{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T20:40:38Z","timestamp":1782420038446,"version":"3.54.5"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Ticks are well-known ectoparasites and vectors responsible for transmitting a diverse range of pathogens, including viruses, bacteria, and protozoa, many of which pose substantial risks to public health and livestock. In recent decades, the incidence and diversity of tick-borne diseases have increased globally, with several novel tick-borne viruses (TBVs) being discovered.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      This study aimed to characterize the virome of ticks collected from various locations in Shanghai, China, using next-generation sequencing (NGS). A total of 2,568 ticks belonging to three dominant species\u2014\n                      <jats:italic>Haemaphysalis flava<\/jats:italic>\n                      ,\n                      <jats:italic>Haemaphysalis longicornis<\/jats:italic>\n                      , and\n                      <jats:italic>Rhipicephalus sanguineus sensu lato<\/jats:italic>\n                      \u2014were collected and analyzed through metagenomic sequencing.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The sequencing analysis identified 214 viral contigs classified into 32 viral families, including Chrysoviridae, Phenuiviridae, Partitiviridae, Nairoviridae, Dicistroviridae, Reoviridae, Botourmiaviridae, and Flaviviridae. Several TBVs with potential relevance to human and animal health, such as Cheeloo Jingmen-like virus (CJLV), Songling virus (SGLV), brown dog tick phlebovirus 1 (BDTPV1), brown dog tick phlebovirus 2 (BDTPV2), and Wuhan mosquito virus 1 (WMV1), were detected. Significant differences in virome composition among tick species based on geographical locations were also observed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>These findings highlight the influence of environmental factors on viral diversity in ticks and underscore the need for ongoing surveillance of TBVs. Implementation of longitudinal virome monitoring across tick developmental stages in Shanghai will provide critical insights for early warning systems, disease prevention strategies, and public health interventions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2025.1699705","type":"journal-article","created":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T05:31:15Z","timestamp":1761111075000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China"],"prefix":"10.3389","volume":"16","author":[{"given":"Wenbo","family":"Zeng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Limin","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuhan","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongxia","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,22]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.14202\/vetworld.2016.1087-1101","article-title":"Morphological and molecular identification of the brown dog tick Rhipicephalus sanguineus and the camel tick Hyalomma dromedarii (Acari: Ixodidae) vectors of rickettsioses in Egypt","volume":"9","author":"Abdullah","year":"2016","journal-title":"Vet. World"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"19","DOI":"10.3325\/cmj.2014.55.19","article-title":"Reliability of long vs short COI markers in identification of forensically important flies","volume":"55","author":"Aly","year":"2014","journal-title":"Croat. Med. J."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1093\/sysbio\/syy036","article-title":"Multiple sequence alignment averaging improves phylogeny reconstruction","volume":"68","author":"Ashkenazy","year":"2019","journal-title":"Syst. Biol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"10034","DOI":"10.1073\/pnas.91.21.10034","article-title":"Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences","volume":"91","author":"Black","year":"1994","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"199006","DOI":"10.1016\/j.virusres.2022.199006","article-title":"Virome analysis of ticks and tick-borne viruses in Heilongjiang and Jilin provinces, China","volume":"323","author":"Cai","year":"2023","journal-title":"Virus Res."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"627327","DOI":"10.3389\/fmicb.2021.627327","article-title":"Unbiased characterization of the microbiome and Virome of questing ticks","volume":"12","author":"Chandra","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1186\/s40249-022-01017-4","article-title":"Transmission and mortality risk assessment of severe fever with thrombocytopenia syndrome in China: results from 11-years\u2019 study","volume":"11","author":"Chen","year":"2022","journal-title":"Infect. Dis. Poverty"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/j.pt.2012.07.003","article-title":"Ticks and tick-borne diseases: a one health perspective","volume":"28","author":"Dantas-Torres","year":"2012","journal-title":"Trends Parasitol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"284","DOI":"10.11604\/pamj.2017.27.284.10341","article-title":"Seasonal distribution and faunistic of ticks in the Alashtar county (Lorestan Province), Iran","volume":"27","author":"Davari","year":"2017","journal-title":"Pan. Afr. Med. J."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1186\/s13071-017-2279-1","article-title":"Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey","volume":"10","author":"Din\u00e7er","year":"2017","journal-title":"Parasites Vectors"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"49","DOI":"10.26444\/aaem\/118134","article-title":"First metagenomic report of Borrelia Americana and Borrelia carolinensis in Poland - a preliminary study","volume":"28","author":"Dunaj","year":"2021","journal-title":"Ann. Agric. Environ. Med."