Porcine Deltacoronavirus Strain Research Articles

Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015.

Porcine deltacoronavirus (PDCoV) in Thailand was first detected in 2015. We performed a retrospective investigation of the presence of PDCoV in intestinal samples collected from piglets with diarrhea in Thailand from 2008 to 2015 using RT-PCR. PDCoV was found to be present as early as February 2013. Phylogenetic analysis demonstrated that all PDCoV variants from Thailand differ from those from other countries and belong to a novel group of PDCoV that is separate from the US and Chinese PDCoV variants. Evolutionary analysis suggested that the Thai PDCoV isolates probably diverged from a different ancestor from that of the Chinese and US PDCoV isolates and that this separation occurred after 1994.Electronic supplementary materialThe online version of this article (doi:10.1007/s00705-017-3331-3) contains supplementary material, which is available to authorized users.

Genome Sequencing and Analysis of a Porcine Delta Coronavirus from Eastern China

Porcine delta coronavirus (PDCoV) has been reported in many countries, including the United States, Canada, South Korea, China, Thailand, Vietnam and Laos. In December 2016, clinical diarrhea similar to that caused by porcine epidemic diarrhea virus (PEDV), but with a lower mortality rate, was reported on a swine farm in Shanghai, China. 6 Intestine samples were collected from dead suckling piglets (<3 weeks old) with clinical diarrhea, and they were assayed for the presence of swine enteric coronaviruses. Polymerase chain reaction results were positive for PDCoV (6/6), but negative for PEDV (0/6), transmissible gastroenteritis virus (TGEV) (0/6) and porcine rotavirus group A (Rota A) (0/6). The full-length genome sequence of the PDCoV strain SHJS/SL/2016 was determined. Phylogenetic trees demonstrated that PDCoV strain SHJS/SL/2016 belongs to the Chinese clade, which might share a common evolutionary ancestor with United States and South Korean clades, but it clustered separately from Thai and Laotian PDCoV strains. This report describes the complete genome sequence of SHJS/SL/2016, and the data will promote a better understanding of the molecular epidemiology and genetic diversity of PDCoV isolates in China.

Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014

Porcine deltacoronavirus (PDCoV) is an emerging swine coronavirus that causes diarrhea in piglets. Since the first outbreak of PDCoV in the United States in 2014, this novel porcine coronavirus has been detected in South Korea, Canada, Mexico, Thailand, and China. In this study, a Chinese PDCoV strain, designated CHN-HN-2014, was isolated from piglets with severe diarrhea on a pig farm in Henan Province, China, and examined with a specific immunofluorescence assay and electron microscopy. Genomic analysis showed that CHN-HN-2014 shares 91.6%–99.4% nucleotide identity with other known PDCoV strains. The pathogenicity of CHN-HN-2014 was further investigated in 5-day-old and 21-day-old piglets. Both kinds of piglets developed clear clinical symptoms, including vomiting, anorexia, lethargy, and severe diarrhea, by 2days postinoculation (DPI), and diarrhea persisted for about 5–6 days. Viral shedding was detected in rectal swabs until 14 DPI in challenged 5-day-old pigs and until 18 DPI in challenged 21-day-old pigs. At necropsy at 4 DPI, macroscopic and microscopic lesions were observed and viral antigen was detected in the small intestines with immunohistochemical staining. These data demonstrate that Chinese PDCoV strain CHN-HN-2014 shares high nucleotide identity with previously reported PDCoV strains and is pathogenic in 5-day-old and 21-day-old piglets.

Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22.

