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Virus genes2020; 56(6); 777-780; doi: 10.1007/s11262-020-01792-y

First identification and genomic characterization of equine hepacivirus sub-type 3 strain in China.

Abstract: Equine Hepacivirus (EqHV) is a newly discovered equine virus that is classified under the Hepacivirus genus of the Flaviviridae family. There are three sub-types of EqHV worldwide namely; sub-types 1-3. The majority of EqHV sub-type 1 strains were found in China. While different sub-types have been found in Japan and USA, therefore, to investigate whether the other sub-types of EqHV strains were present in China, a total of 60 horse serum samples were collected and screened for EqHV RNA through RT-PCR. The results revealed that 19 serum samples were RNA-positive (19/60) and the EqHV detection rate was 31.67%. One EqHV strain named GD23 was obtained and its near-complete genome sequence was acquired. Analysis of nucleotide p-distance with reference to the entire polyprotein gene revealed that GD23 was classified into sub-type 3. In addition, the phylogenetic analysis demonstrated that GD23 was clustered together with EqHV strains of sub-type 3 in other countries. The present study is the first to identify an EqHV sub-type 3 strain in China.
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Publication Date: 2020-09-22 PubMed ID: 32964346DOI: 10.1007/s11262-020-01792-yGoogle Scholar: Lookup
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Summary

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The research discusses the discovery and genomic characterization of a subtype 3 strain of Equine Hepacivirus (EqHV) in China, a virus belonging to the Hepacivirus genus of the Flaviviridae family.

Sampling and Methodology

  • The researchers collected 60 horse serum samples to investigate whether the different subtypes of EqHV strains, particularly sub-type 3, were present in the country. Prior to this study, only subtype 1 strains were predominantly found in the region. Meanwhile, varying subtypes were identified in Japan and the United States.
  • The collected serum samples underwent screening for EqHV RNA through a method known as RT-PCR, a popular laboratory technique used to amplify and detect RNA sequences.

Findings and Analysis

  • The screening results revealed that out of the 60 samples, 19 were RNA-positive, indicating an EqHV detection rate of approximately 31.67%.
  • The researchers were able to isolate a strain of the virus, named GD23, from one of the positive samples. They further managed to acquire its near-complete genome sequence for in-depth study and characterization.
  • The analysis of the nucleotide p-distance with the reference to the entire polyprotein gene revealed that the GD23 strain fell under sub-type 3, making it the first identification of its kind in China.
  • In addition, the phylogenetic analysis, a study that explores the evolutionary relationships between different species or strains based on their genetic characteristics, demonstrated that GD23 was similar to EqHV strains of sub-type 3 found in other countries. This suggests shared evolutionary paths and genetic ties.

Implications

  • This study represents the first identification and genomic characterization of the EqHV sub-type 3 strain in China, which provides crucial insight into EqHV’s diversity. Additionally, it contributes valuable data to the global understanding of the virus and its distribution among horse populations.

Cite This Article

APA
Wu L, Ou J, Cai S, Ji J, Ren Z, Shao R, Li S. (2020). First identification and genomic characterization of equine hepacivirus sub-type 3 strain in China. Virus Genes, 56(6), 777-780. https://doi.org/10.1007/s11262-020-01792-y

Publication

Virus genes
ISSN: 1572-994X
NlmUniqueID: 8803967
Country: United States
Language: English
Volume: 56
Issue: 6
Pages: 777-780

Researcher Affiliations

Wu, Liyan
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China.
Ou, Jiajun
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China.
Cai, Siqi
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China.
Ji, Jinzhao
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China.
Ren, Zixin
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China.
Shao, Ran
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China.
Li, Shoujun
  • College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China. shoujunli@scau.edu.cn.
  • Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People's Republic of China. shoujunli@scau.edu.cn.
  • Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People's Republic of China. shoujunli@scau.edu.cn.

MeSH Terms

  • Animals
  • China
  • Genome, Viral
  • Hepacivirus / classification
  • Hepacivirus / genetics
  • Hepacivirus / isolation & purification
  • Hepatitis C / veterinary
  • Hepatitis C / virology
  • Horses / virology
  • Phylogeny
  • RNA, Viral

Grant Funding

  • 31372448 / The National Natural Science Foundation of China
  • 31672563 / The National Natural Science Foundation of China
  • 201303042 / The Special Fund for Agro-scientific Research in the Public Interest
  • 2016YFD0501004 / The National Key Research and Development Program of China
  • 2016YFD0501010 / The National Key Research and Development Program of China
  • 2013B040200032 / The Promote Scientific and Technological Development Program
  • 2013A061401013 / The Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases

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This article includes 7 references
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Citations

This article has been cited 1 times.
  1. Pacchiarotti G, Nardini R, Scicluna MT. Equine Hepacivirus: A Systematic Review and a Meta-Analysis of Serological and Biomolecular Prevalence and a Phylogenetic Update.. Animals (Basel) 2022 Sep 20;12(19).
    doi: 10.3390/ani12192486pubmed: 36230228google scholar: lookup
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