Introduction
Coronaviruses (CoVs) can infect a wide variety of animals, and cause
respiratory, enteric, and other diseases
(Woo et al., 2006). So far, the most
relevant enteric coronaviruses in pigs include porcine epidemic diarrhea
virus (PEDV), transmissible gastroenteritis virus (TGEV), and recently
identified viruses, such as porcine deltacoronavirus (PDCoV) and swine
acute diarrhea syndrome coronavirus (SADS-CoV)
(Gong et al., 2017;
L. Wang, Byrum, & Zhang, 2014a). Among
them, PEDV has the highest detection rate and up to 100% mortality in
neonatal piglets. The acute diarrhea caused by PEDV was characterized by
severe vomiting, dehydration, and watery diarrhea
(D. Wang, Fang, & Xiao, 2016). Outbreaks
of the disease brought huge economic losses to pig production around the
world (Song & Park, 2012).
PEDV is an enveloped virus, whose genome is composed of a positive
sense, non-segmented, and single-stranded RNA with a size of 28 kb. The
PEDV genome encodes ORF1ab, spike (S), ORF3, envelope (E), membrane (M),
and nucleoprotein (N) from 5’ to 3’ untranslated region (UTR)
(Kocherhans, Bridgen, Ackermann, &
Tobler, 2001). S protein is a glycoprotein peplomer located on the
viral surface, and contains 1383-1386 amino acids (aa) in most strains.
Despite the S protein of PEDV cannot be demarcated by a protease
cleavage site, it is divided into S1 and S2 subunits based on the
homology with other coronaviruses (Duarte
et al., 1994; Millet & Whittaker,
2015). The receptor for PEDV is still unknown. However, S1 protein has
been shown to bind to sialic acid glycans and porcine aminopeptidase N
(pAPN) as a receptor binding domain to facilitate viral invasion. S2
subunit is responsible for a membrane fusion
(B. X. Li, Ge, & Li, 2007;
W. Li, van Kuppeveld, He, Rottier, &
Bosch, 2016). S protein is also the main target for inducing
neutralizing antibodies. The neutralizing epitope region COE (499–638
aa) , four neutralizing B cell epitopes S1A (435-485
aa), SS2 (748–755 aa) , SS6 (764–771 aa), and 2C10 (1368-1374 aa) have
been identified on this protein (C. Y.
Chang et al., 2019; S. H. Chang et al.,
2002; Okda et al., 2017;
Sun et al., 2008). In addition, a
specific linear B-cell epitope SE16 (722-731aa) had been identified to
be required for a reactivity with the mAb 2E10. The epitope SE16 was
localized on the surface of PEDV S protein based on a 3D structure
(Kong et al., 2020).
PEDV was first reported in the United Kingdom in 1971
(Wood, 1977). In China, PEDV was first
identified and isolated in 1984. Since then, PEDV infection occurred
sporadically and regionally. In 2010, a high virulence strain of PEDV
appeared on pig farms in southern China, which caused up to 100 %
mortality in newborn piglets, and immediately swept throughout the
country (Q. Wang, Vlasova, Kenney, &
Saif, 2019). The presence of variant strain in China was identified by
a detection of a field CH/FJND-3/2011 strain
(J. Chen et al., 2012). The AJ1102 strain
isolated from a PEDV positive farm had become the prevalent variant for
the time (Bi, Zeng, Xiao, Chen, & Fang,
2012).
The epidemiological survey proceeded from February 2011 to March 2014 in
29 provinces of China showed that the PEDV positive rates for samples
and pig farms were 61.10%–78.49% and 71.43%–83.47%, respectively.
Genetic drift could be confirmed mainly by the genetic variation of S
protein as compared with Chinese commercialized vaccine strain CV777
(N. Chen et al., 2017;
X. Wang et al., 2016). PEDV is mainly
classified into two genotypes GI (classical) and GII (variant) on the
basis of S gene (J. Chen et al., 2012). In
2013, new PEDV variants containing new insertion and deletion in S gene
versus prototype strain were reported in USA
(L. Wang, Byrum, & Zhang, 2014b).
Subsequently, these variants, named S-INDEL-variant, were also detected
and isolated in China (D. Wang et al.,
2016). S-INDEL strains were associated with milder clinical signs and
lower mortality in suckling pigs.
Currently, PEDV is still the main pathogen that leads to the death of
piglets on pig farms in China. High morbidity, variation, and
recombination of viral genomes make it hard to prevent and control the
prevalence of PEDV. To better understand the prevalence and molecular
characteristics of PEDV in different regions of China, 91 PEDV positive
samples from 17 provinces of China were collected. The full-length S
genes were sequenced and analyzed with a focus on the variation of the
neutralizing epitopes, the emergence of S-INDEL strains, and potential
recombinant between different strains. These data systematically
describe the genetic and evolutionary characteristics of PEDV field
strains in China and promote the development of novel effective vaccines
.