Porcine deltacoronavirus (PDCoV) is a novel enteropathogenic coronavirus in pigs. We have isolated and passaged the PDCoV strain OH-FD22 in an LLC porcine kidney (LLC-PK) cell line. Our study investigated the pathogenicity of the tissue-culture-grown PDCoV (TC-PDCoV) OH-FD22 at cell passages 5, 20 and 40 in LLC-PK cells, in eight 14-day-old gnotobiotic (Gn) pigs. Pigs (n = 3) were euthanized for pathologic examination at post-inoculation day (PID) 3, and the remainder were monitored for clinical signs, virus shedding, and serum antibody responses until PID 28. All inoculated pigs developed watery diarrhea and/or vomiting at PID 1-2 and shed the highest amount of viral RNA in feces at PID 3-5, accompanied by severe atrophic enteritis. They developed high titers of PDCoV-specific IgG/IgA and virus-neutralizing antibodies in serum at PID 23-24. Histologic lesions were limited to the villous epithelium of the jejunum and ileum at PID 3. Two inoculated pigs tested at PID 23-24 had small to moderate numbers of PDCoV antigen-positive cells in the intestinal lamina propria and mesenteric lymph nodes, but not in enterocytes. An analysis of full-length S and N genes of TC- and Gn-pig-passaged OH-FD22 revealed a high genetic stability in cell culture and pigs. TC-PDCoV OH-FD22 (cell passages 5, 20 and 40) was enteropathogenic, and the pathogenicity was similar to that of the original field virus. The TC-PDCoV OH-FD22 will be useful for further pathogenesis studies and for evaluating if higher-level cell-culture passaged virus becomes attenuated for vaccine development.

Occurrence and sequence analysis of porcine deltacoronaviruses in southern China.

BackgroundFollowing the initial isolation of porcine deltacoronavirus (PDCoV) from pigs with diarrheal disease in the United States in 2014, the virus has been detected on swine farms in some provinces of China. To date, little is known about the molecular epidemiology of PDCoV in southern China where major swine production is operated.ResultsTo investigate the prevalence of PDCoV in this region and compare its activity to other enteric disease of swine caused by porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis coronavirus (TGEV), and porcine rotavirus group C (Rota C), 390 fecal samples were collected from swine of various ages from 15 swine farms with reported diarrhea. Fecal samples were tested by reverse transcription-PCR (RT-PCR) that targeted PDCoV, PEDV, TGEV, and Rota C, respectively. PDCoV was detected exclusively from nursing piglets with an overall prevalence of approximate 1.28 % (5/390), not in suckling and fattening piglets. Interestingly, all of PDCoV-positive samples were from 2015 rather than 2012–2014. Despite a low detection rate, PDCoV emerged in each province/region of southern China. In addition, compared to TGEV (1.54 %, 5/390) or Rota C (1.28 %, 6/390), there were highly detection rates of PEDV (22.6 %, 88/390) in those samples. Notably, all five PDCoV-positive piglets were co-infected by PEDV. Furthermore, phylogenetic analysis of spike (S) and nucleocapsid (N) gene sequences of PDCoVs revealed that currently circulating PDCoVs in southern China were more closely related to other Chinese strains of PDCoVs than to those reported in United States, South Korea and Thailand.ConclusionsThis study demonstrated that PDCoV was present in southern China despite the low prevalence, and supported an evolutionary theory of geographical clustering of PDCoVs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0591-6) contains supplementary material, which is available to authorized users.

Detection and Phylogenetic Analysis of Porcine Deltacoronavirus in Korean Swine Farms, 2015.

SummaryThis study applied molecular‐based method to investigate the presence of porcine deltacoronavirus (PDCoV) in 59 commercial pig farms in South Korea. The results of RT‐PCR screening on a relatively large collection of faeces samples (n = 681) from January 2013 to March 2015 did not reveal the presence of PDCoV until the end of 2014. However, on March 2015, PDCoV‐positive samples (SL2, SL5) were detected from SL swine farm in Gyeongbuk province. The phylogenetic trees based on the complete spike‐ and nucleocapsid protein‐coding genes showed that SL2 and SL5 closely related to the US PDCoV strains rather than those in China. Thought Korean strains of PDCoV isolated in 2014 (KNU14.04) and in 2015 (SL2 and SL5) grouped within US PDCoV cluster, the reconstruction of ancestral amino acid changes suggested that they are different.

Full-Length Genome Characterization of Chinese Porcine Deltacoronavirus Strain CH/SXD1/2015.

A porcine deltacoronavirus (PDCoV) was identified in the Chinese mainland and found to be closely related to Hong Kong strain HKU15-155 but differed from PDCoV strains in the United States and South Korea. The complete genome of PDCoV strain CH/SXD1/201 was sequenced and analyzed to further characterize PDCoV in Chinese swine.

