Genotype diversity of hepatitis C virus (HCV) in HCV-associated liver disease patients in Indonesia.
BACKGROUND
Hepatitis C virus (HCV) genotype distribution in Indonesia has been reported. However, the identification of HCV genotype was based on 5'-UTR or NS5B sequence.


OBJECTIVE
This study was aimed to observe HCV core sequence variation among HCV-associated liver disease patients in Jakarta, and to analyse the HCV genotype diversity based on the core sequence.


METHODS
Sixty-eight chronic hepatitis (CH), 48 liver cirrhosis (LC) and 34 hepatocellular carcinoma (HCC) were included in this study. HCV core variation was analysed by direct sequencing.


RESULTS
Alignment of HCV core sequences demonstrated that the core sequence was relatively varied among the genotype. Indeed, 237 bases of the core sequence could classify the HCV subtype; however, 236 bases failed to differentiate several subtypes. Based on 237 bases of the core sequences, the HCV strains were classified into genotypes 1 (subtypes 1a, 1b and 1c), 2 (subtypes 2a, 2e and 2f) and 3 (subtypes 3a and 3k). The HCV 1b (47.3%) was the most prevalent, followed by subtypes 1c (18.7%), 3k (10.7%), 2a (10.0%), 1a (6.7%), 2e (5.3%), 2f (0.7%) and 3a (0.7%). HCV 1b was the most common in all patients, and the prevalence increased with the severity of liver disease (36.8% in CH, 54.2% in LC and 58.8% in HCC). These results were similar to a previous report based on NS5B sequence analysis.


CONCLUSIONS
Hepatitis C virus core sequence (237 bases) could identify the HCV subtype and the prevalence of HCV subtype based on core sequence was similar to those based on the NS5B region.
Utama
Andi
A
Molecular Epidemiology Division, Mochtar Riady Institute for Nanotechnology, Lippo Karawaci, Tangerang, Banten, Indonesia. autama@mrinstitute.org
Tania
Navessa Padma
NP
Dhenni
Rama
R
Gani
Rino Alvani
RA
Hasan
Irsan
I
Sanityoso
Andri
A
Lelosutan
Syafruddin A R
SA
Martamala
Ruswhandi
R
Lesmana
Laurentius Adrianus
LA
Sulaiman
Ali
A
Tai
Susan
S
D001483:Base Sequence; D006528:Carcinoma, Hepatocellular / Q000821:virology*; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D007214:Indonesia; D008103:Liver Cirrhosis / Q000821:virology*; D008113:Liver Neoplasms / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D018709:Statistics, Nonparametric; D014758:Viral Core Proteins / Q000235:genetics*; D019562:Viral Load
D017931:DNA Primers; D014758:Viral Core Proteins