Bioinformatics Tools for Identifying Hepatitis C Virus Subtypes
Michael O. Baclig1*, Juliet Gopez-Cervantes2, and Filipinas F. Natividad1
1Research and Biotechnology Division,
2Liver Disease and Transplant Center, St. Luke's Medical Center,
279 E. Rodriguez Sr., Blvd., Quezon City
corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.
ABSTRACT
With the development of freeware bioinformatics software as well as the availability of web-based software, it is now possible to use various bioinformatics tools to identify viral subtypes such as hepatitis C virus (HCV). This study aimed to demonstrate the role of bioinformatics tools in identifying HCV subtypes and to compare the accuracy of HCV-1 subtyping by 5’UTR PCR-RFLP analysis and DNA sequencing. From a clinical viewpoint, accurate genotype and subtype identification of HCV are important because this may be used as guide for deciding which therapy is appropriate to use for a particular patient. From 2005 up to 2008, we had a total of 30 HCV genotype 1 (HCV-1) positive samples. HCV-1 subtypes were identified by an in-house PCR-RFLP analysis and through direct nucleic acid sequencing using nested primers specific to the 5’UTR and non-structural 5B (NS5B) region. Bioinformatics tools play an important role in identifying HCV-1 subtypes by predicting the size of the amplicon; determining the specific restriction enzyme to cut a given nucleic acid sequence; viewing and editing the electropherogram; aligning nucleotide sequences with prototypes; searching for identical sequences; and understanding the evolution and relationships of various subtypes. The HCV nucleotide sequences reported in this study have been deposited to GenBank. Overall, this information can be utilized to generate molecular diagnostic tests in the future.
INTRODUCTION
There are a number of different methods for HCV genotyping and subtyping. The most frequently used typing methods are line probe assay (LiPA) and sequencing of the 5’UTR. The Versant HCV genotype assay (LiPA) manufactured by Innogenetics has been developed based on hybridization of 5’UTR amplification products with genotype specific probes. On the other hand, the TruGene HCV 5’NCR genotyping kit (Bayer Healthcare, CA) is based on semi-automated sequencing (Verbeeck et al. 2008; Chevaliez et al. 2009). . . . . . . . . . . . . . .
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