Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015

Wang, Enyu; Guo, Donghua; Li, Chunqiu; Shan, Wei; Wang, Zhihui; Liu, Qiujin; Zhang, Bei; Kong, Fanzhi; Feng, Li; Sun, Dongbo

doi:10.1371/journal.pone.0160561

Cited by 39 publications

(47 citation statements)

References 34 publications

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“…It is revealed that the classical PEDV exhibited weaker sugar‐binding activity than the recently uncovered G2 isolates (Deng et al., ). Amino acid substitutions were also reported in the receptor‐binding region (Wang et al., ). Whether the 8‐amino acid insertion observed in VN‐TH15/HY/2015 influences the biological functions of PEDV requires further study.…”

Section: Discussionmentioning

confidence: 85%

Appearance of US-like porcine epidemic diarrhoea virus (PEDV) strains before US outbreaks and genetic heterogeneity of PEDVs collected in Northern Vietnam during 2012-2015

Diep

Sueyoshi

Izzati

et al. 2017

Transbound Emerg Dis

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Summary Porcine epidemic diarrhoea virus (PEDV) is the aetiologic agent of porcine epidemic diarrhoea (PED), a highly contagious enteric disease that is threatening the swine industry globally. Since PED was first reported in Southern Vietnam in 2009, the disease has spread throughout the country and caused substantial economic losses. To identify PEDVs responsible for the recent outbreaks, the full‐length spike (S) gene of 25 field PEDV strains collected from seven northern provinces of Vietnam was sequenced and analysed. The sequence analysis revealed that the S genes of Vietnamese PEDVs were heterogeneous and classified into four genotypes, namely North America and Asian non‐S INDEL, Asian non‐S INDEL, new S INDEL and classical S INDEL. This study reported the pre‐existence of US‐like PEDV strains in Vietnam. Thirteen Vietnamese variants had a truncated S protein that was 261 amino acids shorter than the normal protein. We also detected one novel variant with an 8‐amino acid insertion located in the receptor‐binding region for porcine aminopeptidase N. Compared to the commercial vaccine strains, the emerging Vietnamese strains were genetically distant and had various amino acid differences in epitope regions and N‐glycosylation sites in the S protein. The development of novel vaccines based on the emerging Vietnamese strains may be contributive to the control of the current PED outbreaks.

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Section: Discussionmentioning

confidence: 85%

Appearance of US-like porcine epidemic diarrhoea virus (PEDV) strains before US outbreaks and genetic heterogeneity of PEDVs collected in Northern Vietnam during 2012-2015

Diep

Sueyoshi

Izzati

et al. 2017

Transbound Emerg Dis

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“…For amplification of the 6b gene of FCoV, RNA extraction and cDNA synthesis were carried out according to the protocol described by Wang et al. (). Random primers (six nucleotides) were used for synthesis of the first‐strand cDNA.…”

Section: Methodsmentioning

confidence: 99%

“…Briefly, RNA extraction and cDNA synthesis for the 50 samples were carried out according to the protocol described by Wang et al. () using random primers (six nucleotides) and an oligo dT18 primer. The double‐stranded DNA was synthesized by second strand cDNA synthesis kit (Beyotime Biotechnology, Shanghai, China).…”

Section: Methodsmentioning

confidence: 99%

Circulation and genetic diversity of Feline coronavirus type I andIIfrom clinically healthy andFIP‐suspected cats in China

