Identification of ancient viruses from metagenomic data of the Jomon people
Luca Nishimura, Ryota Sugimoto, Jun Inoue, Hirofumi Nakaoka, Hideaki Kanzawa-Kiriyama, Ken-ichi Shinoda, Ituro Inoue
Journal of Human Genetics 2020 September 30 DOI:10.1038/s10038-020-00841-6
Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human samples such as teeth contain not only ancient human genomes but also microbial ones infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We were able to obtain eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. As a result of the genomic comparison between the Jomon CT89 and the modern CT89 sequences, the Jomon CT89 may reflect the ancestral states. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.