Comprehensive virus detection by high-performance homology search and deep sequencing

• Project/Area Number: 24580430
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Basic veterinary science/Basic zootechnical science
• Research Institution: Rakuno Gakuen University
• Principal Investigator: ENDOH Daiji 酪農学園大学, 獣医学群, 教授 (40168828)
• Co-Investigator(Kenkyū-buntansha): MIZUTANI Tetsuya 東京農工大学, 農学部, 教授 (70281681)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2014: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2013: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: 次世代シーケンサー / 縮重プライマー / バイオインフォマティクス / 網羅的ウイルス検出 / 網羅的細菌検出 / 高速相同性検出 / プライマーの自動設計 / 糞便微生物解析 / 縮重塩基プライマー / 次世代シーケンス / プライマー設計プログラム / グリーディーアルゴリズム / 高速塩基配列整列 / 高速塩基配列相同性検索 / 糞便DNA / 高速相同性検索

Outline of Final Research Achievements

On reports of the emerging viruses, requirement for comprehensive surveillance for viruses has been increased. In this study, we create computer program which design primers for comprehensive detection of viruses. The program automatically designed primers for amplifying 143,557 species (14 families) viruses and 19 genera of bacteria. We also create sequence analysis program for analyzing vast numbers of sequence reads with high-performance homology search. These programs and results suggest the ability of the combination of comprehensive amplification and next-generation sequencer.

