The Prevalence, Genetic Characterization, and Evolutionary Analysis of Porcine Pegivirus in Guangdong, China

Porcine pegivirus(PPgV) is a member of the Pegivirus genus in the Flaviviridae family. PPg V is an emerging virus that has been discovered in swine herds in Germany, the United States, China, Poland, Italy, and the United Kingdom,indicating a wide geographical distribution. In this retrospective study, 339 pig serum samples were collected from 20 different commercial swine farms located in nine cities in Guangdong Province, China, from 2016 to 2018, to investigate the prevalence and genetic diversity of PPg V in this geographical region. PPg V was detected in 55%(11/20) of the farms using nested reverse transcription PCR, with 6.2%(21/339) of pigs testing positive for PPg V. The yearly PPg V-positive rate increased from 2.6% to 7.5% between 2016 and 2018. Sequencing of PPg V-positive samples identified two complete polyprotein genes and seven partial NS5 B genes from different farms. Comparative analysis of the polyprotein genes revealed that PPg V sequences obtained in this study showed 87.4%–97.2% similarity at the nucleotide level and 96.5%–99.4% similarity at the amino acid level with the reference sequences. Sequence alignment and phylogenetic analysis of the complete polyprotein gene and partial NS5 B and NS3 genes demonstrated a high genetic similarity with the samples from the USA. The finding of the wide distribution of PPg V in swine herds in Guangdong Province will contribute to the understanding of the epidemiological characteristics and genetic evolution of PPg V in China.