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Submitted: 01 June 2010 Modified: 21 April 2017
HERDIN Record #: PCHRD05311012055039

Concordance of hepatitis C virus subtyping by non-structural 5A and non-structural 5B sequencing.

1Michael O. Baclig,
2Veronica F. Chan,
3John Donnie A. Ramos,
4Juliet Gopez-Cervantes,
5Filipinas F. Natividad
Graduate School - University of Santo Tomas,
Research and Biotechnology Division - St. Luke's Medical Center,
Research Center for Natural Sciences - University of Santo Tomas,
Center for Liver Diseases - St. Luke's Medical Center


The non-structural 5B (NS5B) gene is the target region to identify hepatitis C virus (HCV) subtypes. However, it is not always possible to amplify this region because of inherently high sequence variability. Nucleotide sequences of the non-structural 5A (NS5A) and NS5B genes and its concordance were determined from patients infected with HCV genotype 1 (HCV-1). Among the 30 HCV-1 samples, 7 (23%) were identified as subtype 1a and 23 (77%) were identified as 1b by NS5A sequencing. Sequence analysis of the NS5B showed that 13 (43%) were identified as 1a and 17 (57%) were identified as 1b. Out of the 13 samples identified as 1a by NS5B, 6 (46%) were correctly identified by NS5A. Of the 17 samples identified as 1b by NS5B, 16 (94%) were correctly identified by NS5A. The presence of glutamic acid (E) or aspartic acid (D) at position 2225 in the NS5A differentiates 1a from 1b subtypes, respectively. This study showed that the NS5A sequencing can identify HCV-1a and 1b subtypes with predictive values of 86% and 70% of cases, respectively. The overall concordance with NS5B was 73%. NS5B sequence analysis remains to be the reference method to identify HCV-1 subtypes. NS5A sequencing may be used to complement NS5B sequencing in case the NS5B gene cannot be successfully amplified.

Publication Type:
Publication Sub Type:
Journal Article, Original
Acta Medica Philippina
Publication Date:
January-March 2010
University of the Phiilippines-Manila

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