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.

The full-length genome characterization, genetic diversity and evolutionary analyses of Senecavirus A isolated in Thailand in 2016.

Senecavirus A (SVA) is a novel picornavirus that causes porcine idiopathic vesicular disease characterized by lameness, coronary band hyperemia, and vesicles on the snout and coronary bands. An increase in the detection rate of SVA in several countries suggests that the disease has become a widespread problem. Herein, we report the detection of SVA in Thailand and the characterization of full-length genomic sequences of six Thai SVA isolates. Phylogenetic, genetic, recombination, and evolutionary analyses were performed. The full-length genome, excluding the poly (A) tail of the Thai SVA isolates, was 7282 nucleotides long, with the genomic organization resembling other previously reported SVA isolates. Phylogenetic and genetic analyses based on full-length genome demonstrated that the Thai SVA isolates were grouped in a novel cluster, separated from SVA isolates from other countries. Although the Thai SVA isolates were closely related to 11-55910-3, the first SVA isolate from Canada, with 97.9-98.2%, but they are different. Evolutionary and recombinant analyses suggested that the Thai SVA isolates shared a common ancestor with the 11-55910-3 isolate. The positive selection in the VP4 and 3D genes suggests that the virus was not externally introduced, but rather continuously evolved in the population prior to the first detection. Addition, the presence of SVA could have been ignored due to the presence of other pathogens causing similar clinical diseases. This study warrants further investigations into molecular epidemiology and genetic evolution of the SVA in Thailand.

Immune response of gilts to single and double infection with porcine epidemic diarrhea virus.

Immune response of gilts following single and double infection with porcine epidemic diarrhea virus (PEDV) at gilt acclimatization and prepartum were investigated. One hundred PEDV-naïve gilts were divided into two groups: negative (Neg) and feedback (FB) groups. Antibody responses in serum, colostrum, and milk samples were measured by IgG/IgA ELISA and virus neutralization assay (VN). Fecal shedding was investigated using RT-PCR. In summary, a single infection at gilt acclimatization resulted in slightly increased serum antibody titers as determined by VN assay and IgG ELISA, but not by IgA ELISA. Viral RNA was detected in fecal samples up to 6 days post-exposure. A double infection at prepartum resulted in significantly increased IgA and VN titers in milk samples compared to the single-infection group. No fecal shedding was detected following the double infection.