Detection and Whole Genome Amplification of the 4d Type of Porcine Hepatitis E Virus in Eastern Tibet, China.

Abstract

Genomic and evolutionary analysis of epidemic porcine hepatitis E virus (HEV) in the Tibetan Plateau was performed. Faecal samples were collected from 216 Tibetan pigs and 78 Tibetan Yorkshire (Large White) and 53 tissue samples from Yorkshire from the Linzhi City slaughterhouse. Total RNA was extracted from faeces and fragments of HEV open reading frame 2 (ORF2) detected by reverse transcription and nested polymerase chain reaction (RT-nPCR) and cloned. Twenty-three samples (23/347; 6.63%) were positive for the virus, including 6.94% (15/216) Tibetan pig and 6.11% (8/131) Yorkshire samples. No tissue samples tested positive for the virus. Cloned sequences were uploaded to GenBank (accession numbers: OR392679-OR392685, OR355817-OR355824 and OR909495-OR909502) and a phylogenetic tree constructed. The entire viral genome was amplified using primers for the 5-month-old Tibetan pig sequence which confirmed that the strain belonged to HEV type 4, subtype d (GenBank accession number: OQ981960) and showed 93.30% homology with Sichuan Tibetan pig sequence, MK410044. Bayesian tree analysis showed that the earliest divergence was in 1999 and evidence of homologous recombination was found. Genomic and evolutionary analysis of HEV in the Tibetan Plateau is presented. The importance of continuous surveillance and genomic analysis of HEV is highlighted, especially in regions like the Tibetan Plateau where new strains may emerge. The findings contribute to our understanding of HEV's genetic diversity, evolutionary history and potential risks to animal and human health.