Brief Articles
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World J Gastroenterol. Mar 28, 2009; 15(12): 1480-1486
Published online Mar 28, 2009. doi: 10.3748/wjg.15.1480
Positional effect of mutations in 5'UTR of hepatitis C virus 4a on patients' response to therapy
Mostafa K El Awady, Hassan M Azzazy, Ahmed M Fahmy, Sherif M Shawky, Noha G Badreldin, Samar S Yossef, Moataza H Omran, Abdel Rahman N Zekri, Said A Goueli
Mostafa K El Awady, Ahmed M Fahmy, Noha G Badreldin, Samar S Yossef, Moataza H Omran, Department of Biomedical Technology, National Research Center, Dokki, Cairo 12622, Egypt
Hassan M Azzazy, Sherif M Shawky, Department of Chemistry and Yousef Jameel Science and Technology Research Center, the American University in Cairo, Cairo 11511, Egypt
Sherif M Shawky, Structural biology department, Free University of Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
Abdel Rahman N Zekri, National Cancer Institute, Cairo 11796, Egypt
Said A Goueli, Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711, United States
Author contributions: El Awady MK designed experiment, wrote manuscript; Azzazy HM wrote the manuscript, analyzed data; Fahmy AM, Shawky SM, Badreldin NG, Yossef SS and Omran MH performed research; Zekri ARN and Goueli SA analyzed data.
Correspondence to: Hassan M Azzazy, PhD, Department of Chemistry and Yousef Jameel Science and Technology Research Center, the American University in Cairo, 113 Kasr El-Aini Street, SSE Rm # 1194, Cairo 11511, Egypt.
Telephone: +2-22-6152543  
Fax: +2-22-7957565
Received: October 29, 2008
Revised: February 19, 2009
Accepted: February 26, 2009
Published online: March 28, 2009

AIM: To investigate the effects of mutations in domain III of the hepatitis C virus (HCV) internal ribosome entry sequences (IRES) on the response of chronic HCV genotype 4a patients to interferon therapy.

METHODS: HCV RNA was extracted from 19 chronic HCV 4a patients receiving interferon/ribavirin therapy who showed dramatic differences in their response to combination therapy after initial viral clearance. IRES domain III was cloned and 15 clones for each patient were sequenced. The obtained sequences were aligned with genotype 4a prototype using the ClustalW program and mutations scored. Prediction of stem-loop secondary structure and thermodynamic stability of the major quasispecies in each patient was performed using the MFOLD 3.2 program with Turner energies and selected constraints on base pairing.

RESULTS: Analysis of RNA secondary structure revealed that insertions in domain III altered Watson-Crick base pairing of stems and reduced molecular stability of RNA, which may ultimately reduce binding affinity to ribosomal proteins. Insertion mutations in domain III were statistically more prevalent in sustained viral response patients (SVR, n = 14) as compared to breakthrough (BT, n = 5) patients.

CONCLUSION: The influence of mutations within domain III on the response of HCV patients to combination therapy depends primarily on the position, but not the frequency, of these mutations within IRES domain III.

Keywords: Hepatitis C virus, Internal ribosome entry sequences, Domain III, Genotype 4a, Ribosomal subunit, Interferon therapy, RNA folding