Phylogenetic and 2D/3D Analysis of HCV 1a NS4A Gene/Protein in Pakistani Isolates

Background: the nonstructural protein ns4a of hepatitis c virus is composed of 54 amino acids. this small size protein has vital role in many cellular functions. the most important reported function is being a cofactor of viral enzymes serine protease and helicase. objectives: the objective of this study was to analyze the phylogenetic variation, its impact in terms of translation and any functional change in protein structure at primary 2d/3d structure using computational tools from pakistani patients isolates. materials and methods: patient sera infected with hepatitis c virus, genotype 1a, were obtained from molecular diagnostics lab, cemb, university of the punjab lahore by using bd vacutainer collection tubes (becton dickenson). results: phylogenetic analysis of the gene revealed that pakistani 1a hcv strains are in the start of third cluster and there is a difference between inter pakistani isolates at primary, secondary and tertiary levels. conclusions: mutations were present in the central domain of ns4a (amino acids 21 - 34).