{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T08:18:13Z","timestamp":1789892293264,"version":"4.0.1"},"reference-count":40,"publisher":"Editorial Committee of Japanese Journal of Infectious Diseases, National Institute of Infectious Dis","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Jpn J Infect Dis"],"published-print":{"date-parts":[[2026,1,30]]},"DOI":"10.7883\/yoken.jjid.2025.027","type":"journal-article","created":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T18:07:27Z","timestamp":1751220447000},"page":"29-37","source":"Crossref","is-referenced-by-count":2,"title":["RNA Virome Analysis of &lt;i&gt;Haemaphysalis longicornis&lt;\/i&gt; Ticks Collected in Hyogo, Japan"],"prefix":"10.7883","volume":"79","author":[{"given":"Alisa Rose","family":"Aboshi","sequence":"first","affiliation":[{"name":"School of Agriculture, Meiji University, Japan"},{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryo","family":"Matsumura","sequence":"additional","affiliation":[{"name":"School of Agriculture, Meiji University, Japan"},{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mizue","family":"Inumaru","sequence":"additional","affiliation":[{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyoko","family":"Sawabe","sequence":"additional","affiliation":[{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mamoru","family":"Watanabe","sequence":"additional","affiliation":[{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshinori","family":"Sasaki","sequence":"additional","affiliation":[{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daisuke","family":"Kobayashi","sequence":"additional","affiliation":[{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyo","family":"Itoyama","sequence":"additional","affiliation":[{"name":"School of Agriculture, Meiji University, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haruhiko","family":"Isawa","sequence":"additional","affiliation":[{"name":"Department of Medical Entomology, National Institute of Infectious Diseases, Japan Institute of Health Security, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4631","reference":[{"key":"1","doi-asserted-by":"crossref","unstructured":"1. Madison-Antenucci S, Kramer LD, Gebhardt LL, et al. Emerging tick-borne diseases. Clin Microbiol Rev. 2020;33:2.","DOI":"10.1128\/CMR.00083-18"},{"key":"2","doi-asserted-by":"crossref","unstructured":"2. McMullan LK, Folk SM, Kelly AJ, et al. A new phlebovirus associated with severe febrile illness in Missouri. N Engl J Med. 2012;367:834-841.","DOI":"10.1056\/NEJMoa1203378"},{"key":"3","doi-asserted-by":"crossref","unstructured":"3. Yu XJ, Liang MF, Zhang SY, et al. Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med. 2011;364:1523-1532.","DOI":"10.1056\/NEJMoa1010095"},{"key":"4","doi-asserted-by":"crossref","unstructured":"4. Takahashi T, Maeda K, Suzuki T, et al. The first identification and retrospective study of severe fever with thrombocytopenia syndrome in Japan. J Infect Dis. 2014;209:816-827.","DOI":"10.1093\/infdis\/jit603"},{"key":"5","doi-asserted-by":"crossref","unstructured":"5. Kim KH, Yi J, Kim G, et al. Severe fever with thrombocytopenia syndrome, South Korea, 2012. Emerg Infect Dis. 2013;19:1892-1894.","DOI":"10.3201\/eid1911.130792"},{"key":"6","doi-asserted-by":"crossref","unstructured":"6. Kobayashi Y, Kato H, Yamagishi T, et al. Severe fever with thrombocytopenia syndrome, Japan, 2013\u20132017. Emerg Infect Dis. 2020;26:692-699.","DOI":"10.3201\/eid2604.191011"},{"key":"7","doi-asserted-by":"crossref","unstructured":"7. Kosoy OI, Lambert AJ, Hawkinson DJ, et al. Novel thogotovirus associated with febrile illness and death, United States, 2014. Emerg Infect Dis. 2015;21:760-764.","DOI":"10.3201\/eid2105.150150"},{"key":"8","doi-asserted-by":"crossref","unstructured":"8. Kobayashi D, Murota K, Itokawa K, et al. RNA virome analysis of questing ticks from Hokuriku District, Japan, and the evolutionary dynamics of tick-borne phleboviruses. Ticks Tick Borne Dis. 2020;11:101364.","DOI":"10.1016\/j.ttbdis.2019.101364"},{"key":"9","doi-asserted-by":"crossref","unstructured":"9. Matsumura R, Kobayashi D, Itoyama K, et al. Detection of novel coltivirus-related sequences in <i>Haemaphysalis megaspinosa<\/i> ticks collected from Kanagawa Prefecture, Japan. J Vet Med Sci. 2024;86:866-871.","DOI":"10.1292\/jvms.24-0124"},{"key":"10","doi-asserted-by":"crossref","unstructured":"10. Luo LM, Zhao L, Wen HL, et al. <i>Haemaphysalis longicornis<\/i> ticks as reservoir and vector of severe fever with thrombocytopenia syndrome virus in China. Emerg Infect Dis. 2015;21:1770-1776.","DOI":"10.3201\/eid2110.150126"},{"key":"11","doi-asserted-by":"crossref","unstructured":"11. Natsuaki M, Tick bites in Japan. J Dermatol. 