Metagenomic research of virus infections in human clinical specimens by high-throughput DNA sequencing in Thailand

• Project/Area Number: 23406033
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 海外学術
• Research Field: Infectious disease medicine
• Research Institution: Kyoto Prefectural University of Medicine
• Principal Investigator: NAKAYA Takaaki 京都府立医科大学, 医学(系)研究科(研究院), 教授 (80271633)
• Co-Investigator(Kenkyū-buntansha): DAIDOJI Tomo 京都府立医科大学, 大学院・医学研究科, 助教 (80432433) ; NAKAMURA Shota 大阪大学, 微生物病研究所, 助教 (90432434)
• Project Period (FY): 2011-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥18,720,000 (Direct Cost: ¥14,400,000、Indirect Cost: ¥4,320,000); Fiscal Year 2013: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2012: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000); Fiscal Year 2011: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
• Keywords: ウイルス / メタゲノム / 次世代シーケンサー / タイ / タイ王国 / ハイスループットシーケンサー / 感染症 / タイ国 / ウイルス感染症 / ハイスループットシークエンサー / インフルエンザウイルス

Research Abstract

Newly developed next-generation sequencing (NGS) technologies can be used to generate large amounts of unbiased data (gigabases) in a single round of operation. So far, we have conducted a direct metagenomic diagnosis of virus infections in human clinical specimens using NGS in Japan. In this study, we collaborated with Osaka University and the Ministry of Public Health, Thailand, to conduct metagenomic research in order to identify causative agents of 36 clinical infectious cases caused by unknown pathogens in Thailand. Several rounds of high-throughput sequencing identified human pathogenic viruses, such as Picornaviridae, Paramyxoviridae, Coronaviridae, Herpesviridae, and Parvoviridae, in 23 specimens.

