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- Title
Comparative Phylogenetic and Residue Analysis of Hepatitis C Virus E1 Protein from the Middle East and North Africa Region.
- Authors
Sohail, Muhammad Umar; Al Thani, Asma A.; Yassine, Hadi Mohamad
- Abstract
Hepatitis 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, weperformed 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 1.601x10-3 substitutions/site/year and the meannucleotide 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. Maybe 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 glycosylationmaydeduce heterogeneity and subsequent escape from vaccine-generated immune response, thereby ascertaining necessary interventions for disease management and control.
- Subjects
AFGHANISTAN; ALGERIA; ARABIAN Peninsula; EGYPT; IRAN; PAKISTAN; TUNISIA; YEMEN (Republic); NORTH Africa; MIDDLE East; GLYCOSYLATION; HEPATITIS C; PHYLOGENY; PROTEINS; GENETIC markers; DESCRIPTIVE statistics; GENOTYPES
- Publication
Hepatitis Monthly, 2019, Vol 19, Issue 8, p1
- ISSN
1735-143X
- Publication type
Article
- DOI
10.5812/hepatmon.92437