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1002\/arch.21327","article-title":"Translating ecology, physiology, biochemistry, and population genetics research to meet the challenge of tick and tick-borne diseases in North America","volume":"92","author":"Esteve-Gassent","year":"2016","journal-title":"Arch. Insect Biochem. Physiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1016\/s1473-3099(15)00177-2","article-title":"Emerging tick-borne infections in mainland China: an increasing public health threat","volume":"15","author":"Fang","year":"2015","journal-title":"Lancet Infect. Dis."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1093\/cid\/cix349","article-title":"Viruses in the 21st century: from the curiosity-driven discovery of Giant viruses to new concepts and definition of life","volume":"65","author":"Forterre","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1007\/s00248-020-01611-9","article-title":"Changes in bacterial diversity, composition and interactions during the development of the seabird tick Ornithodoros maritimus (Argasidae)","volume":"81","author":"Gomard","year":"2021","journal-title":"Microb. Ecol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"966735","DOI":"10.3389\/fmicb.2022.966735","article-title":"Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China","volume":"13","author":"Guo","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1186\/s13071-020-04061-x","article-title":"Under the skin: Ixodes ticks in the subcutaneous tissue of red foxes (Vulpes vulpes) from Germany","volume":"13","author":"Haut","year":"2020","journal-title":"Parasites Vectors"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1186\/s13071-017-2424-x","article-title":"Contributions to the phylogeny of Ixodes (Pholeoixodes) canisuga, I. (Ph.) kaiseri, I. (Ph.) hexagonus and a simple pictorial key for the identification of their females","volume":"10","author":"Hornok","year":"2017","journal-title":"Parasites Vectors"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"138","DOI":"10.7589\/jwd-d-21-00137","article-title":"Tacheng tick virus 1 and Songling virus infection in great gerbils (Rhombomys opimus) in northwestern China","volume":"59","author":"Ji","year":"2023","journal-title":"J. Wildl. Dis."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"5539","DOI":"10.1038\/s41467-021-25857-0","article-title":"A novel nairovirus associated with acute febrile illness in Hokkaido, Japan","volume":"12","author":"Kodama","year":"2021","journal-title":"Nat Commun"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e0324537","DOI":"10.1371\/journal.pone.0324537","article-title":"Evaluation of metatranscriptomic sequencing protocols to obtain full-length RNA virus genomes from mammalian tissues","volume":"20","author":"Li","year":"2025","journal-title":"PLoS One"},{"key":"ref23","doi-asserted-by":"publisher","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":"ref24","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1002\/rmv.1776","article-title":"Systematic review of severe fever with thrombocytopenia syndrome: virology, epidemiology, and clinical characteristics","volume":"24","author":"Liu","year":"2014","journal-title":"Rev. Med. Virol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1016\/s1473-3099(14)70718-2","article-title":"Severe fever with thrombocytopenia syndrome, an emerging tick-borne zoonosis","volume":"14","author":"Liu","year":"2014","journal-title":"Lancet Infect. Dis."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1375852","DOI":"10.3389\/fvets.2024.1375852","article-title":"Identification and phylogenetic analysis of Jingmen tick virus in Jiangxi Province, China","volume":"11","author":"Liu","year":"2024","journal-title":"Front. Vet. Sci."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"e0011017","DOI":"10.1371\/journal.pntd.0011017","article-title":"Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China","volume":"16","author":"Liu","year":"2022","journal-title":"PLoS Negl. Trop. Dis."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/j.ijppaw.2021.06.003","article-title":"Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing","volume":"15","author":"Luo","year":"2021","journal-title":"Int. J. Parasitol. Parasites Wildl."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1186\/1756-3305-7-93","article-title":"Assessment of four DNA fragments (COI, 16S rDNA, ITS2, 12S rDNA) for species identification of the Ixodida (Acari: Ixodida)","volume":"7","author":"Lv","year":"2014","journal-title":"Parasites Vectors"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1038\/s41591-020-01228-y","article-title":"Identification of a new orthonairovirus associated with human febrile illness in China","volume":"27","author":"Ma","year":"2021","journal-title":"Nat. Med."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1056\/NEJMoa1203378","article-title":"A new phlebovirus associated with severe febrile illness in Missouri","volume":"367","author":"McMullan","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1016\/j.ttbdis.2018.12.002","article-title":"Virome analysis of tick-borne viruses in Heilongjiang Province, China","volume":"10","author":"Meng","year":"2019","journal-title":"Ticks Tick Borne Dis."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1146\/annurev.genet.41.110306.130119","article-title":"Genomics and evolution of heritable bacterial symbionts","volume":"42","author":"Moran","year":"2008","journal-title":"Annu. Rev. Genet."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/s13071-020-3908-7","article-title":"The scale affects our view on the identification and distribution of microbial communities in ticks","volume":"13","author":"Pollet","year":"2020","journal-title":"Parasites Vectors"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"10421","DOI":"10.1038\/s41598-019-46914-1","article-title":"Viral diversity of tick species parasitizing cattle and dogs in Trinidad and Tobago","volume":"9","author":"Sameroff","year":"2019","journal-title":"Sci. Rep."