Prevalence, phylogenetic and evolutionary analysis of porcine deltacoronavirus in Henan province, China

Zhang, Honglei; Liang, Qingqing; Li, Bingxiao; Cui, Xiaoxu; Xuelei, Wei; Ding, Qingwen; Wang, Yabin; Hu, Hui

doi:10.1016/j.prevetmed.2019.02.017

Cited by 48 publications

(48 citation statements)

References 36 publications

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“…PDCoV has been detected in many countries, and previous researches showed that the prevalence of PDCoV was mainly focus on suckling piglets with the mortality rate from 40 to 80% [14,15]. PDCoV was reported in Ohio of U.S.A. in February 2014 that with diarrhea in sows and piglets [4].…”

Section: Discussionmentioning

confidence: 99%

“…PDCoV could cause acute diarrhea, vomiting, dehydration and even lead to death in nursing piglets, with the main lesion of villous atrophy in intestines [10][11][12][13]. The prevalence of PDCoV in Henan province of China was about 23.49%, and up to 36.43% in suckling piglets [14,15]. Infected sows usually did not show obviously clinical signs so that the PDCoV detection in sows was often ignored.…”

Section: Introductionmentioning

confidence: 99%

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Porcine deltacoronavirus causes diarrhea in various ages of field-infected pigs in China

Zheng

et al. 2019

Bioscience Reports

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Porcine deltacoronavirus (PDCoV) is a novel coronavirus that causes acute diarrhea in suckling piglets. In Henan province of China, three swine farms broke out diarrhea in different ages of pigs during June of 2017, March of 2018 and January of 2019, respectively. PCR method, Taqman real-time RT-PCR method, sequencing, histopathology and immunohistochemistry (IHC) were conducted with the collected samples, and the results showed that PDCoV was detected among the suckling piglets, commercial fattening pigs and sows with diarrhea. PDCoV-infected suckling piglets were characterized with thin and transparent intestinal walls from colon to caecum, spot hemorrhage at mesentery and intestinal bleeding. PDCoV RNA was detected in multiple organs and tissues by Taqman real-time RT-PCR, which had high copies in ileum, inguinal lymph node, rectum and spleen. PDCoV antigen was detected in the basal layer of jejunum and ileum by IHC. In this research, we found that PDCoV could infect various ages of farmed pigs with watery diarrhea and anorexia in different seasons in a year.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Porcine deltacoronavirus causes diarrhea in various ages of field-infected pigs in China

Zheng

et al. 2019

Bioscience Reports

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“…The USA/Japan/South Korea lineage has a worldwide distribution (Jang et al, 2017;Nelson et al, 2019;Niederwerder and Hesse, 2018;Perez-Rivera et al, 2019;Suzuki et al, 2018). The China lineage has been the predominant lineage in China since 2014 Zhang et al, 2019a). S protein-based phylogenetic trees showed that 7 strains belonging to the China lineage were classified into a minor branch with CHN-HG-2017.…”

Section: Novel Amino Acid Deletions or Insertions Were Detected In Thmentioning

confidence: 99%

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

et al. 2020

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Porcine deltacoronavirus (PDCoV) is the etiological agent of acute diarrhoea and vomiting in pigs, threatening the swine industry worldwide. Although several PDCoV studies have been conducted in China, more sequence information is needed to understand the molecular characterization of PDCoV. In this study, the partial ORF1a, spike protein (S) and nucleocapsid protein (N) were sequenced from Shandong Province between 2017 and 2018. The sequencing results for the S protein from 10 PDCoV strains showed 96.7 %-99.7 % nucleotide sequence identity with the China lineage strains, while sharing a lower level of nucleotide sequence identity, ranging from 95.7 to 96.8%, with the Vietnam/Laos/Thailand lineage strains. N protein sequencing analysis showed that these strains showed nucleotide homologies of 97.3%-99.3% with the reference strains. Phylogenetic analyses based on S protein sequences showed that these PDCoV strains were classified into the China lineage. The discontinuous 2 + 3 aa deletions at 400-401 and 758-760 were found in the Nsp2 and Nsp3 coding region in five strains, respectively, with similar deletions having been identified in Vietnam, Thailand, and Laos. Three novel patterns of deletion were observed for the first time in the Nsp2 and Nsp3 regions. Importantly, those findings suggest that PDCoV may have undergone a high degree of variation since PDCoV was first detected in China.

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“…Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine rotavirus (PoRV) are the most common viral agents causing piglet diarrhea [2]. Moreover, porcine deltacoronavirus (PDCoV), since first reported in 2009, has become an important cause of newborn piglet diarrhea [3][4][5][6][7][8][9]. Sometimes, mixed infections in clinics are frequent.…”

Section: Introductionmentioning

confidence: 99%

“…Like TGEV, PEDV can cause severe enteritis in newborn piglets, but has higher mortality rate that may reach 100% during epidemics [12,13]. PDCoV, as a newly emerging porcine intestinal coronavirus, can also cause enteritis and severe diarrhea in piglets [9], leading to numerous economic losses for farmers in China. Its infection appears to be clinically milder with lower neonatal mortality rate of 30-40% compared to typical PEDV infection.…”

Section: Introductionmentioning

confidence: 99%

Dual priming oligonucleotide (DPO)-based real-time RT-PCR assay for accurate differentiation of four major viruses causing porcine viral diarrhea

Jia

Feng

Wang

et al. 2019

Molecular and Cellular Probes

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A B S T R A C TCurrently in China, porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus (PoRV), and porcine deltacoronavirus (PDCoV) are the major causes of porcine viral diarrhea, and mixed infections in clinics are common, resulting in significant economic losses in pig industry. Here, a dual priming oligonucleotide (DPO)-based multiplex real-time SYBR Green RT-PCR assay were developed for accurately differentiating PEDV, TGEV, PoRV, and PDCoV in clinical specimens targeting the N gene of TGEV, PEDV, and PDCoV, and the VP7 gene of PoRV. Results showed that the DPO primer allowed a wider annealing temperature range (40-65°C) and had a higher priming specificity compared to conventional primer, in which more than 3 nucleotides in the 3′-or 5′-segment of DPO primer mismatched with DNA template, PCR amplification efficiency would decrease substantially or extension would not proceed. DPO-based multiplex real-time RT-PCR method had analytical detection limit of 8.63 × 10 2 copies/μL, 1.92 × 10 2 copies/μL, 1.74 × 10 2 copies/μL, and 1.76 × 10 2 copies/μL for PEDV, TGEV, PoRV, and PDCoV in clinical specimens, respectively. A total of 672 clinical specimens of piglets with diarrheal symptoms were collected in Northeastern China from 2017 to 2018 followed by analysis using the assay, and epidemiological investigation results showed that PEDV, TGEV, PoRV, and PDCoV prevalence was 19.05%, 5.21%, 4.32%, and 3.87%, respectively. The assay developed in this study showed higher detection accuracy than conventional RT-PCR method, suggesting a useful tool for the accurate differentiation of the four major viruses causing porcine viral diarrhea in practice.

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Prevalence, phylogenetic and evolutionary analysis of porcine deltacoronavirus in Henan province, China

Cited by 48 publications

References 36 publications

Porcine deltacoronavirus causes diarrhea in various ages of field-infected pigs in China

Porcine deltacoronavirus causes diarrhea in various ages of field-infected pigs in China

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

Dual priming oligonucleotide (DPO)-based real-time RT-PCR assay for accurate differentiation of four major viruses causing porcine viral diarrhea

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