{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T14:09:00Z","timestamp":1780668540431,"version":"3.54.1"},"reference-count":30,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T00:00:00Z","timestamp":1719532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Agriculture, Forestry, and Fisheries of Japan","award":["JPJ008617.18065101"],"award-info":[{"award-number":["JPJ008617.18065101"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>We performed whole genome sequencing (WGS) of 15 Palyam serogroup virus (PALV) strains isolated from cattle or Culicoides biting midges in Japan from 1984 to 2018. We found that the PALV strains consisted of Chuzan (Kasba) virus (CHUV), D\u2018Aguilar virus (DAGV), Bunyip Creek virus, and another PALV, Marrakai virus (MARV). The Japanese MARV strains isolated in 1997 were closely related to Australian PALV strains isolated in 1968\u20131976 in genome segments 2 and 10, but they were most closely related to other Japanese PALV strains in the other genome segments. Our data suggest that the Japanese MARV strains were reassortant viruses between Asian and Australian PALVs. In addition to the WGS, we developed a real-time reverse-transcription polymerase chain reaction assay that can broadly detect PALV and specifically detect CHUV and DAGV, utilizing the data obtained by the WGS in this study. We detected the DAGV gene in bovine stillborn fetuses and congenitally abnormal calves in 2019 using the newly developed assay. To our knowledge, this is the first report of isolation of MARV outside of Australia and the first report of detection of PALV in bovine fetuses or calves with congenital abnormality outside of Africa.<\/jats:p>","DOI":"10.3390\/pathogens13070550","type":"journal-article","created":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T10:14:46Z","timestamp":1719828886000},"page":"550","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genetic Characterization of Palyam Serogroup Viruses Isolated in Japan from 1984 to 2018 and Development of a Real-Time RT-PCR Assay for Broad Detection of Palyam Serogroup Viruses and Specific Detection of Chuzan (Kasba) and D\u2019Aguilar Viruses"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8912-6544","authenticated-orcid":false,"given":"Hiroaki","family":"Shirafuji","sequence":"first","affiliation":[{"name":"Exotic Disease Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), 6-20-1 Josuihoncho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natsumi","family":"Kishida","sequence":"additional","affiliation":[{"name":"Virus Group, Division of Infectious Animal Disease Research, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba 305-0856, Ibaraki, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katsunori","family":"Murota","sequence":"additional","affiliation":[{"name":"Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), 2702 Chuzan, Kagoshima 891-0105, Kagoshima, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuto","family":"Suda","sequence":"additional","affiliation":[{"name":"Virus Group, Division of Infectious Animal Disease Research, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba 305-0856, Ibaraki, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tohru","family":"Yanase","sequence":"additional","affiliation":[{"name":"Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), 2702 Chuzan, Kagoshima 891-0105, Kagoshima, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,28]]},"reference":[{"key":"ref_1","unstructured":"Coetzer, J.A.W., Penrith, M.L., Maclachlan, N.J., and Thomson, G.R. (2020). Palyam serogroup orbivirus infections. Infectious Diseases of Livestock, Oxford University Press. [3rd ed.]."},{"key":"ref_2","first-page":"2022","article-title":"Isolation of Chuzan virus, a new member of the Palyam subgroup of the genus Orbivirus, from cattle and Culicoides oxystoma in Japan","volume":"49","author":"Miura","year":"1988","journal-title":"Am. J. Vet. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1111\/j.1751-0813.1994.tb06155.x","article-title":"Identification of Kagoshima and Chuzan viruses of Japan as Kasba virus, an orbivirus of the Palyam serogroup","volume":"71","author":"Jusa","year":"1994","journal-title":"Aust. Vet. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1292\/jvms1939.52.689","article-title":"Hydranencephaly-cerebellar hypoplasia in a newborn calf after infection of its dam with Chuzan virus","volume":"52","author":"Miura","year":"1990","journal-title":"Nihon Juigaku Zasshi"},{"key":"ref_5","first-page":"2026","article-title":"Serologic evidence for the etiologic role of Chuzan virus in an epizootic of congenital abnormalities with hydranencephaly-cerebellar hypoplasia syndrome of calves in Japan","volume":"49","author":"Goto","year":"1988","journal-title":"Am. J. Vet. Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1292\/jvms1939.50.405","article-title":"Epidemiological survey of an epidemic of congenital abnormalities with hydranencephaly-cerebellar hypoplasia syndrome of calves occurring in 1985\/86 and seroepidemiological investigations on Chuzan virus, a putative causal agent of the disease, in Japan","volume":"50","author":"Goto","year":"1988","journal-title":"Nihon Juigaku Zasshi"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4610","DOI":"10.1128\/JCM.42.10.4610-4614.2004","article-title":"Evidence of an antigenic shift among Palyam serogroup orbiviruses","volume":"42","author":"Ohashi","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1099\/0022-1317-69-9-2221","article-title":"Characterization of potentially foetotropic Palyam serogroup orbiviruses isolated in Zimbabwe","volume":"69","author":"Whistler","year":"1988","journal-title":"J. Gen. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1099\/0022-1317-80-4-937","article-title":"Molecular analysis of the genome of Chuzan virus, a member of the Palyam serogroup viruses, and its phylogenetic relationships to other orbiviruses","volume":"80","author":"Yamakawa","year":"1999","journal-title":"J. Gen. