Viral Metagenomics and Applications

Project: National Science and Technology CouncilNational Science and Technology Council Academic Grants

Project Details

Abstract

Metagenomics is a newly emerged discipline that focuses on the research of microbial organism communities by modern genomics technologies directly from their natural environment without the need for being cultured and isolated. Viruses are the most abundant biological entities in the world. Unlike other eukaryotic and prokaryotic (bacterial) organisms with distinct ribosomal RNAs for being classified by sequence comparison, viruses are currently classified by only their pathogenic effects on the hosts they infected, not the genomic content they have. Other problems for virus identification/classification lie on the fact that they are often difficult to be cultured or isolated. As a result, it is generally believed that there are yet much more viruses to be disclosed, without saying that many RNA viruses do evolve into new species from time to time. Next-generation sequencing(also known as NGS)technologies are important tools in investigating viral metagenomics. In addition to their ultra-high capacity for generating sequence fragments, they do not need, or only need little sample cultivation and isolation. As a result, viruses are much easier to be detected, if the analysis of these NGS fragments can make sense. With the ultra-high depth the NGS sequences may provide, it is also now possible to investigate virus quasispecies, which are virus sub-populations that are only apart from their primary population by single nucleotide polymorphisms (SNPs). In this 3-year project, we will develop a computational pipeline for NGS reads from viral metagenome. We will build a comprehensive nucleotide and taxonomy database so that the NGS reads can be compared and classified, and a microbial catalog can be established from clinical samples. For any viruses found, we will investigate their genetic difference with other database strains to estimate their genetic drifts. We will detect virus SNPs from these reads, and investigate how these variations may contribute to, for example, new amino acids that are related to antigenicity, epitope, receptor-binding, etc. We will also detect the existence of any microRNAs (miRNAs) or other small RNAs in the sample, as to understand possible virus-host interactions. We will collaborate with other component projects too. For example, component project #1 will help us in de novo assembly, component project #2 will help in researching important genomic structures on unknown contigs, component project #4 will help in gene findings on unknown contigs too, and component project #6 will help in small RNA searching. We expect to gain virus knowledge through our co-investigator – Dr. Shin-Ru Shih of the Research Center for Emerging Viral Infections, Chang Gung University. Dr. Shih is an expert in virus detection and evolution too. She will also help in getting clinical samples, NGS reads, and interpreting the analysis results. We truly believe this project will greatly aid the virus diagnosis, virus epidemiology, and potentially in finding novel viruses.

Project IDs

Project ID:PB10202-0715
External Project ID:NSC100-2221-E182-056-MY3
StatusFinished
Effective start/end date01/08/1331/07/14

Keywords

  • virus
  • genomics
  • metagenomics
  • next-generation-sequencing (NGS)
  • BLAST

Fingerprint

Explore the research topics touched on by this project. These labels are generated based on the underlying awards/grants. Together they form a unique fingerprint.