The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015

Lorsirigool, Athip; Saeng‐chuto, Kepalee; Madapong, Adthakorn; Temeeyasen, Gun; Tripipat, Thitima; Kaewprommal, Pavita; Tantituvanont, Angkana; Piriyapongsa, Jittima; Nilubol, Dachrit

doi:10.1007/s11262-016-1413-z

Cited by 36 publications

(27 citation statements)

References 21 publications

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“…Studies of genomic sequences analyses using S protein genes have shown that PDCoV can be further divided into three lineages: the China lineage, USA/Japan/South Korea lineage and Vietnam/Laos/Thailand lineage Zhang et al, 2019d). The Vietnam/Laos/Thailand lineage has been detected in Southeast Asia (Janetanakit et al, 2016;Lorsirigool et al, 2017Lorsirigool et al, , 2016Saeng-Chuto et al, 2017). 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).…”

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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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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“…cDNA was synthesized from the extracted RNA using random primers and a Takara RNA PCR Kit (Takara, Japan). The whole genome of CHN-HG-2017 was sequenced using 26 pairs of primers reported by Lorsirigool et al [23]. Based on the sequence that was obtained, a pair of primers (PDCoV-5′GSP, 5′-GAT TAC GCC AAG CTT TAG ATC GCA AGG TGG GTT GGG CTC C-3′; PDCoV-3′GSP, 5′-GAT TAC GCC AAG CTT CGT CGT AAG ACC CAA CAT CAA GCT -3′) was designed to verify the 5′-and 3′-terminal sequences of CHN-HG-2017 using a SMARTer RACE 5′/3′ Kit (Takara) according to manufacturer′s instructions.…”

Section: Phylogenetic and Recombination Analysismentioning

confidence: 99%

Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China

Zhang

Liu

et al. 2018

Arch Virol

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Porcine deltacoronavirus (PDCoV) was first detected in Hong Kong and has recently spread to many countries around the world. PDCoV causes acute diarrhea and vomiting in pigs, resulting in significant economic losses in the global pork industry. In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Subsequently, the virus was identified by an indirect immunofluorescence assay and electron microscopy. A nucleotide sequence alignment showed that the whole genome of CHN-HG-2017 is 97.6%-99.1% identical to other PDCoV strains. Analysis of potential recombination sites showed that CHN-HG-2017 is a possible recombinant originating from the strains CH/SXD1/2015 and Vietnam/HaNoi6/2015. Furthermore, the pathogenicity of this recombinant PDCoV strain was investigated in 5-day-old piglets by oral inoculation. The challenged piglets developed typical symptoms, such as vomiting, anorexia, diarrhea and lethargy, from 1 to 7 days post-inoculation (DPI). Viral shedding was detected in rectal swabs until 14 DPI in the challenged piglets. Interestingly, high titers of virus-neutralizing antibodies in sera were detected at 21 DPI. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. Our analysis of the full genome sequence of a recombinant PDCoV and its virulence in suckling piglets might provide new insights into the pathogenesis of PDCoV and facilitate further investigation of this newly emerged pathogen.

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“…Samples positive for PDCoV were then subjected to fulllength genome sequence characterization. Twenty-six pairs of primers were used to amplify the different regions of PDCoV [8]. PCR amplification was performed using Platinum Ò Taq DNA Polymerase High Fidelity (Invitrogen, CA, USA) in accordance with the manufacturer's protocol.…”

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confidence: 99%

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

et al. 2017

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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.

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The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015

Cited by 36 publications

References 21 publications

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

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

Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China

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

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