Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 1 (3), 236-44

Correlation of the 5'untranslated Region (5'UTR) and Non-Structural 5B (NS5B) Nucleotide Sequences in Hepatitis C Virus Subtyping

Correlation of the 5'untranslated Region (5'UTR) and Non-Structural 5B (NS5B) Nucleotide Sequences in Hepatitis C Virus Subtyping

Michael O Baclig et al. Int J Mol Epidemiol Genet.

Abstract

The 5'untranslated region (5'UTR) is often targeted to detect major genotypes in hepatitis C virus (HCV) but its insufficient sequence variation limits its usefulness for differentiating HCV subtypes. Subtyping has important implications to epidemiologic studies, clinical management, and vaccine development. Analysis of the nucleotide sequence of variable regions such as the non-structural 5B (NS5B) is considered the reference method for identifying HCV subtypes. We evaluated the accuracy of subtyping of HCV genotype 1 (HCV-1) samples from the Philippines by 5'UTR sequencing as compared with the NS5B sequence. A total of 30 patients infected with HCV-1 previously confirmed by PCR-RFLP and clinically diagnosed with chronic hepatitis C were analyzed. Nucleotide sequencing of the 5'UTR showed that 15 (50%) were identified as 1a and 15 (50%) were identified as 1b. Sequence analysis of the NS5B revealed that 13 (43%) belonged to subtype 1a while 17 (57%) belonged to subtype 1b. The most predominant subtype was 1b by NS5B sequencing. The predictive value of 5'UTR sequencing to subtype 1a was 73% while for subtype 1b, predictive value was 87%. Overall concordance between 5'UTR and NS5B sequencing was 80%. NS5B sequence and phylogenetic analysis is still the reference method for identifying HCV-1a and 1b subtypes.

Keywords: 5′untranslated region; hepatitis C virus; non-structural 5B; sequencing; subtyping.

Figures

Figure 1
Figure 1
Deduced amino acid alignment of NS5B of 13 HCV-1a-confirmed samples. At the top, HCV-1a reference sequence (GenBank accession number M62321) is given. At the left, the sample identification numbers are shown. The key amino acids associated with 1a are boxed.
Figure 2
Figure 2
Deduced amino acid alignment of NS5B of 17 HCV-1b-confirmed samples. At the top, HCV-1b reference sequence (GenBank accession number D90208) is given. At the left, the sample identification numbers are shown. The key amino acids associated with 1b are boxed.
Figure 3
Figure 3
Phylogenetic analysis of partial NS5B sequences of 30 HCV-1 samples. HCV prototype sequences from GenBank/EMBL/DDBJ were included. The evolutionary history was inferred using the Neighbor-Joining (NJ) method. The numbers at the nodes represent the percent bootstrap support for 1000 replicates. Only values over 70% are shown. Bar at the base of the tree shows the genetic divergence. Phylogenetic analysis was conducted in MEGA4.
Figure 4
Figure 4
Alignment of partial HCV-1a 5′UTR sequences. At the top, HCV-1a reference sequence (GenBank accession number M62321) is given. At the left, the sample identification numbers are shown. The key nucleotide associated with 1a is boxed. At the right, the subtyping results observed by the 5′UTR sequencing are shown.
Figure 5
Figure 5
Alignment of partial HCV-1b 5′UTR sequences. At the top, HCV-1b reference sequence (GenBank accession number D90208) is given. At the left, the sample identification numbers are shown. The key nucleotide associated with 1b is boxed. At the right, the subtyping results observed by the 5′UTR sequencing are shown.
Figure 6
Figure 6
Phylogenetic analysis of partial 5′UTR sequences of 30 HCV-1 samples. HCV prototype sequences from GenBank/EMBL/DDBJ were included. The evolutionary history was inferred using the Neighbor-Joining (NJ) method. Phylogenetic analysis was conducted in MEGA4.

Similar articles

See all similar articles

Cited by 4 PubMed Central articles

LinkOut - more resources

Feedback