Molecular Epidemiology And Characterization Of Rotavirus Group A, Group C And Porcine Epidemic Diarrhea Virus In Pigs With Gastroenteritis Among The Commercial Swine Farms In Thailand, 2011-2016

Abstract

The most frequent viruses associated with pig gastroenteritis have been previously reported as porcine epidemic diarrhea virus (PEDV) and rotavirus (RV). Rotavirus is an important cause of diarrhea in piglets and pigs worldwide, and group A (RVA) and group C (RVC) are mostly affected. In Thailand, studies on RVA and PEDV have been reported periodically, whereas information on RVC is still limited. In this study, 769 samples (fecal and intestinal content) from pigs with diarrhea were collected from pig herds located in difference provinces throughout Thailand between 2011 and 2016. The specimens were tested using virus-specific RT-PCR to detect the gene encoding capsid protein VP7 and VP4 for RVC, complete 11 gene segments of RVA and S, ORF3, N genes for PEDV. Sequencing analyses showed that 6.6% (51/769) of samples were positive for RVC, 9.5% (73/769) for RVA and 19.9% (153/769) for PEDV. Co-infections of RVA/RVC accounted for 21.6% (11/51) of samples and of PEDV/RVC for 7.8% (4/51) of samples, while only three samples (3/51) or 5.8% tested positive for all three viruses. RV was detected in piglets up to 8 weeks old, while PEDV was often demonstrated from newborn up to 4 weeks of age. Infection severities were not associated with seasonality, since the virus was detected throughout the year. From our study, the G9 and P[13] as the dominant genotypes for RVA, while predominant genotypes of RVC were G1 and P[5]. Furthermore, genome constellation of the Thai RVA strains showed the predominance of Wa-like genotype with significant of reassortment between the porcine and human RVA strains. Comparison of 95 PEDV-positive samples indicated those Thai strains had close genetic relationship and resembled to previously identified PEDV from Thailand and China. Interestingly, eight Thai PEDV strains possessed the amino acid deletions in the N protein. Our findings provide substaintial information in regional rotavirus and PEDV strains in field circulations and may assist inclusions of suitable strains for future vaccine development.