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AuthorSohail, Muhammad Umar
AuthorHadi Muhamad, Yassine
AuthorAsma A, Al Thani
Available date2019-09-08T07:52:01Z
Publication Date2019-08-31
Publication NameHepatitis monthlyen_US
Identifierhttp://dx.doi.org/10.5812/hepatmon.92437
CitationSohail M U, Al Thani A A, Yassine H M. Comparative Phylogenetic and Residue Analysis of Hepatitis C Virus E1 Protein from the Middle East and North Africa Region, Hepat Mon. 2019 ; 19(8):e92437. doi: 10.5812/hepatmon.92437.
ISSN1735-143X
Identifiere92437
URIhttp://hepatmon.com/en/index.html
URIhttp://hdl.handle.net/10576/11788
AbstractHepatitis C virus (HCV) is a major public health problem in the Middle East and North Africa (MENA) region with an estimate of over 15 million chronically infected patients. However, molecular characterization of circulating genotypes in the MENA region remains elusive. Here, we performed a comparative phylogenomic analysis of so-far available E1 gene sequences (937), originating from eight countries in the MENA region. All HCV E1 protein sequences present in NCBI from the MENA region were retrieved and cataloged per year and country of origin. Phylogenetic analysis revealed a maximum diversity of genotypes and subtypes in South Arabia [G-1 (1a, 1b, 1g), G-2 (2a, 2c), G-3 (3a) and G-4 (4a, 4d, 4n, 4o, 4r, 4s)] followed by Egypt [G-1 (1b, 1g) and G-4 (4a, 4l, 4n, 4m, 4u)], Iran [G-1 (1b) and G-3 (3a) G-6 (6a)], Tunisia [G-1 (1b) and G-2 (2a, 2b, 2c)], Algeria [G-1 (1i), 4(4f), Pakistan [G-1 (1a), G-3(3a, 3b)], Afghanistan [G-1 (1a), GT-3 (3a)], and 5(5a), and Yemen [G-4 (4r)]. The calculated evolution rate of retrieved sequences was 1.601 × 10−3 substitutions/site/year and the mean nucleotide diversity rate was 0.2684 (P < 0.001). The ratio of synonymous to non-synonymous (mean dN/dS) substitutions was higher in genotypes 2 and 4 compared to the genotypes 1 and 3. A higher degree of nucleotide identity in E1 gene was found between subtypes 1a and 1b, between 2c and 2g, and between 4a, 4d, and 4o. Comparative residue analysis of E1 protein epitope sequences of previously reported H111, A4, and A6 monoclonal antibodies showed relatively poor and genotype-specific conservancy. Perhaps, none of the reported epitope sequences had immunogenicity score higher than 0.4 (A minimum threshold for vaccine sequence prediction). Furthermore, these epitope sequences were heavily glycosylated at amino acid 196, 209, and 234 sites in all GTs. In conclusion, a high genetic variability in E1 protein coupled with increased glycosylation may deduce heterogeneity and subsequent escape from vaccine-generated immune response, thereby ascertaining necessary interventions for disease management and control.
SponsorThe work was performed at BRC internal resources
Languageen
PublisherKowsar (Research Center for Gastroenterology and Liver Diseases, Tehran, Iran)
SubjectE1 Protein
SubjectN- Glycosylation
SubjectGenotyping
SubjectImmune Epitopes
SubjectNucleotide Diversity
TitleComparative Phylogenetic and Residue Analysis of Hepatitis C Virus E1 Protein from the Middle East and North Africa Region
TypeArticle
Issue Number8
Volume Number19
ESSN1735-3408


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