Abstract
The 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome contains the internal ribosome entry site (IRES), a highly conserved RNA structure essential for cap-independent translation of the viral polyprotein. HCV, apart from the liver, is thought to be associated with lymphocyte subpopulations of peripheral blood mononuclear cells (PBMCs), in lymph nodes and brain tissue. In this study, RT-PCR, cloning, and sequence analysis were employed to investigate the quasispecies nature of the 5'UTR following extraction of viral RNA from PBMCs and plasma of HCV infected individuals. The nucleotide variation between IRES-derived sequences from PBMCs and plasma indicated the existence of polymorphic sites within the IRES. HCV isolates had divergent variants with unique mutations particularly at positions 107, 204, and 243 of the IRES. Most of the PBMC-derived sequences contained an A-A-A variant at these positions. The mutations associated with the IRESes suggested the presence of unique quasispecies populations in PBMCs compared with plasma.
Highlights
Hepatitis C virus (HCV), a member of the Hepacivirus genus in the Flaviviridae family, is an enveloped virus with an icosahedral capsid that encloses a single-stranded positive sense genomic RNA of approximately 9.5 kb in length [1, 2]
The nucleotide differences among all the 225 sequences derived from peripheral blood mononuclear cells (PBMCs) and all of the 225 sequences derived from plasma samples are highlighted on the secondary RNA structure of the 5’untranslated regions (UTR) HCV (nt. 1-383 genotype 1b (GenBank, AJ238799.1) where numbers indicate internal ribosome entry site (IRES) nucleotide positions relative to strain HCV 1a (GenBank, NC 004102) (Figure 1)
As the two-dimensional structure of HCV genotype 1b 5’UTR was used as an outline to position the nucleotide substitutions detected in HCV IRESes, mainly genotype 1a (Figure 1), the HCV IRES genotype 1b was aligned with consensus sequence genotype 1a to pinpoint any differences between the two IRESes
Summary
Hepatitis C virus (HCV), a member of the Hepacivirus genus in the Flaviviridae family, is an enveloped virus with an icosahedral capsid that encloses a single-stranded positive sense genomic RNA of approximately 9.5 kb in length [1, 2]. The presence of HCV RNA in extrahepatic sites has been detected in HCV infected individuals where HCV negative strands (replicative intermediate) have been associated with PBMCs, CD4+, CD8+, CD19+, T-cells, monocytes, and macrophages [12]. The virus has been shown to persist in the PBMCs of patients who had received successful antiviral treatment with Pegylated-IFNα (Peg-IFNα) in combination with ribavirin. In such patients, HCV RNA was associated with PBMCs but not present in the serum [13,14,15]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
