Coexistence of multiple genotypes of porcine epidemic diarrhea virus with novel mutant S genes in the Hubei Province of Chinain 2016

摘要

The emergence of highly virulent porcine epidemic diarrhea virus （PEDV） variants in China causedhuge economic losses in 2010. Since then, large-scale sporadic outbreaks of PED caused by PEDVvariants have occasionally occurred in China. However, the molecular diversity and epidemiologyof PEDV in different provinces has not been completely understood. To determine the moleculardiversity of PEDV in the Hubei Province of China, we collected 172 PED samples from 34 farmsacross the province in 2016 and performed reverse transcription polymerase chain reaction （RT-PCR） by targeting the nucleocapsid （N） gene. Seventy-four samples were found to be PEDV-positive. We further characterized the complete spike （S） glycoprotein genes from the positivesamples and found 21 different S genes with amino acid mutations. The PEDV isolates herepresented most of the genotypes which were found previously in field isolates in East and South-East Asia, North America, and Europe. Besides the typical Genotypes I and II, the INDEX groupswere also found. Importantly, 58 new amino acids mutant sites in the S genes, including 44 sites inS1 and 14 sites in S2, were first described. Our results revealed that the S genes of PEDV showedvariation and that diverse genotypes of PEDV coexisted and were responsible for the PEDoutbreaks in Hubei in 2016. This work highlighted the complexity of the epidemiology of PEDV andemphasized the need for reassessing the efficacy of classic PEDV vaccines against emergingvariant strains and developing new vaccines to facilitate the prevention and control of PEDV infields.