{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:16:53Z","timestamp":1790799413828,"version":"4.1.0"},"reference-count":38,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T00:00:00Z","timestamp":1662076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31972707"],"award-info":[{"award-number":["31972707"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Pangolins are endangered animals and are listed in the CITES Appendix I of the Convention International Trade Endangered Species of Wild Fauna and Flora as well as being the national first-level protected wild animal in China. Based on a few reports on pangolins infected with pestiviruses of the Flaviviridae family, <jats:italic>Pestivirus<\/jats:italic> infections in pangolins have attracted increasing attention. Pangolin pestivirus is a pathogen that may cause diseases such as acute diarrhea and acute hemorrhagic syndrome. To better understand the epidemiology and genomic characterization of pestiviruses carried by pangolins, we detected pestiviruses in dead Malayan pangolin using metavirome sequencing technology and obtained a <jats:italic>Pestivirus<\/jats:italic> sequence of 12,333 nucleotides (named Guangdong pangolin <jats:italic>Pestivirus<\/jats:italic>, GDPV). Phylogenetic tree analysis based on the entire coding sequence, <jats:italic>NS3<\/jats:italic> gene or <jats:italic>RdRp<\/jats:italic> gene sequences, showed that GDPV was closely related to previously reported pangolin-derived <jats:italic>Pestivirus<\/jats:italic> and clustered into a separate branch. Molecular epidemiological investigation revealed that 15 <jats:italic>Pestivirus<\/jats:italic>-positive tissues from two pangolins individuals with a positivity rate of 5.56%, and six <jats:italic>Amblyomma javanense<\/jats:italic> carried pestiviruses with a positivity rate of 19.35%. Moreover, the <jats:italic>RdRp<\/jats:italic> gene of the <jats:italic>Pestivirus<\/jats:italic> carried by <jats:italic>A. javanense<\/jats:italic> showed a high similarity to that carried by pangolins (93\u2013100%), indicating <jats:italic>A. javanense<\/jats:italic> is likely to represent the vector of <jats:italic>Pestivirus<\/jats:italic> transmission. This study expands the diversity of viruses carried by pangolins and provides an important reference value for interrupting the transmission route of the virus and protecting the health of pangolins.<\/jats:p>","DOI":"10.3389\/fmicb.2022.988730","type":"journal-article","created":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T13:46:43Z","timestamp":1662126403000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Detection of a novel Pestivirus strain in Java ticks (Amblyomma javanense) and the hosts Malayan pangolin (Manis javanica) and Chinese pangolin (Manis pentadactyla)"],"prefix":"10.3389","volume":"13","author":[{"given":"Yuan-Ni","family":"Shi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin-Miao","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Bin","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Hua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi-Liao","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye-Pin","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi-Guo","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin-Ping","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,9,2]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"86","DOI":"10.3390\/v9040086","article-title":"Classical swine fever\u2014an updated review","volume":"9","author":"Blome","year":"2017","journal-title":"Viruses"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e0117199","DOI":"10.1371\/journal.pone.0117199","article-title":"Knowledge and uses of African pangolins as a source of traditional medicine in Ghana","volume":"10","author":"Boakye","year":"2015","journal-title":"PLoS One"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1177\/03009858211002198","article-title":"Canine parvovirus infections in Taiwanese pangolins (Manis pentadactyla pentadactyla)","volume":"58","author":"Chang","year":"2021","journal-title":"Vet. Pathol."},{"key":"ref4","first-page":"371","article-title":"Bovine viral diarrhea virus: biotypes and disease","volume":"36","author":"Deregt","year":"1995","journal-title":"Can. Vet. J."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1590\/0037-8682-0014-2012","article-title":"Approaches towards tick and tick-borne diseases control","volume":"46","author":"Domingos","year":"2013","journal-title":"Rev. Soc. Bras. Med. Trop."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1186\/s12864-017-4140-5","article-title":"Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae","volume":"18","author":"du Toit","year":"2017","journal-title":"BMC Genomics"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1111\/mve.12403","article-title":"Mitochondrial genome of Amblyomma javanense: a hard tick parasite of the endangered Malayan pangolin (Manis javanica)","volume":"34","author":"Duan","year":"2020","journal-title":"Med. Vet. Entomol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"veaa020","DOI":"10.1093\/ve\/veaa020","article-title":"Newly identified viral genomes in pangolins with fatal disease","volume":"6","author":"Gao","year":"2020","journal-title":"Virus Evol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1093\/jhered\/esx097","article-title":"The complete phylogeny of pangolins: scaling up resources for the molecular tracing of the most trafficked mammals on earth","volume":"109","author":"Gaubert","year":"2018","journal-title":"J. Hered."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1111\/j.1348-0421.2000.tb02583.x","article-title":"Giraffe strain of pestivirus: its taxonomic status based on the 5\u2032-untranslated region","volume":"44","author":"Harasawa","year":"2000","journal-title":"Microbiol. Immunol."},{"key":"ref11","doi-asserted-by":"publisher","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":"ref12","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1016\/j.cell.2022.02.014","article-title":"Virome characterization of game animals in China reveals a spectrum of emerging pathogens","volume":"185","author":"He","year":"2022","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1093\/nsr\/nwaa031","article-title":"Genomic consequences of population decline in critically endangered pangolins and their demographic histories","volume":"7","author":"Hu","year":"2020","journal-title":"Natl. Sci. Rev."