2021;48:423-430.","DOI":"10.1111\/1346-8138.15779"},{"key":"12","doi-asserted-by":"crossref","unstructured":"12. Shao L, Pang Z, Fu H, et al. Identification of recently identified tick-borne viruses (Dabieshan tick virus and SFTSV) by metagenomic analysis in ticks from Shandong province, China. J Infect. 2020;81:973-978.","DOI":"10.1016\/j.jinf.2020.10.022"},{"key":"13","doi-asserted-by":"crossref","unstructured":"13. Yang Z, Zhang J, Yang S, et al. Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence. Virol J. 2021;18:163.","DOI":"10.1186\/s12985-021-01632-x"},{"key":"14","doi-asserted-by":"crossref","unstructured":"14. Itokawa K, Sekizuka T, Maekawa Y, et al. High-throughput genotyping of a full voltage-gated sodium channel gene via genomic DNA using target capture sequencing and analytical pipeline MoNaS to discover novel insecticide resistance mutations. PLoS Negl Trop Dis. 2019;13:e0007818.","DOI":"10.1371\/journal.pntd.0007818"},{"key":"15","doi-asserted-by":"crossref","unstructured":"15. Kobayashi D, Komatsu N, Faizah AN, et al. A novel nyavirus lacking matrix and glycoprotein genes from <i>Argas japonicus<\/i> ticks. Virus Res. 2021;292:198254.","DOI":"10.1016\/j.virusres.2020.198254"},{"key":"16","doi-asserted-by":"crossref","unstructured":"16. Barnes M, Price DC. Endogenous viral elements in Ixodid tick genomes. Viruses. 2023;15:2201.","DOI":"10.3390\/v15112201"},{"key":"17","doi-asserted-by":"crossref","unstructured":"17. Russo AG, Kelly AG, Tuipulotu DE, et al. Novel insights into endogenous RNA viral elements in <i>Ixodes scapularis<\/i> and other arbovirus vector genomes. Virus Evol. 2019;5:vez010.","DOI":"10.1093\/ve\/vez010"},{"key":"18","doi-asserted-by":"crossref","unstructured":"18. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160-1166.","DOI":"10.1093\/bib\/bbx108"},{"key":"19","doi-asserted-by":"crossref","unstructured":"19. Katoh K, Kuma K, Toh H, et al. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33:511-518.","DOI":"10.1093\/nar\/gki198"},{"key":"20","doi-asserted-by":"crossref","unstructured":"20. Katoh K, Misawa K, Kuma K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059-3066.","DOI":"10.1093\/nar\/gkf436"},{"key":"21","doi-asserted-by":"crossref","unstructured":"21. Kumar S, Stecher G, Li M, et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547-1549.","DOI":"10.1093\/molbev\/msy096"},{"key":"22","doi-asserted-by":"crossref","unstructured":"22. Felsenstein J. Phylogenies and the comparative method. Am Nat. 1985;125:1-15.","DOI":"10.1086\/284325"},{"key":"23","doi-asserted-by":"crossref","unstructured":"23. Li CX, Shi M, Tian JH, et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife. 2015;4:e05378.","DOI":"10.7554\/eLife.05378"},{"key":"24","doi-asserted-by":"crossref","unstructured":"24. Shi M, Lin XD, Tian JH, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540:539-543.","DOI":"10.1038\/nature20167"},{"key":"25","doi-asserted-by":"crossref","unstructured":"25. Xu L, Guo M, Hu B, et al. Tick virome diversity in Hubei Province, China, and the influence of host ecology. Virus Evol. 2021;7:veab089. Erratum in Virus Evol. 2022;7:veab108.","DOI":"10.1093\/ve\/veab108"},{"key":"26","doi-asserted-by":"crossref","unstructured":"26. Mekata H, Kobayashi I, Okabayashi T. Detection and phylogenetic analysis of Dabieshan tick virus and Okutama tick virus in ticks collected from Cape Toi, Japan. Ticks Tick Borne Dis. 2023;14:102237.","DOI":"10.1016\/j.ttbdis.2023.102237"},{"key":"27","doi-asserted-by":"crossref","unstructured":"27. Kobayashi D, Kuwata R, Kimura T, et al. Detection of quaranjavirus-like