Abstract
Porcine epidemic diarrhea virus (PEDV) is the major pathogen that causes diarrhea and high mortality in newborn piglets with devastating impact to the pig industry. Recombination and mutation are the main driving forces of viral evolution and genetic diversity of PEDV. In 2016, an outbreak of diarrhea in piglets occurred in an intensive pig farm in Central China. A novel PEDV isolate (called HNAY) was successfully isolated from clinical samples. Sequence analysis and alignment showed that HNAY possessed 21-nucleotide (nt) insertion in its S1 gene, which has never been reported in other PEDV isolates. Moreover, the sequence of the insertion was identical with the sequence fragment in PEDV N gene. Notably, the HNAY strain exhibited two unique mutations (T500A and L521Y) in the neutralizing epitopes of the S1 protein that were different from those of other PEDV variant strains and CV777-based vaccine strains. Additionally, PEDV HNAY might be derived from a natural recombination between two Chinese variant PEDV strains. Animal experiments demonstrated that HNAY displayed higher pathogenicity compared with two other clinical isolates. This study lays the foundation for better understanding of the genetic evolution and molecular pathogenesis of PEDV.
Highlights
Coronaviruses (CoVs) belong to RNA viruses and infect different vertebrates, such as mammalian and avian species (Durham et al, 1979; Law et al, 2005)
Phylogenetic analysis based on S gene can divide Porcine epidemic diarrhea virus (PEDV) into two major genotypes in the United States (US): the original non-S-INDEL (S-INDEL standing for insertions/deletions in the S gene) and the variant S-INDEL (Vlasova et al, 2014; Lin et al, 2016)
We identified potential breakpoints for recombination in the ORF1b and S region
Summary
Coronaviruses (CoVs) belong to RNA viruses and infect different vertebrates, such as mammalian and avian species (Durham et al, 1979; Law et al, 2005). Since 2010, PEDV variant strain has emerged in Asia, which can infect the pigs of all ages but most severely in suckling pigs, reaching up to 95% mortality (Bi et al, 2012; Li et al, 2012; Pan et al, 2012). PEDVs can be divided into genome 1 (G1) and genome 2 (G2) clades and further divided into four subgroups: G1a, G1b, G2a, and G2b (Wang et al, 2016). Despite they have relatively conserved neutralizing epitopes, commercial vaccines based on CV777 strains cannot provide complete protection in piglets against variant PEDV infections which are currently circulating in China and the US (Zhu et al, 2019). Monitoring the genetic alterations in the S gene of PEDV could provide more clues for understanding the epidemic characteristics of PEDV and adjusting the immunization program of PED in pig farms
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