Liu

Kong

et al. 2018

Transbound Emerg Dis

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Feline infectious peritonitis (FIP) is a fatal infectious disease of wild and domestic cats, and the occurrence of FIP is frequently reported in China. To trace the evolution of type I and II feline coronavirus in China, 115 samples of ascetic fluid from FIP‐suspected cats and 54 fecal samples from clinically healthy cats were collected from veterinary hospitals in China. The presence of FCoV in the samples was detected by RT‐PCR targeting the 6b gene. The results revealed that a total of 126 (74.6%, 126/169) samples were positive for FCoV: 75.7% (87/115) of the FIP‐suspected samples were positive for FCoV, and 72.2% (39/54) of the clinically healthy samples were positive for FCoV. Of the 126 FCoV‐positive samples, 95 partial S genes were successfully sequenced. The partial S gene‐based genotyping indicated that type I FCoV and type II FCoV accounted for 95.8% (91/95) and 4.2% (4/95), respectively. The partial S gene‐based phylogenetic analyses showed that the 91 type I FCoV strains exhibited genetic diversity; the four type II FCoV strains exhibited a close relationship with type II FCoV strains from Taiwan. Three type I FCoV strains, HLJ/HRB/2016/10, HLJ/HRB/2016/11 and HLJ/HRB/2016/13, formed one potential new clade in the nearly complete genome‐based phylogenetic trees. Further analysis revealed that FCoV infection appeared to be significantly correlated with a multi‐cat environment (p < 0.01) and with age (p < 0.01). The S gene of the three type I FCoV strains identified in China, BJ/2017/27, BJ/2018/22 and XM/2018/04, exhibited a six nucleotide deletion (C4035AGCTC4040). Our data provide evidence that type I and type II FCoV strains co‐circulate in the FIP‐affected cats in China. Type I FCoV strains exhibited high prevalence and genetic diversity in both FIP‐affected cats and clinically healthy cats, and a multi‐cat environment and age (<6 months) were significantly associated with FCoV infection.

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“…Further, the novel PEDV strains with new amino acid deletions in their S genes have been found in fields in China. The S proteins of strains FJAX1 and FJAX2 were found to have a 66–67 amino acid deletion28 and the S protein of HLJ2015/DP1–1 had a 377–380 amino acid deletion29 compared with the CV777 S protein. However, the pathogenicity of these three strains has not been reported so far.…”

Section: Discussionmentioning

confidence: 98%

“…Concurrently, several variant PEDV strains, characterised by insertions and deletions (INDELs) in the S gene and designated S-INDEL PEDV, were found to be circulating in United States swine farms2425. Several strains with different deletions in the S gene were also reported in previous studies222627282930. Thus, the S gene may be important for understanding the genetic relatedness of PEDV field isolates, the epidemiological status of the virus, and for vaccine development.…”

mentioning

confidence: 90%

Characterization of Chinese Porcine Epidemic Diarrhea Virus with Novel Insertions and Deletions in Genome

Fan

Jiao

Zhao

et al. 2017

Sci Rep

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Outbreaks of porcine epidemic diarrhoea virus (PEDV) have caused great economic losses to the global pig industry. PEDV strains with variants in the spike (S) gene have been reported in several countries. To better understand the molecular epidemiology and genetic diversity of PEDV field isolates, in this study, we characterised the complete genome sequence of a novel PEDV variant JSCZ1601 from a outbreak in China in 2016. The PEDV isolate was 28,033 nucleotides (nt) in length without the polyadenylated sequences. Phylogenetic analysis based on the full-length genome sequence of JSCZ1601 grouped it with the pandemic variants determined post-2010 into group 2 (G2). However, the S gene of JSCZ1601 formed a new subgroup separated from the subgroups containing the other G2 strains. Comparative analysis of the amino acids encoded by the S genes revealed the N-terminal of the deduced JSCZ1601 S protein had a novel two-amino-acid deletion (N58 and S59) compared with all identified genogroups. Further, compared with the reference strains, a ‘G’ insertion was detected in the 5′ terminal of the 5′UTR of the JSCZ1601. The animal experiment revealed that this strain was high pathogenic to neonatal pigs. Taken together, a PEDV strain with the new molecular characterizations and phylogenies was found in mainland China. It is necessary to strengthen the monitoring of PEDV variations.

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Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015

Cited by 39 publications

References 34 publications

Appearance of US-like porcine epidemic diarrhoea virus (PEDV) strains before US outbreaks and genetic heterogeneity of PEDVs collected in Northern Vietnam during 2012-2015

Appearance of US-like porcine epidemic diarrhoea virus (PEDV) strains before US outbreaks and genetic heterogeneity of PEDVs collected in Northern Vietnam during 2012-2015

Circulation and genetic diversity of Feline coronavirus type I andIIfrom clinically healthy andFIP‐suspected cats in China

Characterization of Chinese Porcine Epidemic Diarrhea Virus with Novel Insertions and Deletions in Genome

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