{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T20:44:30Z","timestamp":1790628270450,"version":"4.1.0"},"reference-count":48,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T00:00:00Z","timestamp":1635811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Hepaciviruses represent a group of viruses that pose a significant threat to the health of humans and animals. New members of the genus Hepacivirus in the family Flaviviridae have recently been identified in a wide variety of host species worldwide. Similar to the Hepatitis C virus (HCV), bovine hepacivirus (BovHepV) is hepatotropic and causes acute or persistent infections in cattle. BovHepVs are distributed worldwide and classified into two genotypes with seven subtypes in genotype 1. In this study, three BovHepV strains were identified in the samples of ticks sucking blood on cattle in the Guangdong province of China, through unbiased high-throughput sequencing. Genetic analysis revealed the polyprotein-coding gene of these viral sequences herein shared 67.7\u201384.8% nt identity and 76.1\u201395.6% aa identity with other BovHepVs identified worldwide. As per the demarcation criteria adopted for the genotyping and subtyping of HCV, these three BovHepV strains belonged to a novel subtype within the genotype 1. Additionally, purifying selection was the dominant evolutionary pressure acting on the genomes of BovHepV, and genetic recombination was not common among BovHepVs. These results expand the knowledge about the genetic diversity and evolution of BovHepV distributed globally, and also indicate genetically divergent BovHepV strains were co-circulating in cattle populations in China.<\/jats:p>","DOI":"10.3390\/v13112206","type":"journal-article","created":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T22:14:52Z","timestamp":1635891292000},"page":"2206","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["A Novel Subtype of Bovine Hepacivirus Identified in Ticks Reveals the Genetic Diversity and Evolution of Bovine Hepacivirus"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9548-3831","authenticated-orcid":false,"given":"Jian-Wei","family":"Shao","sequence":"first","affiliation":[{"name":"School of Life Sciences and Engineering, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luan-Ying","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Engineering, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao-Xian","family":"Yuan","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Engineering, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Engineering, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0404-0830","authenticated-orcid":false,"given":"Ji-Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Engineering, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3411-3196","authenticated-orcid":false,"given":"Quan","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Engineering, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nrmicro1645","article-title":"Replication of hepatitis C virus","volume":"5","author":"Moradpour","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/hep.20032","article-title":"Structural biology of hepatitis C virus","volume":"39","author":"Penin","year":"2004","journal-title":"Hepatology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1002\/hep.23138","article-title":"Experimental models for hepatitis C viral infection","volume":"50","author":"Boonstra","year":"2009","journal-title":"Hepatology"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"11608","DOI":"10.1073\/pnas.1101794108","article-title":"Characterization of a canine homolog of hepatitis C virus","volume":"108","author":"Kapoor","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1976","DOI":"10.3201\/eid1812.120498","article-title":"Nonprimate hepaciviruses in domestic horses, United Kingdom","volume":"18","author":"Lyons","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"8971","DOI":"10.1128\/JVI.00888-13","article-title":"A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate","volume":"87","author":"Lauck","year":"2013","journal-title":"J. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"8194","DOI":"10.1073\/pnas.1303037110","article-title":"Bats are a major natural reservoir for hepaciviruses and pegiviruses","volume":"110","author":"Quan","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s40168-018-0554-9","article-title":"Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases","volume":"6","author":"Wu","year":"2018","journal-title":"Microbiome"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Drexler, J.F., Corman, V.M., M\u00fcller, M.A., Lukashev, A.N., Gmyl, A., Coutard, B., Adam, A., Ritz, D., Leijten, L.M., and Van Riel, D. (2013). Evidence for novel hepaciviruses in rodents. PLoS Pathog., 9.","DOI":"10.1371\/journal.ppat.1003438"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"7007","DOI":"10.1128\/JVI.00534-15","article-title":"Identification of a novel hepacivirus in domestic cattle from Germany","volume":"89","author":"Baechlein","year":"2015","journal-title":"J. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5876","DOI":"10.1128\/JVI.00393-15","article-title":"Highly divergent hepaciviruses from African cattle","volume":"89","author":"Corman","year":"2015","journal-title":"J. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e01711","DOI":"10.1128\/JVI.01711-16","article-title":"Differential infection patterns and recent evolutionary origins of equine hepaciviruses in donkeys","volume":"91","author":"Walter","year":"2017","journal-title":"J. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1099\/jgv.0.000672","article-title":"ICTV Report, C., ICTV virus taxonomy profile: Flaviviridae","volume":"98","author":"Simmonds","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1128\/JVI.02036-15","article-title":"Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the flaviviridae and related viruses","volume":"90","author":"Shi","year":"2016","journal-title":"J. