Genetic Characteristics and Pathogenicity of a Novel Porcine Deltacoronavirus Southeast Asia-Like Strain Found in China

Abstract

Farmers involved in the lucrative pork trading business between China and Southeast Asian countries should be aware of a recently discovered novel porcine deltacoronavirus (PDCoV) in Guangxi province, China. A PDCoV strain, CHN/GX/1468B/2017, was isolated from the small intestinal contents of piglets with diarrhea from this region, with a titer of 1 × 108.0 TCID50/mL on LLC-PK cells. The full-length genome sequence consists of 25,399 nt as determined by next-generation sequencing and this was deposited in the GenBank (accession number MN025260.1). Genomic analysis showed that CHN/GX/1468B/2017 strain had 96.9~99.4% nucleotide homology with other 87 referenced PDCoV strains from different areas, and contained 6 and 9-nt deletions at positions 1,733~1,738 and 2,804~2,812, respectively, in the ORF1a gene. Phylogenetic analyses based on the whole gene sequence as well as S protein and ORF1a/1b protein sequences all showed that this strain was closely related to the Southeast Asia strain. When 7-day-old piglets were inoculated orally with the CHN/GX/1468B/2017 strain, they developed severe diarrhea, with a peak of fecal viral shedding at 4 days post-infection. Although no death or fever were observed, the CHN/GX/1468B/2017 strain produced a wide range of tissue tropism, with the main target being the intestine. Importantly, the VH:CD ratios of the jejunum and ileum in infected piglets were significantly lower than controls. These results indicate that CHN/GX/1468B/2017, isolated in China, is a novel PDCoV Southeast Asia-like strain with distinct genetic characteristics and pathogenicity. This finding enriches the international information on the genetic diversity of PDCoV.

An Updated Review of Porcine Deltacoronavirus in Terms of Prevalence, Pathogenicity, Pathogenesis and Antiviral Strategy

“…PDCoV mainly aggregates in the duodenum in the early stage, while in the peak of stage and the later period, the virus transfers to ileum ( 42 ). Occasionally, a small number of PDCoV antigen-positive cells were detected in the cecum and colon ( 36 , 39 ), and fewer PDCoV antigen-positive cells were detected in mesenteric lymph nodes (MLN) ( 36 ), peyer's patches ( 39 ) and stomach ( 45 ). One study reported that the percentage of pigs that tested positive for PDCoV antigen decreased significantly at 7–8 dpi, and no positive cells were detected in samples from 10 dpi and thereafter ( 39 ).…”

“…Although the strain and dose of the virus, the age of pigs or the time of euthanasia varied in different studies, PDCoV RNA was usually detected in the duodenum, jejunum, ileum, cecum, colon, liver, spleen, kidney, lung and MLN ( 2 , 12 , 39 – 41 , 45 ), and the quantities are relatively high in the duodenum, jejunum, ileum, cecum and colon. Low to moderate quantities of viral RNA are occasionally detected in the rectum, stomach, diaphragm, heart, inguinal lymph node, tonsil and muscle from rear leg ( 41 , 45 ). One study using 5-day-old piglets orally inoculated with PDCoV (CHN-GD16–05) with 5 mL at 10 8.6 TCID 50 /mL declared that viral RNA was detected from duodenum, jejunum, and ileum at the early stage.…”

“…Based on experimental findings, fecal viral shedding occurs on 24–48 hpi, peaks at 2–7 dpi ( 12 , 40 , 41 , 44 , 45 ). Fecal viral RNA is still detectable at 14–35 dpi ( 12 , 40 ).…”

Genomic characterization and pathogenicity analysis of a porcine deltacoronavirus strain isolated in western China

“…However, recently isolated Chinese PDCoV strains belonging to the Chinese lineage have been found to cause much milder disease in sucking piglets. In those studies, although typical symptoms were observed in infected piglets, most recovered from the infection [40][41][42]. Our results suggest that BN23 is more pathogenic than with other PDCoV strains belonging to the Chinese lineage.…”

Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential

“…This may have contributed to PDCoV transmission from China to Haiti. The Southeast Asian (or Vietnam/Laos/Thailand) lineage contains PDCoV strains prevailing in these countries and a novel strain detected in China (CHN/GX/1468B/2017), indicating that these strains may derive from common evolutionary ancestors [52]. In addition, another Thailand-like PDCoV isolate (CHN-GX81-2018) was also discovered in Guangxi Province of China [53].…”