Phylogenetic sub
Phylogenetic subtyping of hepatitis C virus 5' UTR isolated in Egypt and the effect of 2 transitions in subdomain IIId on the apical loop structure
*Amal Mahmoud and Medhat H. Hashem
Genetic Engineering & Biotechnology Research Institute, Menoufia University, Sadat City Branch, Menoufia, Egypt. *[email protected]
Abstract: HCV 5′-UTR of 3 non-responding isolates (Sohag 1, 2 and 3), collected from Sohag-Egypt was compared with the 6 genotypes collected from GenBank and HCV database sequences included a responder isolate from Egypt. Multiple alignment comparison showed that TTGGGT sequence located in the IIId subdomain loop was conserved in all genotypes. Phylogenetic tree revealed that isolate Sohag 1 was clustered with the responder isolate within subtype 4a. Sohag 2 was clustered with isolates of subtypes g and o, however, isolate 3 was grouped with isolates from subtype 4a and q. Two transitions T175→C and C183→T were detected in the stem of IIId subdomain and were highly represented in genotype 2 followed by genotype 6: 1.0, 95.5, 2.0, 14.5, 0.0 and 33.5% for genotypes 1, 2, 3, 4, 5 and 6, respectively.The predicted secondary structure of HCV 5′-UTR showed that the formation of UUGGGU loop was affected by the 2 transitions T175→C and C183→T. In the absence of these 2 transitions, the apical loop was replaced by double helix structure in most predicted folding. Taken together, the % of the 2 transitions in different genotypes and the modification in the apical loop structure could affect the response to therapeutic treatment.
[Amal Mahmoud and Medhat H. Hashem. Phylogenetic subtyping of hepatitis C virus 5' UTR isolated in Egypt and the effect of 2 transitions in subdomain IIId on the apical loop structure. Life Science Journal. 2012;9(1):903-909] (ISSN:1097-8135). http://www.lifesciencesite.com. 133
Keywords: Hepatitis C virus; 5` UTR; IIId subdomain; Secondary structure Full Text 133
