sheep disease virus

Nairobi sheep disease virus (NSDV) is a tick-borne orthonairovirus causing severe hemorrhagic gastroenteritis in small ruminants, with case fatality rate up to 90% among naive populations. Despite its veterinary and zoonotic importance, the evolution and spatiotemporal dynamics of NSDV remain poorly understood. We analysed S, M, and L segment sequences collected from the 1950s to 2024 in China, India, and Kenya, and identified three geographically structured lineages (Lineage A from India, Lineage B from China, and Lineage C from Kenya). No host-specific clustering was observed, indicating geographic isolation, rather than host adaptation, is the primary driver of diversification. Recombination events exhibited strong geographic structuring, with Jilin province as a major hotspot (likely reflecting higher sampling density in the region). Occasional intercontinental gene flow from Africa into China contributed parental lineages, and recombinant strains were detected in ticks, with parental contributions from sheep and saiga antelope hosts. Selection analyses revealed strong purifying selection on L segment (dN/dS = 0.365), but relaxed or positive selection on M glycoprotein (dN/dS = 3.020) and S segment (dN/dS = 5.360). Substitution rates ranged from 1.56 × 10^-4 (L) to 6.81 × 10^-4 (S) substitutions/site/year. Time-to-most-recent-common-ancestor (tMRCA) of all NSDV strains was estimated at ~ 1732 ce (95% highest posterior density [HPD]: 1624-1833), representing the divergence between the Chinese lineage and the common ancestor of the Indian and Kenyan lineages. The Indian and Kenyan lineages subsequently diverged from their common ancestor ~ 1763 ce (95% HPD: 1677-1845), followed by the Indian lineage (~1883 ce) and the Chinese lineage (~1934 ce). The ancestral location at the root node is highly uncertain (maximum a posteriori, MAP = India_Karnataka), and sparse sampling from intermediate regions limits robust phylogeographic inference. Among the well-supported intra-continental routes, migration from India (Maharashtra/Karnataka) to eastern China (Liaoning, Shandong) received moderate support (BF = 6.40-22.57). A route from Liaoning to Kenya was also detected (BF = 11.84), but this inference should be interpreted with caution given the limited Kenyan sampling and potential unsampled intermediate populations.