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Abstract

Hepatitis C virus (HCV) infection remains a significant global health problem, affecting millions of individuals with confirmed liver conditions. Despite recent advancements in antiviral therapies, the development of an effective Vaccine remains a top priority. Understanding the molecular epidemiology and viral evolution of hepatitis C virus (HCV) infection requires sequencing. Due in part to the tremendous genomic variety found in HCV, there is currently limited uniformity among sequencing methodologies. HCV envelope proteins, in particular E1 and E2, are critical targets for vaccine development because they play a critical role in the infection's entrance into host cells. These envelope proteins, particularly E1 and E2, are pivotal in facilitating the original intercourse between the virus and the host's vulnerable system, making them ideal targets for vaccine design. E1 and E2 are complex molecules with different structures, featuring glycosylation sites and containing essential antigenic regions that are critical for the host's vulnerable response. Still, their structural diversity poses a significant challenge in vaccine development. HCV is well- known for its inheritable variability, with multiple genotypes and quasi species circulating globally. This inheritable diversity has implications for the effectiveness of any potential vaccine, as a single strain may not give sufficient protection against the wide range of HCV variants. To address this challenge, innovative strategies are being explored. A general time-reversible substitution model was used to build phylogenetic trees, and sensitivity studies were carried out for each subregion.