Identification of viruses using CRISPR spacer sequences.

2022 Fiscal Year Final Research Report

• Project/Area Number: 20K21405
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
• Research Institution: National Institute of Genetics
• Principal Investigator: Inoue Ituro 国立遺伝学研究所, ゲノム・進化研究系, 特任教授 (00192500)
• Project Period (FY): 2020-07-30 – 2023-03-31
• Keywords: 新規ウイルス / CRISPR-Cas / ファージ / 縄文人

Outline of Final Research Achievements

Viruses are the most abundant population of organisms on earth that possess the most abundant genetic materials. All viruses infect and multiply in specific cells. Horizontal gene spread and arms race evolutionary competition between viruses and cells have been the driving forces of evolution. Analysis of the genomes of many viruses will provide insight into the evolution and origin of not only viruses but also cellular life.
Previous studies exploring viral genomes have been limited to species closely related to known viruses, as detected by homology searches. The objectives of this study are (1) to search phage genomes using CRISPR immuno-memory in a manner that does not rely on homology search, and to use the obtained genome sequences to elucidate the evolution and origin of entire viruses, (2) To examine ancient viral sequences to establish the chronology of viral evolution.

Free Research Field

人類遺伝学, ゲノム医科学

Academic Significance and Societal Importance of the Research Achievements

本研究では得られるメタゲノムデータからCRISPR-Casシステムを用いホモロジーに頼らないウイルス同定を確立できた。縄文人をはじめ多数の年代の日本列島人の歯髄と歯石から得られた76の全ゲノムデータと縄文人糞石由来DNA4検体の提供を受け、全ゲノムデータを取得した。縄文人から得られた歯髄および糞石由来の全ゲノムデータを用い、ウイルスの網羅的探索を行った。ウイルス同定のために、データベース上に登録のある既知のウイルスを参照配列として相同性検索を行い、11種類の現代のウイルスと類似のゲノムを持つ縄文ウイルスを同定した。