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1292\/jvms1939.50.777","article-title":"Biochemical characteristics of Chuzan virus, a new serotype of Palyam serogroup","volume":"50","author":"Harasawa","year":"1988","journal-title":"Nihon Juigaku Zasshi"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Ebersohn, K., Coetzee, P., Snyman, L.P., Swanepoel, R., and Venter, E.H. (2019). Phylogenetic Characterization of the Palyam Serogroup Orbiviruses. Viruses, 11.","DOI":"10.3390\/v11050446"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S0168-1702(00)00163-5","article-title":"Genetic diversity of RNA segments 5, 7 and 9 of the Palyam serogroup orbiviruses from Japan, Australia and Zimbabwe","volume":"68","author":"Yamakawa","year":"2000","journal-title":"Virus Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1007\/s00705-015-2734-2","article-title":"Complete genome sequence of a Chuzan virus strain isolated for the first time in mainland China","volume":"161","author":"Yang","year":"2016","journal-title":"Arch. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1007\/s11262-015-1282-x","article-title":"Isolation, complete genome sequencing, and phylogenetic analysis of the first Chuzan virus in China","volume":"52","author":"Wang","year":"2016","journal-title":"Virus Genes."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"001662","DOI":"10.1099\/jgv.0.001662","article-title":"Orbiviruses in biting midges and mosquitoes from the Zambezi region, Namibia","volume":"102","author":"Guggemos","year":"2021","journal-title":"J. Gen. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1071\/BI9820343","article-title":"Preliminary characterization of D\u2019Aguilar virus and three Palyam group viruses new to Australia","volume":"35","author":"Cybinski","year":"1982","journal-title":"Aust. J. Biol. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.jviromet.2004.04.006","article-title":"Simultaneous detection of bovine arboviruses using single-tube multiplex reverse transcription-polymerase chain reaction","volume":"120","author":"Ohashi","year":"2004","journal-title":"J. Virol. Methods"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Ebersohn, K. (2018). Phylogenetic Characterisation of the Palyam Serogroup Orbiviruses and Development of a Real-Time RT-PCR. [Master\u2019s Thesis, University of Pretoria].","DOI":"10.3390\/v11050446"},{"key":"ref_19","unstructured":"Yang, H., Liao, D., Li, Z., Li, Z., Yang, Z., Xiao, L., and Li, H. (2024, May 08). Real-Time Fluorescent Quantitative RT-PCR Detection Primers for Serotype of Palyam Serogroup Virus (PALV), Probes and Detection Kit. Available online: https:\/\/patentscope2.wipo.int\/search\/en\/detail.jsf?docId=CN282352475&docAn=201910979854.1."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.meegid.2017.05.010","article-title":"Characterization of genome segments 2, 3 and 6 of epizootic hemorrhagic disease virus strains isolated in Japan in 1985\u20132013: Identification of their serotypes and geographical genetic types","volume":"53","author":"Shirafuji","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.jviromet.2007.02.016","article-title":"Rapid cDNA synthesis and sequencing techniques for the genetic study of bluetongue and other dsRNA viruses","volume":"143","author":"Maan","year":"2007","journal-title":"J. Virol. Methods"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.jviromet.2006.11.007","article-title":"Bluetongue virus detection by two real-time RT-qPCRs targeting two different genomic segments","volume":"140","author":"Toussaint","year":"2007","journal-title":"J. Virol. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1292\/jvms.14-0492","article-title":"Occurrence of bovine ephemeral fever in Okinawa Prefecture, Japan, in 2012 and development of a reverse-transcription polymerase chain reaction assay to detect bovine ephemeral fever virus gene","volume":"77","author":"Niwa","year":"2015","journal-title":"J. Vet. Med. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Kato, T., Yanase, T., Suzuki, M., Katagiri, Y., Ikemiyagi, K., Takayoshi, K., Shirafuji, H., Ohashi, S., Yoshida, K., and Yamakawa, M. (2016). Monitoring for bovine arboviruses in the most southwestern islands in Japan between 1994 and 2014. BMC Vet. Res., 12.","DOI":"10.1186\/s12917-016-0747-z"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1071\/BI9840351","article-title":"Isolation of arboviruses from insects collected at Beatrice Hill, Northern Territory of Australia, 1974\u20131976","volume":"37","author":"Standfast","year":"1984","journal-title":"Aust. J. Biol. Sci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.virusres.2009.07.012","article-title":"Genetic and phylogenetic analysis of the outer-coat proteins VP2 and VP5 of epizootic haemorrhagic disease virus (EHDV): Comparison of genetic and serological data to characterise the EHDV serogroup","volume":"145","author":"Anthony","year":"2009","journal-title":"Virus Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1099\/vir.0.040717-0","article-title":"Genetic and phylogenetic characterization of genome segments 2 and 6 of bluetongue virus isolates in Japan from 1985 to 2008","volume":"93","author":"Shirafuji","year":"2012","journal-title":"J. Gen. Virol."},{"key":"ref_30","unstructured":"Sakai, Y., and Suzuta, F. (2019). Occurrence of Congenital Abnormalities in Cattle Suspected to be Caused by D\u2019Aguilar Virus Infection and Molecular Epidemiology of D\u2019Aguilar Virus Isolates Obtained from Sentinel Cattle, Nagasaki Prefectural Government. (Unpublished work)."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/13\/7\/550\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:07:28Z","timestamp":1760108848000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/13\/7\/550"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,28]]},"references-count":30,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7]]}},"alternative-id":["pathogens13070550"],"URL":"https:\/\/doi.org\/10.3390\/pathogens13070550","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,28]]}}}