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/s41426-018-0093-2","article-title":"A novel tick-borne phlebovirus, closely related to severe fever with thrombocytopenia syndrome virus and heartland virus, is a potential pathogen","volume":"7","author":"Shen","year":"2018","journal-title":"Emerg Microbes Infect"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/nature20167","article-title":"Redefining the invertebrate RNA virosphere","volume":"540","author":"Shi","year":"2016","journal-title":"Nature"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"e3001007","DOI":"10.1371\/journal.pbio.3001007","article-title":"ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference","volume":"18","author":"Steenwyk","year":"2020","journal-title":"PLoS Biol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1111\/j.1462-2920.2011.02438.x","article-title":"Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities","volume":"14","author":"Suenaga","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1186\/s13071-019-3707-1","article-title":"Prevalence of the emerging novel Alongshan virus infection in sheep and cattle in Inner Mongolia, northeastern China","volume":"12","author":"Wang","year":"","journal-title":"Parasites Vectors"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"2116","DOI":"10.1056\/NEJMoa1805068","article-title":"A new segmented virus associated with human febrile illness in China","volume":"380","author":"Wang","year":"","journal-title":"N. Engl. J. Med."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1080\/22221751.2021.1936197","article-title":"A new nairo-like virus associated with human febrile illness in China","volume":"10","author":"Wang","year":"2021","journal-title":"Emerg. Microbes Infect."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e0121609","DOI":"10.1371\/journal.pone.0121609","article-title":"Metagenomic profile of the viral communities in Rhipicephalus spp. ticks from Yunnan, China","volume":"10","author":"Xia","year":"2015","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"veab089","DOI":"10.1093\/ve\/veab089","article-title":"Tick virome diversity in Hubei Province, China, and the influence of host ecology","volume":"7","author":"Xu","year":"2021","journal-title":"Virus Evol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e1002369","DOI":"10.1371\/journal.ppat.1002369","article-title":"Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (FTLS) in Henan Province, China: discovery of a new bunyavirus","volume":"7","author":"Xu","year":"2011","journal-title":"PLoS Pathog."},{"key":"ref47","first-page":"1","article-title":"Ticks of Japan, Korea and the Ryukyu islands","volume":"15","author":"Yamaguti","year":"1971","journal-title":"Brighan Young Univ. Sci. Bull."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"e0268822","DOI":"10.1128\/spectrum.02688-22","article-title":"Meta-Viromic sequencing reveals virome characteristics of mosquitoes and Culicoides on Zhoushan Island, China","volume":"11","author":"Yang","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/s40168-024-01753-9","article-title":"Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis","volume":"12","author":"Ye","year":"2024","journal-title":"Microbiome"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.7679\/j.issn.2095?1353.2015.128","article-title":"Progress in research on tick borne diseases and vector ticks","volume":"52","author":"Yu Zhijun","year":"2015","journal-title":"Chin. J. Appl. Entomol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"413","DOI":"10.3390\/tropicalmed7120413","article-title":"Identification of bacterial communities and tick-borne pathogens in Haemaphysalis spp. Collected from Shanghai, China","volume":"7","author":"Zeng","year":"2022","journal-title":"Trop. Med. Infect. Dis."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1007\/s12250-016-3931-1","article-title":"Current status of severe fever with thrombocytopenia syndrome in China","volume":"32","author":"Zhan","year":"2017","journal-title":"Virol. Sin."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1186\/s12879-021-06877-z","article-title":"A tick bite patient with fever and meningitis co-infected with Rickettsia raoultii and Tacheng tick virus 1: a case report","volume":"21","author":"Zhang","year":"2021","journal-title":"BMC Infect. Dis."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1016\/j.coviro.2016.02.006","article-title":"The emergence and cross species transmission of newly discovered tick-borne Bunyavirus in China","volume":"16","author":"Zhang","year":"2016","journal-title":"Curr. Opin. Virol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1007\/s12250-020-00197-3","article-title":"Comparison of Viromes in ticks from different domestic animals in China","volume":"35","author":"Zhao","year":"2020","journal-title":"Virol. Sin."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"2136","DOI":"10.3201\/eid2511.190512","article-title":"Tamdy virus in Ixodid ticks infesting Bactrian camels, Xinjiang, China, 2018","volume":"25","author":"Zhou","year":"2019","journal-title":"Emerg. Infect. Dis."}],"updated-by":[{"DOI":"10.3389\/fmicb.2025.1731347","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T00:00:00Z","timestamp":1762732800000}}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1699705\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T13:52:55Z","timestamp":1762782775000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1699705\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,22]]},"references-count":55,"alternative-id":["10.3389\/fmicb.2025.1699705"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1699705","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,22]]},"article-number":"1699705"}}