Sequence comparison and phylogenetic analysis of Hepatitis C virus genotype 3 polymerase

Waheed,Yasir; Bhatti,Attya; Anjum,Sadia; Ashraf,Muhammad

doi:10.3892/mmr.2014.1926

Sequence comparison and phylogenetic analysis of Hepatitis C virus genotype 3 polymerase

Authors:
- Yasir Waheed
- Attya Bhatti
- Sadia Anjum
- Muhammad Ashraf
View Affiliations

Affiliations: Atta‑ur‑Rahman School of Applied BioSciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
Published online on: January 30, 2014 https://doi.org/10.3892/mmr.2014.1926
Pages: 1266-1270

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Hepatitis C virus (HCV) is a worldwide health problem with high morbidity and mortality. HCV polymerase is an attractive target for the development of antiviral strategies. The aim of the present study was to report the sequence variation in the HCV NS5B gene from genotype 3 patient samples. The gene was amplified, cloned and sequenced. A nucleotide and amino acid sequence comparison of conserved motifs of HCV NS5B from the current reported sequences and previously reported genotype 3 sequences was performed. The sequence comparison indicated that the motifs A, B, C and F and β loop sequences are conserved in the reported sequences, while sequence variation was observed in motifs D and E. Amino acids E18, Y191, C274, Y276 and H502, which are involved in the interaction between template and primer, are highly conserved in the reported sequences. R48, R158, D225, S367, R386 and R394 amino acids interact with initiating GTP, and are also highly conserved in the reported sequences. A phylogenetic tree revealed that the sequences are clustered with sequences from India. HCV polymerase lacks proofreading ability and has high error rates. The present study revealed that the residues that form the important motifs of HCV NS5B remain conserved. However, it was observed that numerous place changes in the nucleotide sequences did not affect the amino acid sequences of HCV NS5B. The conserved motifs are strong targets for the development of peptide vaccines against HCV.

View Figures

View References

1	Pfannkuche A, Büther K, Karthe J, Poenisch M, Bartenschlager R, Trilling M, Hengel H, Willbold D, Haussinger D and Bode GJ: c-Src is required for complex formation between the hepatitis C virus encoded proteins NS5A and NS5B: a prerequisite for replication. Hepatology. 53:1127–1136. 2011. View Article : Google Scholar : PubMed/NCBI
2	Waheed Y, Shafi T, Safi SZ and Qadri I: Hepatitis C virus in Pakistan: a systematic review of prevalence, genotypes and risk factors. World J Gasteroenterol. 15:5647–5653. 2009. View Article : Google Scholar : PubMed/NCBI
3	Lemon SM, Walker C, Alter MJ and Yi M: Hepatitis C viruses. Knipe D, Howley P, Griffin DE, Martin MA, Lamb RA, et al: Fields’ virology. 5th edition. Lippincott Williams and Wilkins; Philadelphia, PA: pp. 1253–1304. 2007
4	Waheed Y, Safi SZ and Qadri I: Role of Potash Alum in hepatitis C virus transmission at barber’s shop. Virol J. 8:2112011.PubMed/NCBI
5	Quinkert D, Bartenschlager R and Lohmann V: Quantitative analysis of the hepatitis C virus replication complex. J Virol. 79:13594–13605. 2005. View Article : Google Scholar : PubMed/NCBI
6	Hijikata M, Shimizu YK, Kato H, Iwamoto A, Shih JW, Alter HJ, Purcell RH and Yoshikura H: Equilibrium centrifugation studies of hepatitis C virus: evidence for circulating immune complexes. J Virol. 67:1953–1958. 1993.PubMed/NCBI
7	Pawlotsky JM: Hepatitis C virus genetic variability: pathogenic and clinical implications. Clin Liver Dis. 7:45–66. 2003. View Article : Google Scholar : PubMed/NCBI
8	Yan Y, Li Y, Munshi S, Sardana V, Cole JL, Sardana M, Steinkuehler C, Tomei L, De Francesco R, Kuo LC and Chen Z: Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form. Protein Sci. 7:837–847. 1998. View Article : Google Scholar : PubMed/NCBI
9	Penin F, Dubuisson J, Rey FA, Moradpour D and Pawlotsky JM: Structural biology of hepatitis C virus. Hepatology. 39:5–19. 2004. View Article : Google Scholar
10	Waheed Y, Saeed U, Anjum S, Afzal MS and Ashraf M: Development of global consensus sequence and analysis of highly conserved domains of HCV NS5B protein. Hepat Mon. 12:e61422012.PubMed/NCBI
11	Waheed Y, Bhatti A and Ashraf M: RNA dependent RNA polymerase of HCV: a potential target for the development of antiviral drugs. Infect Genet Evol. 14:247–257. 2013. View Article : Google Scholar : PubMed/NCBI
12	Lohmann V, Körner F, Herian U and Bartenschlager R: Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. J Virol. 71:8416–8428. 1997.PubMed/NCBI
13	Ranjith-Kumar CT and Kao CC: Biochemical activities of the HCV NS5B RNA dependent RNA polymerase. Hepatitis C Viruses: Genomes and Molecular Biology. Tan S: Horizon Bioscience; Norfolk: pp. 293–310. 2006
14	Bressanelli S, Tomei L, Rey FA and De Francesco R: Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides. J Virol. 76:3482–3492. 2002. View Article : Google Scholar : PubMed/NCBI
15	Hong Z, Cameron CE, Walker MP, Castro C, Yao N, Lau JY and Zhong W: A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase. Virology. 285:6–11. 2001. View Article : Google Scholar : PubMed/NCBI
16	Brass V, Gouttenoire J, Wahl A, Pal Z, Blum HE, Penin F and Moradpour D: Hepatitis C virus RNA replication requires a conserved structural motif within the transmembrane domain of the NS5B RNA-dependent RNA polymerase. J Virol. 84:11580–11584. 2010. View Article : Google Scholar : PubMed/NCBI
17	Sanger F, Nicklen S and Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA. 74:5463–5467. 1977. View Article : Google Scholar : PubMed/NCBI
18	O’Reilly EK and Kao CC: Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure. Virology. 252:287–303. 1998.PubMed/NCBI
19	Waheed Y, Tahir S, Ahmad T and Qadri I: Sequence comparison and phylogenetic analysis of core gene of hepatitis C virus from Pakistani population. Afr J Biotech. 9:4561–4567. 2010.
20	Herrmann E, Neumann AU, Schmidt JM and Zeuzem S: Hepatitis C virus kinetics. Antivir Ther. 5:85–90. 2000.
21	Neumann AU, Lam NP, Dahari H, Gretch DR, Wiley TE, Ladyen TJ and Perelson AS: Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science. 282:103–107. 1998. View Article : Google Scholar
22	Bartenschlager R and Lohmann V: Replication of hepatitis C virus. J Gen Virol. 81:1631–1648. 2000.PubMed/NCBI
23	Legrand-Abravanel F, Nicot F and Izopet J: New NS5B polymerase inhibitors for hepatitis C. Expert Opin Inves Drugs. 19:963–975. 2010. View Article : Google Scholar
24	Sadia A, Afzal MS, Ahmad T, Aslam B, Waheed Y, Shafi T and Qadri I: Mutation in the STAT1-interacting domain of the hepatitis C virus core protein modulate the response to antiviral therapy. Mol Med Rep. 8:487–492. 2013.PubMed/NCBI