The phylodynamics of emerging porcine deltacoronavirus in Southeast Asia

Porcine deltacoronavirus (PDCoV), a recently emerging pathogen, causes diarrhoea in pigs. A previous phylogenetic analysis based on spike genes suggested that PDCoV was divided into three different groups, including China, the United States, and Southeast Asia (SEA). SEA PDCoV, however, is genetically separated from China and the United States but shares a common ancestor. Its origin and evolution have yet been identified. Herein, phylodynamic analyses based on the full-length genome were performed to investigate the origin and evolution of SEA PDCoV. In the study, 18 full-length genome sequences of SEA PDCoV identified in 2013-2016 together with PDCoV from other regions were used in analyses. The results demonstrated that PDCoV was classified into two genogroups including G1 and G2. G1 is further evolved into G1a (China) and G1b (US). G2 (SEA) group is further evolved into three clades, including SEA-1 (Thailand), SEA-2 (Vietnam) and SEA-2r (Vietnam recombinant) clades. The time to the most recent common ancestor (MRCA) of global PDCoV was estimated to be approximately 1989-1990 and possibly have been circulated in SEA more than a decade. SEA PDCoV is genetically diverse compared to China and U.S. PDCoV. The substitution rate of SEA PDCoV was lower than those of China and the United States, but the recombination rate of SEA was higher. Recombination analyses revealed four potential recombinant events in SEA PDCoV, suggesting that they were derived from the same ancestor of China PDCoV. The SEA-2r subgroup was potentially recombinant between SEA-2 and U.S. strains. In conclusion, the major mechanisms driving the complex evolution and genetic diversity of SEA PDCoV were multiple introductions of exotic PDCoV strains followed by recombination.