Mutational Frequencies in the Immune System Interacting Proteins NS2A and NS2B in Dengue Virus Isolates

Abstract

Background: The genome of the dengue virus (DENV) encodes a total of ten proteins, three of which are structural and seven of which are non-structural (NS). Among the NS proteins, nonstructural protein 2A (NS2A) and NS2B play pivotal roles in the replication and assembly of DENV. This study aimed to determine the frequency of mutations occurring in the NS2A and NS2B regions of DENV within the Punjab Province of Pakistan. Methods: About 4 mL of blood was collected from DENV patients. RNA was isolated from serum samples and confirmed using an RNA Kit. The RNA was converted to complementary DNA (cDNA) followed by amplification using polymerase chain reaction. The cDNA was subjected to library preparation for whole genome sequencing. We selected 23 samples to undergo whole genome sequencing. Among these, 19 isolates exhibited a significant number of mutations. Results: In the NS2A, a total of 25 mutations were detected, with 23 being novel in the N-terminal and domains. The most common mutation, I15V, was found in seven genomic isolates, followed by I171A (n = 4), M150R (n = 2), and T34A (n = 2). Within NS2B, there were 20 different mutations, 18 of which were novel. Notably, the N and C-terminal regions exhibited a higher mutation frequency compared to the central two helices of NS2B. Specifically, seven mutations were located in the α1 helix of NS2B. Additionally, four mutations (A10E, V11F, I73F, and K127E) were detected in two isolates, respectively. Conclusions: The most conserved region was the C-terminal domains extending beyond the 181 amino acids. This study represents the first comprehensive analysis of mutations in the NS2A and NS2B regions, which may help design effective vaccines and antiviral therapies for DENV.