Cloning and Molecular Pattern Of HCV 1a NS5a Complete Coding Sequence as Predicting Factor for Resistance Therapy

Abstract

The hepatitis C virus (HCV) NS5A protein is known essential for virus replication and suggested play important role in therapy resistance mechanism. To predict and more understanding the molecular pattern of HCV 1a NS5A we cloned the NS5A gene of HCV 1a isolated in Central of Java Indonesia using standard cloning procedure. The sequence results were then aligned with all of HCV 1a NS5A complete coding sequences reported in GenBank. In total, 441 sequences were retrieved and aligned by ClustalW. We revealed the nucleotide and amino acid sequence consensus of HCV NS5A gene. Overall, only aa 5, 9-11, 13-15, 18-19, 22-23, 25-27, 29, 32-33, 35, 38-43, 45, 47, 50-51, 55, 57, 59-60, 63, 65-67, 70, 72, 76, 80, 82, 84, 86, 88-91, 94-97, 100, 102, 104-106, 109-113, 115-116, 118-120, 125, 128-129, 132, 134, 136, 140-143, 145, 147, 149-152, 154-157, 159, 162-163, 165, 167-168, 170, 173, 175, 178-179, 184-187, 189-193, 195, 201, 203, 207-208, 210, 216-218, 220, 222-225, 227-235, 238, 243, 249, 252, 257, 268, 270, 271, 274, 278, 283, 291-292, 298, 300, 306, 309-311, 313-314, 318-321, 324, 326, 329, 331, 336, 338-339, 342, 348, 350, 353, 356, 360, 363, 368-369, 377, 405-406, 409, 411-414, 416-419, 421-424, 427, 430-432, and 443 were found have no variation. Amino acid variations may have relevant changes of physicochemical properties so that influence the replication efficiency, therefore, the amino acid variations found in the present report need further study