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1099\/jgv.0.001298","article-title":"A highly divergent hepacivirus-like flavivirus in domestic ducks","volume":"100","author":"Chu","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/s41586-018-0012-7","article-title":"The evolutionary history of vertebrate RNA viruses","volume":"556","author":"Shi","year":"2018","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"veaa064","DOI":"10.1093\/ve\/veaa064","article-title":"Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates","volume":"6","author":"Porter","year":"2020","journal-title":"Virus Evol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s42522-019-0006-x","article-title":"Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and a novel hepacivirus in Australian brushtail possums","volume":"1","author":"Chang","year":"2019","journal-title":"One Health Outlook"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Williams, S.H., Levy, A., Yates, R.A., Somaweera, N., Neville, P.J., Nicholson, J., Lindsay, M.D.A., Mackenzie, J.S., Jain, K., and Imrie, A. (2020). Discovery of Jogalong virus, a novel hepacivirus identified in a Culex annulirostris (Skuse) mosquito from the Kimberley region of Western Australia. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0227114"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e01358","DOI":"10.1128\/JVI.01358-18","article-title":"Extensive diversity of RNA viruses in Australian ticks","volume":"93","author":"Harvey","year":"2019","journal-title":"J. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2401","DOI":"10.1007\/s00705-019-04303-z","article-title":"Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China","volume":"164","author":"Li","year":"2019","journal-title":"Arch. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1099\/jgv.0.001082","article-title":"Comprehensive evolutionary and phylogenetic analysis of Hepacivirus N (HNV)","volume":"99","author":"Junqueira","year":"2018","journal-title":"J. Gen. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1111\/tbed.12999","article-title":"Further characterization of bovine hepacivirus: Antibody response, course of infection, and host tropism","volume":"66","author":"Baechlein","year":"2019","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3133","DOI":"10.1007\/s00705-019-04419-2","article-title":"Highly divergent cattle hepacivirus N in Southern Brazil","volume":"164","author":"Weber","year":"2019","journal-title":"Arch. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"4732520","DOI":"10.1155\/2017\/4732520","article-title":"A novel genetic group of bovine hepacivirus in archival serum samples from Brazilian cattle","volume":"2017","author":"Canal","year":"2017","journal-title":"Biomed. Res. Int."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.vetmic.2018.09.001","article-title":"Presence of bovine hepacivirus in Turkish cattle","volume":"225","author":"Baechlein","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.biologicals.2016.12.009","article-title":"Virome of US bovine calf serum","volume":"46","author":"Sadeghi","year":"2017","journal-title":"Biologicals"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Lu, G., Ou, J., Zhao, J., and Li, S. (2019). Presence of a novel subtype of bovine hepacivirus in China and expanded classification of bovine hepacivirus strains worldwide into 7 subtypes. Viruses, 11.","DOI":"10.3390\/v11090843"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s41426-018-0055-8","article-title":"Novel bovine hepacivirus in dairy cattle, China","volume":"7","author":"Lu","year":"2018","journal-title":"Emerg. Microbes. Infect."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"6216853","DOI":"10.1155\/2018\/6216853","article-title":"The detection and phylogenetic analysis of bovine hepacivirus in China","volume":"2018","author":"Deng","year":"2018","journal-title":"Biomed. Res. Int."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1007\/s00705-020-04611-9","article-title":"Complete genome sequence of a novel bovine hepacivirus from Yunnan, China","volume":"165","author":"Qiang","year":"2020","journal-title":"Arch. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1111\/tbed.13628","article-title":"Genetic heterogeneity of bovine hepacivirus in Italy","volume":"67","author":"Elia","year":"2020","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1186\/s13071-016-1764-2","article-title":"Characterization of rickettsiae in ticks in northeastern China","volume":"9","author":"Liu","year":"2016","journal-title":"Parasit. Vectors."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration","volume":"14","author":"Robinson","year":"2013","journal-title":"Brief Bioinform."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e05378","DOI":"10.7554\/eLife.05378","article-title":"Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses","volume":"4","author":"Li","year":"2015","journal-title":"Elife"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and analysis of recombination patterns in virus genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"ref_43","first-page":"418","article-title":"Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions","volume":"3","author":"Nei","year":"1986","journal-title":"Mol. Biol. Evol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"veaa051","DOI":"10.1093\/ve\/veaa051","article-title":"Diversity and circulation of Jingmen tick virus in ticks and mammals","volume":"6","author":"Guo","year":"2020","journal-title":"Virus Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2894","DOI":"10.1099\/jgv.0.000612","article-title":"Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family","volume":"97","author":"Smith","year":"2016","journal-title":"J. Gen. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"veaa033","DOI":"10.1093\/ve\/veaa033","article-title":"Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths","volume":"6","author":"Sander","year":"2020","journal-title":"Virus Evol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.meegid.2013.10.021","article-title":"Phylogeny and molecular evolution of the hepatitis C virus","volume":"21","author":"Jackowiak","year":"2014","journal-title":"Infect. Genet. Evol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/11\/2206\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:24:40Z","timestamp":1760167480000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/11\/2206"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,2]]},"references-count":48,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,11]]}},"alternative-id":["v13112206"],"URL":"https:\/\/doi.org\/10.3390\/v13112206","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,2]]}}}