First identification and genomic characterization of equine hepacivirus sub-type 3 strain in China
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First identification and genomic characterization of equine hepacivirus sub‑type 3 strain in China Liyan Wu1,2,3 · Jiajun Ou1,2,3 · Siqi Cai1,2,3 · Jinzhao Ji1,2,3 · Zixin Ren1,2,3 · Ran Shao1,2,3 · Shoujun Li1,2,3 Received: 22 December 2019 / Accepted: 7 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
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. Keywords Equine hepacivirus · China · Horse · Emerging disease · Sub-type Hepatitis C virus (HCV) is typically asymptomatic and is strongly associated with the development of severe liver diseases such as liver fibrosis and hepatocellular carcinoma [1]. Originally, humans were believed to be the only hosts for HCV. However, Kapoor and his team (2011) discovered a virus similar to HCV in some respiratory tissue samples from domestic dogs in the USA [2]. Furthermore, viruses that resemble HCV are continuously detected in different Edited by Takeshi Noda. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11262-020-01792-y) contains supplementary material, which is available to authorized users. * Shoujun Li [email protected] 1
College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, People’s Republic of China
2
Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong, People’s Republic of China
3
Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangzhou, Guangdong, People’s Republic of China
animals including horses [3], rodents [4] and bats [5]. The first report of horses being infected with Equine Hepacivirus (EqHV) was in the USA in 2012 [3]. However, the prevalence of EqHV in China was 3.4% in 2016 [6]. In 2019, Lu et al. classified the EqHV strains from around the world into one unique genotype and three sub-types using cut-off values for HCV genotyping [7]. In 2018, 60 serum samples were collected from horses in Guangdong, China. Tot
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