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Published on: April 17, 2017
Sequence and structural analysis of 3' untranslated region of hepatitis C virus, genotype 3a, from pakistani isolates
Sadia Anjum1, Sidra Ali, Tahir Ahmad
1Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
Insights
Hepatitis C virus (HCV) 3' untranslated region (UTR) sequences from Pakistan show unique structural variations. These differences in the HCV 3'UTR may influence viral replication and infectivity in local populations.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Hepatitis C virus (HCV) causes significant global morbidity and mortality.
- The HCV genome contains conserved structural elements crucial for replication, particularly in the 3' untranslated region (UTR).
- The 3'UTR regulates key stages of the viral life cycle.
Purpose of the Study:
- To analyze the sequence and secondary structure of the HCV 3'UTR subtype 3a from Pakistan.
- To characterize potential differences in regulatory elements contributing to varied infectivity of local HCV isolates.
Main Methods:
- Amplification, cloning, and sequencing of the HCV 3'UTR from five Pakistani patients.
- Sequence and secondary structure analysis of the obtained 3'UTR fragments.
- Phylogenetic analysis using publicly available NCBI nucleotide sequences.
Main Results:
- The Pakistani HCV 3'UTR sequences (214-235 nts) feature a type-specific variable region (26 nts, one stem loop), a variable poly U/UC region (79-100 nts), and a conserved 98 nt X-tail.
- The Pakistani 3a isolates' X-tail lacks terminal U residues, unlike genotype 1b variants.
- Substitutions in the X-tail did not alter its predicted secondary structure, suggesting a role in replication, stabilization, and packaging.
Conclusions:
- Sequence and structural diversity in the 3'UTR variable and poly U/UC regions of Pakistani HCV isolates suggest specific regulatory elements.
- These variations may correlate with differential replication efficacy and pathogenicity of local HCV strains.
- Further functional studies are needed to understand the role of these regulatory elements in inter-geographical isolate variability.
Background:
Hepatitis C virus (HCV) is the cause of high morbidity and mortality worldwide, inflicting around one million people in Pakistan alone. The HCV genomic RNA harbors conserved structural elements that are indispensable for its replication. The 3' untranslated region (UTR) contains several of these elements essentially involved in regulating the major steps of the viral life cycle.
Objectives:
Differences in regulatory elements of HCV may contribute towards differential infectivity of local isolates. The present study explicates sequence analysis and secondary structure prediction of HCV 3'UTR region of subtype 3a from Pakistan to characterize this particular region.
Patients And Methods:
HCV 3'UTR region was amplified, cloned and sequenced from five different patients. Sequence and structural analysis was performed and phylogenetic analysis was carried out using the 3'UTR sequence reported in NCBI nucleotide data base (http://www.ncbi.nlm.nih.gov/nuccore) by other studies.
Results:
Sequence analysis of the amplified fragment from five patients indicated that the 3'UTR is composed of 214-235 nts. Its sequence contains a type-specific variable region followed by a poly U/UC region and a highly conserved X-tail of 98 nts. The variable region reported here has 26 nts and one stem loop at the secondary structure that differentiate it from HCV genotype 1a ( GT1a) 3'UTR which contains additional 14 nts and two stem loops. The poly U/UC region varied in length (100-79 nts) and nucleotide sequence within the Pakistani isolates, and among different genotypes. Some substitutions found in the X-tail do not affect secondary structure of this element suggesting that this region might play an important role in replication, stabilization and packaging of HCV genome. Additionally, U residues are not present at the end of the X-tail in Pakistani 3a isolates as otherwise reported for the variants of genotype 1b.
Conclusions:
Sequence and structural diversity of the 3'UTR variable region and Poly U/UC region found in the local isolates indicate specificity in the regulating elements of 3'UTR that might be associated with differential replication efficacy of the HCV Pakistani isolates. The study necessitates functional characterization of these regulating elements to elucidate variable viral efficiency and pathogenicity associated with inter-geographical isolates.