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"10917","DOI":"10.1038\/s41598-017-11384-w","article-title":"Virome analysis for identification of novel mammalian viruses in bats from Southeast China","volume":"7","author":"Hu","year":"2017","journal-title":"Sci. Rep."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","article-title":"MRBAYES: Bayesian inference of phylogenetic trees","volume":"17","author":"Huelsenbeck","year":"2001","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1007\/s10493-019-00393-1","article-title":"Identifying the tick Amblyomma javanense (Acari: Ixodidae) from Chinese pangolin: generating species barcode, phylogenetic status and its implication in wildlife forensics","volume":"78","author":"Jabin","year":"2019","journal-title":"Exp. Appl. Acarol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"728","DOI":"10.3390\/pathogens10060728","article-title":"Molecular detection of novel Borrelia species, Candidatus Borrelia javanense in Amblyomma javanense ticks from pangolins","volume":"10","author":"Jiang","year":"2021","journal-title":"Pathogens"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.1016\/j.ttbdis.2016.07.007","article-title":"Surveillance of ticks and associated pathogens in free-ranging Formosan pangolins (Manis pentadactyla pentadactyla)","volume":"7","author":"Khatri-Chhetri","year":"2016","journal-title":"Ticks Tick Borne Dis."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.vetpar.2016.05.025","article-title":"Molecular detection of Anaplasma spp. in pangolins (Manis javanica) and wild boars (Sus scrofa) in peninsular Malaysia","volume":"227","author":"Koh","year":"2016","journal-title":"Vet. Parasitol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1038\/438575a","article-title":"Fruit bats as reservoirs of Ebola virus","volume":"438","author":"Leroy","year":"2005","journal-title":"Nature"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with burrows-wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ymeth.2016.02.020","article-title":"MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices","volume":"102","author":"Li","year":"2016","journal-title":"Methods"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"979","DOI":"10.3390\/v11110979","article-title":"Viral Metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica)","volume":"11","author":"Liu","year":"2019","journal-title":"Viruses"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/0378-1135(90)90135-i","article-title":"Pestiviruses: a review","volume":"23","author":"Moenning","year":"1990","journal-title":"Vet. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1542","DOI":"10.3390\/v13081542","article-title":"Proposed update to the taxonomy of Pestiviruses: eight additional species within the genus Pestivirus, family Flaviviridae","volume":"13","author":"Postel","year":"2021","journal-title":"Viruses"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"950","DOI":"10.3390\/v13060950","article-title":"Global distribution and genetic heterogeneity of border disease virus","volume":"13","author":"Righi","year":"2021","journal-title":"Viruses"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1847","DOI":"10.3201\/eid1312.071115","article-title":"Studies of reservoir hosts for Marburg virus","volume":"13","author":"Swanepoel","year":"2007","journal-title":"Emerg. Infect. Dis."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/bs.aivir.2015.03.002","article-title":"The molecular biology of Pestiviruses","volume":"93","author":"Tautz","year":"2015","journal-title":"Adv. Virus Res."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"3829","DOI":"10.1007\/s10531-020-02053-y","article-title":"Do not blame bats and pangolins! Global consequences for wildlife conservation after the SARS-CoV-2 pandemic","volume":"29","author":"Turcios-Casco","year":"2020","journal-title":"Biodivers. Conserv."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.vetmic.2006.06.003","article-title":"Pestiviruses in wild animals","volume":"116","author":"Vilcek","year":"2006","journal-title":"Vet. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"947","DOI":"10.7589\/2018-09-211","article-title":"Complete genome sequence of Parainfluenza virus 5 (PIV5) from a Sunda pangolin (Manis javanica) in China","volume":"55","author":"Wang","year":"2019","journal-title":"J. Wildl. Dis."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1834","DOI":"10.3201\/eid1212.060401","article-title":"Review of bats and SARS","volume":"12","author":"Wang","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.actbio.2016.05.028","article-title":"Pangolin armor: overlapping, structure, and mechanical properties of the keratinous scales","volume":"41","author":"Wang","year":"2016","journal-title":"Acta Biomater."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"2562","DOI":"10.3389\/fmicb.2018.02562","article-title":"Discovery of diverse rodent and bat pestiviruses with distinct genomic and phylogenetic characteristics in several Chinese provinces","volume":"9","author":"Wu","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"5312","DOI":"10.1128\/jvi.71.7.5312-5322.1997","article-title":"Bovine viral diarrhea virus NS3 serine proteinase: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication","volume":"71","author":"Xu","year":"1997","journal-title":"J. Virol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"410","DOI":"10.3967\/bes2021.055","article-title":"Tick-borne pathogens in Shanxi Province, China","volume":"34","author":"Yang","year":"2021","journal-title":"Biomed. Environ. Sci."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"874003","DOI":"10.3389\/fcimb.2022.874003","article-title":"Multiple novel mosquito-borne zoonotic viruses revealed in pangolin virome","volume":"12","author":"Zhang","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.988730\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T13:46:48Z","timestamp":1662126408000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.988730\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,2]]},"references-count":38,"alternative-id":["10.3389\/fmicb.2022.988730"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.988730","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,2]]},"article-number":"988730"}}