Research Products

• [Journal Article] Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses (2015)
  • Author(s): Shimada S, Nagai M, Moriyama H, Fukuhara T, Koyama S, Omatsu T, Furuya T, Shirai J, MizutaniT.
  • Journal Title: Journal of Veterinary Medical Science Volume: 77 Issue: 9 Pages: 1163-1166
  • DOI: 10.1292/jvms.14-0607
  • NAID: 130005100711
  • ISSN: 0916-7250, 1347-7439
  • Peer Reviewed
• [Journal Article] Identification, characterization, and full-length sequence analysis of a novel double-stranded RNAvirus isolated from an arboreal ant, Camponotus yamaokai. (2015)
  • Author(s): Koyama S, Urayama SI, Ohmatsu T, Sassa Y, Sakai C, Takata M, Hayashi S, Nagai M, Furuya T, Moriyama H, Satoh T, Ono SI, Mizutani T.
  • Journal Title: J Gen Virol. Volume: 96 Issue: 7 Pages: 1930-1937
  • DOI: 10.1099/vir.0.000126
  • Peer Reviewed
• [Journal Article] Characterization of self-assembled virus-like particles of Merkel cell polyomavirus. (2015)
  • Author(s): Li TC, Iwasaki K, Katano H, Kataoka M, Nagata N, Kobayashi K, Mizutani T, Takeda N, Wakita T, Suzuki T.
  • Journal Title: PLOS ONE Volume: 10 Issue: 2 Pages: 524-531
  • DOI: 10.1371/journal.pone.0115646
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Detection of enterovirus genome sequence from diarrheal feces of goat (2014)
  • Author(s): Omatsu T, Tsuchiaka S, Hirata T, Shiroma Y, Okazaki S, Katayama Y, Oba M, Nishiura N, Sassa Y, Furuya T, Nagai M, Ochiai H, Tamaki S, Mizutani T.
  • Journal Title: Virus Genes Volume: 48(3) Issue: 3 Pages: 550-2
  • DOI: 10.1007/s11262-014-1057-9
  • Peer Reviewed
• [Journal Article] Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer. (2014)
  • Author(s): Masuda T, Nagai M, Yamasato H, Tsuchiaka S, Okazaki S, Katayama Y, Oba M, Nishiura N, Sassa Y, Omatsu T, Furuya T, Koyama S, Shirai J, Taniguchi K, Fujii Y, Todaka R, Katayama K, Mizutani T.
  • Journal Title: Vet Microbiol. Volume: 171 Issue: 1-2 Pages: 66-73
  • DOI: 10.1016/j.vetmic.2014.03.009
  • Peer Reviewed / Open Access
• [Journal Article] Characterization of a genetic and antigenic variant of avian paramyxovirus 6 isolated from a migratory wild bird, the red-necked stint (Calidris ruficollis). (2014)
  • Author(s): Bui VN, Mizutani T, Nguyen TH, Trinh DQ, Awad SS, Minoungou GL, Yamamoto Y, Nakamura K, Saito K, Watanabe Y, Runstadler J, Huettmann F, Ogawa H, Imai K.
  • Journal Title: Arch Virol. Volume: 159 Issue: 11 Pages: 3101-3105
  • DOI: 10.1007/s00705-014-2162-8
  • Peer Reviewed
• [Journal Article] Molecular, biological, and antigenic characterization of a Border disease virus isolated from a pig during classical swine fever surveillance in Japan (2014)
  • Author(s): Nagai, M., Aoki, H., Sakoda, Y., Kozasa, T., Tominaga-Teshima, K., Mine, J., Abe Y., Tamura, T., Kobayashi, T., Nishine, K., Tateishi, K., Suzuki, Y., Fukuhara, M., Ohmori, K., Todaka, R., Katayama, K., Mizutani, T., Nakamura, S., Kida, H., Shirai, J.
  • Journal Title: Journal of Veterinary Diagnostic Investigation Volume: 26 Issue: 4 Pages: 547-552
  • DOI: 10.1177/1040638714541837
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Detection of Japanese eel endothelial cells-infecting virus (JEECV) in the Japanese eel Anguilla japonica (Temminck & Schlegel), living in natural habitats. (2014)
  • Author(s): Okazaki S, Manabe H, Omatsu T, Tsuchiaka S, Yamamoto T, Chow S, Shibuno T, Watanabe K, Ono S, Kuwada H, Mizutani T.
  • Journal Title: J Fish Dis. Volume: 173 Issue: 9 Pages: 136-140
  • DOI: 10.1111/jfd.12294
  • Peer Reviewed
• [Presentation] アカバネウイルスによるアポトーシスメカニズムの解明 (2014)
  • Author(s): 三友俊平、長井誠、大松勉、古谷哲也、岡崎祥子、土赤忍、水谷哲也
  • Organizer: 第157回日本獣医学会学術集会
  • Place of Presentation: 北海道札幌市 北海道大学
  • Year and Date: 2014-09-09 – 2014-09-12
• [Presentation] コウモリマルヒメダニから分離された新規ブニヤウイルスについて (2014)
  • Author(s): 大場 真己、大松 勉、安藤 秀二、川端 寛樹、高野 愛 4、片山 幸枝、 古谷 哲也、長井 誠、水谷 哲也
  • Organizer: 第157回日本獣医学会学術集会
  • Place of Presentation: 北海道札幌市 北海道大学
  • Year and Date: 2014-09-09 – 2014-09-12
• [Presentation] G 15P［14］遺伝子型A群ロタウイルス（RVA）による搾乳牛の下痢症 (2014)
  • Author(s): 増田恒幸、山里比呂志、水谷 哲也、長井 誠、片山 和彦
  • Organizer: 第157回日本獣医学会学術集会
  • Place of Presentation: 北海道札幌市 北海道大学
  • Year and Date: 2014-09-09 – 2014-09-12
• [Presentation] 日本で分離されたG3およびG14型ウマロタウイルスの全ゲノム解析 (2014)
  • Author(s): 根本 学、長井 誠、恒光 裕、大松 勉、白井 淳資、近藤 高志、藤井 克樹、戸高 玲子、片山 和彦、水谷 哲也
  • Organizer: 第157回日本獣医学会学術集会
  • Place of Presentation: 北海道札幌市 北海道大学
  • Year and Date: 2014-09-09 – 2014-09-12
• [Presentation] 新規遺伝子型トリボルナウイルス（ABV-BF）の解析 (2014)
  • Author(s): 佐々 悠木子、堀江 真行、鈴木 研太、加藤 真樹、香川 紘子、鈴木 和彦、 渋谷 淳、Chanathip Thammakarn、竹原 一明、古谷 哲也、本田 知之、 朝長 啓造、岡ノ谷 一夫、水谷 哲也
  • Organizer: 第157回日本獣医学会学術集会
  • Place of Presentation: 北海道札幌市 北海道大学
  • Year and Date: 2014-09-09 – 2014-09-12
• [Presentation] EPIC-PCRによる北海道のネズミ類の種判別法の開発
  • Author(s): 小山内佑太，遠藤大二，浅川満彦，長雄一，藤井啓，大沼学
  • Organizer: 日本野生動物医学会
  • Place of Presentation: 京都市 京都大学