Characterization and evolution of the coronavirus porcine epidemic diarrhoea virus HLJBY isolated in China

Abstract

A strain of porcine epidemic diarrhoea virus (PEDV), namely HLJBY, was isolated in Heilongjiang province, China. To provide insight into the understanding of the phylogenetic and the current epidemiological status of PEDV, PEDV HLJBY was compared with CV777 and other PEDV strains deposited in the GenBank. The homology between the entire genomic nucleotide sequences of PEDV HLJBY and CV777 was 97.7%. The homology of M gene was the highest (99.0%). However, the homology of ORF3 gene was 97.7%, and protein of ORF3 was 90.1%. In addition, HLJBY showed the highest nucleotide identity (99.9%) with PEDV‐SX/China/2017 strain and lowest similarity (91.2%) to PEDV/Belgorod/dom/2008 strain. We analysed the changes in S gene and its protein of PEDV HLJBY with 65 historic PEDV strains. The highest nucleotide identity was 99.9% compared with PEDV‐SX/China/2017 strain, and the lowest nucleotide identity was 60.0% compared with PEDV/Belgorod/dom/2008 strain. The length of deduced amino acid sequences of S proteins varied from 1,372 to 1,390 amino acids (aa). Compared with most aa sequences of S proteins, HLJBY exhibited 5 aa deletions (position 55, 59–61, 144). Analysis and comparison of open reading frame 3 (ORF3) proteins between HLJBY strain and other PEDV strains were also focused in this study. We revealed that the length of deduced amino acid sequences of ORF3 proteins was 80–224 aa among tested strains and the identity of HLJBY ORF3 amino acids with other PEDV strains was 71.4%–98.9%. ORF3 protein of both HLJBY strain and PEDV‐SX/China/2017 strain consists of 91 aa, with 133 aa deletions at their C' end in relation to the other tested PEDV strains. The phylogenetic tree based on different proteins or genes resulted in different phylogenetic groups. For pathogenicity evaluation of PEDV HLJBY strain, colostrum deprivation piglets were challenged with PEDV HLJBY, and PEDV reference strain CV777 as a control, the results showed that animals challenged with either of these PEDV strains developed diarrhoea, and histopathological examination of small intestines of challenged animals showed acute viral enteritis with villous atrophy in either PEDV HLJBY‐P10 or PEDV CV777‐P8 inoculated piglets.

Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review

“…Future pandemics may not only come from α-CoV or β-CoV but also from γ-CoV that are found in domestic birds such as turkeys, guinea fowls, or quails and more recently in beluga whales and bottleneck dolphins ( 302 – 304 ). δ-CoVs have potential to spillover to humans and are present in different mammalian (Asian leopard cat CoV, Chinese ferret badger CoV, porcine CoV HKU15) and avian (bulbul CoV HKU11, thrush CoV HKU12, munia CoV HKU13, white-eye CoV HKU16, sparrow CoV HKU17, magpie-robin CoV HKU18, night heron CoV HKU19, wigeon CoV HKU20, and common moorhen CoV HKU21) species ( 158 , 305 – 307 ).…”

Genetic Diversity of Porcine Epidemic Diarrhea Virus With a Naturally Occurring Truncated ORF3 Gene Found in Guangxi, China

“…With the deletion, the ORF3 gene of an attenuated-type virus has 49 nucleotide deletions, and this leads to a reading frame-shift and an early termination of translation ( 20 ). It is mainly represented by the strains of truncated CV777, Zhejiang-08, JS2008, HLJBY, and attenuated DR13, which only has a 91aa truncated protein ( 18 , 24 , 37 – 39 ). It is noteworthy that the ORF3 protein of the Guangxi naturally truncated strains contain only residues of 89aa, since the 382-nucleotide deletion in the ORF3 results in a frameshift mutation and an early termination of translation.…”

Molecular Characterization of a Variant Subgroup GII-a Porcine Epidemic Diarrhea Virus Strain in China

“…Point mutations, insertions, or deletions in structural proteins and non-structural proteins have resulted in changes in tropism and virulence of coronaviruses [17][18][19]. In the case of PEDV, deletions or insertions are frequently observed in the spike protein or ORF3 [20][21][22]. For example, HM2017 has two insertions in the S gene [20], HLJBY has a 133-aa deletion in ORF3 [21], and 15 novel eld PEDV variants with large genomic deletions have been identi ed in Japan [22].…”

“…In the case of PEDV, deletions or insertions are frequently observed in the spike protein or ORF3 [20][21][22]. For example, HM2017 has two insertions in the S gene [20], HLJBY has a 133-aa deletion in ORF3 [21], and 15 novel eld PEDV variants with large genomic deletions have been identi ed in Japan [22].…”