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Genomics Inform > Volume 16(4); 2018 > Article
DOI: https://doi.org/10.5808/GI.2018.16.4.e23    Published online December 28, 2018.
Identification of Viral Taxon-Specific Genes (VTSG): Application to Caliciviridae
Shinduck Kang, Young-Chang Kim
Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea
Corresponding author:  Young-Chang Kim
Tel: +82-43-261-2302   Fax: +82-50-4477-6563   Email: youngkim@chungbuk.ac.kr
Received: July 31, 2018   Revised: December 5, 2018   Accepted: December 16, 2018
Abstract
Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current ICTV taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide [1]. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database(CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CD database. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovius, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.
Keywords: CDS, RPS-BLAST, CD database, Caliciviridae, Picornaviridae, PASC


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