Porcine deltacoronavirus: histological lesions and genetic characterization.

First identified in 2012 in a surveillance study in Hong Kong, porcine deltacoronavirus (PDCoV) is a proposed member of the genus Deltacoronavirus of the family Coronaviridae. In February of 2014, PDCoV was detected in pigs with clinical diarrheal symptoms for the first time in the USA. Since then, it has been detected in more than 20 states in the USA and in other countries, including Canada, South Korea, and mainland China. So far, histological lesions in the intestines of pigs naturally infected with PDCoV under field conditions have not been reported. In this report, we describe the characteristic histological lesions in the small intestine that were associated with PDCoV infection, as evidenced by detection of viral nucleic acid by RT-PCR. In addition, we performed genomic analysis to determine the genetic relationship of all PDCoV strains from the four countries. We found that PDCoV mainly caused histological lesions in the small intestines of naturally infected piglets. Sequence analysis demonstrated that the PDCoV strains of different countries are closely related and shared high nucleotide sequence similarity; however, deletion patterns in the spike and 3’ untranslated regions are different among the strains from mainland China, Hong Kong, the USA, and South Korea. Our study highlights the fact that continual surveillance is needed to trace the evolution of this virus.

Complete Genome Sequence of Porcine Deltacoronavirus Strain CH/Sichuan/S27/2012 from Mainland China.

We report the first complete genome sequence of porcine deltacoronavirus (PDCoV) strain CH/Sichuan/S27/2012 identified in feces of diarrheic piglets from mainland China in 2012. This strain has two unique in-frame deletions within the ORF1a gene and is phylogenetically between the prototype PDCoV (HKU15) and the 2014 U.S. strains.

Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis.

SummaryTo identify and characterize aetiologic agent(s) associated with an outbreak of a severe diarrhoea in piglets in Jiangxi, China, in March 2015, a nested reverse transcription–polymerase chain reaction (RT‐PCR) for the detection of porcine deltacoronavirus (PDCoV) was developed. A survey based on the nested RT‐PCR established indicated that the monoinfection of PDCoV (33.71%) and coinfection of PDCoV (19.66%) with porcine epidemic diarrhoea virus (PEDV) were common in diarrhoeal pigs in Jiangxi, China. A high prevalence of PDCoV (58.33%) in diarrhoeal samples which were PEDV negative was observed. The complete genome sequence of a representative PDCoV strain, PDCoV/CHJXNI2/2015, was determined. Phylogenetic analysis of complete genome and S protein sequences of PDCoV/CHJXNI2/2015 demonstrated that it was most closely related to Hong Kong and US PDCoVs. To our knowledge, this is the first report on the identification, prevalence, complete genome sequencing and molecular characterizations of PDCoV in diarrhoeal samples in pigs in China.

Pathogenicity of 2 porcine deltacoronavirus strains in gnotobiotic pigs.

To verify whether porcine deltacoronavirus infection induces disease, we inoculated gnotobiotic pigs with 2 virus strains (OH-FD22 and OH-FD100) identified by 2 specific reverse transcription PCRs. At 21–120 h postinoculation, pigs exhibited severe diarrhea, vomiting, fecal shedding of virus, and severe atrophic enteritis. These findings confirm that these 2 strains are enteropathogenic in pigs.

Complete Genome Characterization of Korean Porcine Deltacoronavirus Strain KOR/KNU14-04/2014.

In April 2014, porcine deltacoronavirus (PDCoV) was first identified in feces from diarrheic piglets in South Korea and found to be closely related to other PDCoV strains. The complete genome of the Korean PDCoV strain, KOR/KNU14-04/2014, was sequenced and analyzed to characterize PDCoV circulating in South Korea.

Rapid Detection, Complete Genome Sequencing, and Phylogenetic Analysis of Porcine Deltacoronavirus

In February 2014, porcine deltacoronavirus (PDCoV) was identified in the United States. We developed a PDCoV real-time reverse transcription PCR that identified PDCoV in 30% of samples tested. Four additional PDCoV genomes from the United States were sequenced; these had ≈99%–100% nt similarity to the other US PDCoV strains.