{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:18:02Z","timestamp":1785403082926,"version":"3.56.0"},"reference-count":38,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003993","name":"Ministry of Agriculture, Forestry and Fisheries","doi-asserted-by":"crossref","award":["JPJ008837"],"award-info":[{"award-number":["JPJ008837"]}],"id":[{"id":"10.13039\/501100003993","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003993","name":"Ministry of Agriculture, Forestry and Fisheries","doi-asserted-by":"crossref","award":["22682125"],"award-info":[{"award-number":["22682125"]}],"id":[{"id":"10.13039\/501100003993","id-type":"DOI","asserted-by":"crossref"}]},{"award":["JPJ008837"],"award-info":[{"award-number":["JPJ008837"]}],"id":[{"id":"https:\/\/ror.org\/02zdz1m23","id-type":"ROR","asserted-by":"publisher"}]},{"award":["22682125"],"award-info":[{"award-number":["22682125"]}],"id":[{"id":"https:\/\/ror.org\/02zdz1m23","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>African swine fever (ASF) is a highly fatal, febrile infectious disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). Recently, highly virulent recombinant ASFVs with chimeric genomes derived from p72 genotype I and II viruses have emerged in China, Vietnam, and Russia. These genotype I\/II recombinants can evade immunity induced by genotype II\u2013based vaccines, thereby complicating disease control efforts. To address this challenge, a novel duplex quantitative PCR (qPCR) assay was developed to simultaneously detect and differentiate genotypes I, II, and I\/II recombinants in a single reaction. The assay exhibited high sensitivity and specificity, with a reliable detection limit of 10 copies\/reaction for genotype I and II ASFV DNA. Validation using clinical samples collected in northern Vietnam in 2025 confirmed a robust performance in accurately distinguishing circulating genotype II viruses from recombinant genotype I\/II viruses, including the detection of potential co-infection. Whole-genome sequencing of selected positive samples further corroborated these findings. Overall, this qPCR assay provides a precise and efficient tool for identifying currently circulating ASFV genotypes, thereby facilitating improved disease surveillance and supporting a comprehensive understanding of the evolving epidemiological landscape of ASF in regions with increasing viral genetic diversity.<\/jats:p>","DOI":"10.3390\/v18060677","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T08:22:56Z","timestamp":1781684576000},"page":"677","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Establishment of a Duplex Quantitative PCR Assay for the Detection and Differentiation of African Swine Fever Virus Genotype I, Genotype II, and Genotype I\/II Recombinants"],"prefix":"10.3390","volume":"18","author":[{"given":"Naoki","family":"Yoshida","sequence":"first","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiho","family":"Oka","sequence":"additional","affiliation":[{"name":"Saitama Prefectural Chuo Livestock Hygiene Service Center, 107-1 Bessho-cho, Kita-ku, Saitama 331-0821, Saitama, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2472-8165","authenticated-orcid":false,"given":"Anh Duc","family":"Truong","sequence":"additional","affiliation":[{"name":"Department of Veterinary Immunology and Epidemiology, Vietnam Institute of Animal and Veterinary Science, 86, Truong Chinh, Kim Lien, Hanoi 100000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mizuki","family":"Watanabe","sequence":"additional","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8449-0229","authenticated-orcid":false,"given":"Mitsutaka","family":"Ikezawa","sequence":"additional","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hien Thi Thu","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Veterinary Immunology and Epidemiology, Vietnam Institute of Animal and Veterinary Science, 86, Truong Chinh, Kim Lien, Hanoi 100000, Vietnam"},{"name":"Faculty of Agriculture, Forestry and Fisheries, Nghe An University, 51 Ly Tu Trong, Ha Huy Tap, Vinh 460000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le Thi Hai","family":"Vo","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, Forestry and Fisheries, Nghe An University, 51 Ly Tu Trong, Ha Huy Tap, Vinh 460000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuong Dinh","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, Forestry and Fisheries, Nghe An University, 51 Ly Tu Trong, Ha Huy Tap, Vinh 460000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0251-7543","authenticated-orcid":false,"given":"Tomoya","family":"Kitamura","sequence":"additional","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatsuya","family":"Nishi","sequence":"additional","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8869-1402","authenticated-orcid":false,"given":"Takehiro","family":"Kokuho","sequence":"additional","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoang Vu","family":"Dang","sequence":"additional","affiliation":[{"name":"Department of Veterinary Immunology and Epidemiology, Vietnam Institute of Animal and Veterinary Science, 86, Truong Chinh, Kim Lien, Hanoi 100000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ha Thi Thanh","family":"Tran","sequence":"additional","affiliation":[{"name":"Department of Veterinary Immunology and Epidemiology, Vietnam Institute of Animal and Veterinary Science, 86, Truong Chinh, Kim Lien, Hanoi 100000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kentaro","family":"Masujin","sequence":"additional","affiliation":[{"name":"Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,17]]},"reference":[{"key":"ref_1","unstructured":"(2026, February 12). 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