Research Products

• [Journal Article] Human monoclonal antibodies broadly neutralizing against influenza B virus. (2013)
  • Author(s): Yasugi, M., Kubota-Koketsu, R., Yamashita, A., Kawashita, N., Du, A., Sasaki, T., Nishimura, M., Misaki, R., Kuhara, M., Boonsathorn, N., Fujiyama, K., Okuno, Y., Nakaya, T., and Ikuta, K.
  • Journal Title: PLoS Pathog. Volume: 9 Issue: 2 Pages: e1003150-e1003150
  • DOI: 10.1371/journal.ppat.1003150
  • Peer Reviewed
• [Journal Article] The lipid mediator protectin D1 inhibits influenza virus replication and improves severe influenza (2013)
  • Author(s): Morita M, Kuba K, Ichikawa A, Nakayama M, Katahira J, Iwamoto R, Watanebe T, Sakabe S, Daidoji T, Nakamura S, Kadowaki A, Ohto T, Nakanishi H, Taguchi R, Nakaya T, Murakami M, Yoneda Y, Arai H, Kawaoka Y, Penninger JM, Arita M, Imai Y.
  • Journal Title: Cell Volume: 153 Issue: 1 Pages: 112-125
  • DOI: 10.1016/j.cell.2013.02.027
  • Peer Reviewed
• [Journal Article] Tropism of pandemic 2009 H1N1 influenza A virus. (2012)
  • Author(s): Ramadhany, R., Yasugi, M., Nakamura, S., Daidoji, T., Watanabe, Y., Takahashi, K., Ikuta, K., and Nakaya, T.
  • Journal Title: Front. Microbiol. Volume: 3 Pages: 128-128
  • DOI: 10.3389/fmicb.2012.00128
  • Peer Reviewed
• [Journal Article] Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010 (2012)
  • Author(s): Yasugi M, Nakamura S, Daidoji T, Kawashita N, Ramadhany R, Yang CS, Yasunaga T, Iida T, Horii T, Ikuta K, Takahashi K, Nakaya T
  • Journal Title: PLoS One Volume: 7 Issue: 2 Pages: e30946-e30946
  • DOI: 10.1371/journal.pone.0030946
  • Peer Reviewed
• [Journal Article] 次世代シークエンサーのウイルス性疾患同定への適用 (2012)
  • Author(s): 中屋隆明
  • Journal Title: 臨床とウイルス Volume: 40(4) Pages: 177-183
  • NAID: 10031123614
• [Journal Article] メタゲノム解析を応用した網羅的病原体検出法 (2012)
  • Author(s): 中村昇太, 中屋隆明, 飯田哲也
  • Journal Title: 最新医学 Volume: 67(No.9) Pages: 131-133
  • NAID: 40019431074
• [Journal Article] Emergence of HA mutants during influenza virus pneumonia (2012)
  • Author(s): Manriquez ME, Nakaya T, Shinya K. et al.
  • Journal Title: Int. J. Clin. Exp. Pathol. Volume: 5(8) Pages: 787-795
  • Peer Reviewed
• [Journal Article] Antigenic analysis of highly pathogenic avian influenza virus H5N1 sublineage co-circulating in Egypt. (2012)
  • Author(s): Watanabe, Y., Ibrahim, M.S., Ellakany, H.F., Kawashita, N., Daidoji, T., Takagi, T., Yasunaga, T., Nakaya, T., and Ikuta, K.
  • Journal Title: J. Gen. Virol. Volume: 93 Issue: 10 Pages: 2215-2226
  • DOI: 10.1099/vir.0.044032-0
  • Peer Reviewed
• [Journal Article] Gut microbiota of healthy and malnourished children in bangladesh (2011)
  • Author(s): Monira S, Nakamura S, Gotoh K, Izutsu K, Watanabe H, Alam NH, Endtz HP, Cravioto A, Ali SI, Nakaya T, Horii T, Iida T, Alam M
  • Journal Title: Front Microbiol Volume: 228 Pages: 1-7
  • DOI: 10.3389/fmicb.2011.00228
  • Peer Reviewed
• [Journal Article] Metagenomic analysis of bacterial infections by means of high-throughput DNA sequencing (2011)
  • Author(s): Nakamura S, Nakaya T, Iida T
  • Journal Title: Exp.Biol.Med. Volume: 236(8) Issue: 8 Pages: 968-71
  • DOI: 10.1258/ebm.2011.010378
  • Peer Reviewed
• [Presentation] 血液感染症の治療戦略 (2013)
  • Author(s): 中屋隆明
  • Organizer: 京滋血液感染症研究会2013
  • Place of Presentation: 京都市
  • Year and Date: 2013-09-13
• [Presentation] 新興・再興ウイルス感染症のダイナミクス (2012)
  • Author(s): 中屋隆明
  • Organizer: びわ湖国際医療フォーラム
  • Place of Presentation: 大津市
  • Year and Date: 2012-07-14
• [Presentation] 次世代シークエンサーが切り拓く感染症のメタゲノム学 (2012)
  • Author(s): 中屋隆明, 他
  • Organizer: 第11回京都産業大学・総合生命科学部・バイオフォーラム
  • Place of Presentation: 京都市
  • Year and Date: 2012-01-16
  • Invited
• [Presentation] 次世代シークエンサーが切り拓く感染症のメタゲノム (2012)
  • Author(s): 中屋隆明
  • Organizer: 京都産業大学総合生命科学部第11回バイオフォーラム
  • Place of Presentation: 京都市
  • Year and Date: 2012-01-16
• [Presentation] H1N1 2009-HAゲノムのディープシークエンス解析
  • Author(s): 中屋 隆明
  • Organizer: インフルエンザ研究者交流の会シンポジウム
  • Place of Presentation: 福島県耶麻郡
• [Presentation] 新興・再興ウイルス感染症のダイナミクス
  • Author(s): 中屋 隆明
  • Organizer: びわ湖国際医療フォーラム
  • Place of Presentation: 滋賀県大津市
  • Invited
• [Presentation] インフルエンザウイルスの宿主域拡大戦略
  • Author(s): 中屋 隆明
  • Organizer: CREST公開シンポジウム「光が拓く細胞解析の新展開」
  • Place of Presentation: 東京都品川区
• [Presentation] 鳥インフルエンザ
  • Author(s): 中屋 隆明
  • Organizer: 日本神経感染症学会
  • Place of Presentation: 京都府京都市
  • Invited
• [Book] "Direct metagenomic detection of viral pathogens in human specimens using an unbiased high-throughput sequencing approach", Handbook ofMolecular Microbial Ecology II, pp.73-82. Metagenomics in Different Habitats. Wiley-Blackwell (2011)
  • Author(s): *T. Nakaya, S. Nakamura, Y. Okamoto, Y. Nagai, J. Kawai, Y. Hayashizaki, T. Iida, T. Horii
  • Publisher: Hoboken, NJ, USA
• [Book] Handbook of Molecular Microbial Ecology II (2011)
  • Author(s): Nakaya T, Nakamura S, Iida T, Horii T
  • Total Pages: 609
  • Publisher: Wiley-Blackwell, Hoboken, NJ, USA
• [Remarks]
  • URL: http://www.f.kpu-m.ac.jp/k/did/
• [Remarks]
  • URL: http://www.kpu-m.ac.jp/doc/classes/basicmedicine/221.html