sequences from <i>Haemaphysalis hystricis<\/i> ticks collected in Japan. Jpn J Infect Dis. 2022;75:195-198.","DOI":"10.7883\/yoken.JJID.2021.129"},{"key":"28","doi-asserted-by":"crossref","unstructured":"28. Sameroff S, Tokarz R, Jain K, et al. Novel quaranjavirus and other viral sequences identified from ticks parasitizing hunted wildlife in Trinidad and Tobago. Ticks Tick Borne Dis. 2021;12:101730.","DOI":"10.1016\/j.ttbdis.2021.101730"},{"key":"29","doi-asserted-by":"crossref","unstructured":"29. Guo L, Ma J, Lin J, et al. Virome of <i>Rhipicephalus<\/i> ticks by metagenomic analysis in Guangdong, southern China. Front Microbiol. 2022;13:966735.","DOI":"10.3389\/fmicb.2022.966735"},{"key":"30","doi-asserted-by":"crossref","unstructured":"30. Bratuleanu BE, Temmam S, Munier S, et al. Detection of <i>Phenuiviridae<\/i>, <i>Chuviridae<\/i> members, and a novel <i>quaranjavirus<\/i> in hard ticks from Danube Delta. Front Vet Sci. 2022;9:863814.","DOI":"10.3389\/fvets.2022.863814"},{"key":"31","doi-asserted-by":"crossref","unstructured":"31. Yong DL, Liu Y, Low BW, et al. Migratory songbirds in the East Asian-Australasian Flyway: a review from a conservation perspective. Bird Conserv Int. 2015;25:1-37.","DOI":"10.1017\/S0959270914000276"},{"key":"32","unstructured":"32. Ministry of the Environment, Government of Japan. Survey of migratory bird flights. Available at &lt;https:\/\/www.env.go.jp\/nature\/dobutsu\/bird_flu\/migratory\/ap_wr_transit\/index.html&gt;. Accessed June 6, 2024. Japanese."},{"key":"33","doi-asserted-by":"crossref","unstructured":"33. Yun Y, Heo ST, Kim G, et al. Phylogenetic analysis of severe fever with thrombocytopenia syndrome virus in South Korea and migratory bird routes between China, South Korea, and Japan. Am J Trop Med Hyg. 2015;93:468-474.","DOI":"10.4269\/ajtmh.15-0047"},{"key":"34","doi-asserted-by":"crossref","unstructured":"34. Ma C, Zhang R, Zhou H, et al. Prevalence and genetic diversity of Dabieshan tick virus in Shandong Province, China. J Infect. 2022;85:90-122.","DOI":"10.1016\/j.jinf.2022.04.002"},{"key":"35","doi-asserted-by":"crossref","unstructured":"35. Qin T, Shi M, Zhang M, et al. Diversity of RNA viruses of three dominant tick species in North China. Front Vet Sci. 2023;9:1057977.","DOI":"10.3389\/fvets.2022.1057977"},{"key":"36","doi-asserted-by":"crossref","unstructured":"36. Ye RZ, Li YY, Xu DL, et al. Virome diversity shaped by genetic evolution and ecological landscape of <i>Haemaphysalis longicornis<\/i>. Microbiome. 2024;12:35.","DOI":"10.1186\/s40168-024-01753-9"},{"key":"37","doi-asserted-by":"crossref","unstructured":"37. Tamm T, Truve E. Sobemoviruses. J Virol. 2000;74:6231-6241.","DOI":"10.1128\/JVI.74.14.6231-6241.2000"},{"key":"38","doi-asserted-by":"crossref","unstructured":"38. Dolja VV, Koonin EV. Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer. Virus Res. 2018;244:36-52.","DOI":"10.1016\/j.virusres.2017.10.020"},{"key":"39","doi-asserted-by":"crossref","unstructured":"39. Presti RM, Zhao G, Beatty WL, et al. Quaranfil, Johnston Atoll, and Lake Chad viruses are novel members of the family <i>Orthomyxoviridae<\/i>. J Virol. 2009;83:11599-11606.","DOI":"10.1128\/JVI.00677-09"},{"key":"40","doi-asserted-by":"crossref","unstructured":"40. Salvati MV, Salaris C, Monteil V, et al. Virus-derived DNA forms mediate the persistent infection of tick cells by Hazara virus and Crimean-Congo hemorrhagic fever virus. J Virol. 2021;95:e01638-21.","DOI":"10.1128\/JVI.01638-21"}],"container-title":["Japanese Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/yoken\/79\/1\/79_JJID.2025.027\/_pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T03:19:00Z","timestamp":1769224740000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/yoken\/79\/1\/79_JJID.2025.027\/_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,30]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026]]}},"URL":"https:\/\/doi.org\/10.7883\/yoken.jjid.2025.027","relation":{},"ISSN":["1344-6304","1884-2836"],"issn-type":[{"value":"1344-6304","type":"print"},{"value":"1884-2836","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,30]]},"article-number":"JJID.2025.027"}}