ABSTRACT
@# This study is focused towards developing a global consensus sequence of nonstructural protein 2 (NSP2), a protease of Chikungunya Virus (CHIKV) and predict immunogenic promiscuous T-cell epitopes based on various bioinformatics tools. To date, no epitope data is available for the Chikungunya virus in the IEDB database. In this study, 100 available nucleotide sequences of NSP2-CHIKV belonging to different strains were downloaded from the National Centre for Biotechnology Information (NCBI) database. The nucleotide sequences were subjected to translated sequencing using the EXPASY tool followed by protein alignment using the CLC workbench and a global consensus sequence for the respective protein was developed. IEDB tool was used to predict HLA-I and HLA-II binding promiscuous epitopes from the consensus sequence of NSP2-CHIKV. Thirty-four B-cell based epitopes are predicted and the promiscuous epitope is VVDTTGSTKPDPGD at position 341-354. Twenty-six MHC-I short peptide epitopes are predicted to bind with HLA-A. The promiscuous epitopes predicted to bind with HLA-A*01:01 are VTAIVSSLHY, SLSESATMVY, FSKPLVYY, QPTDHVVGEY at positions 317-326, 84-93, 535-544 and 15-24 with percentile ranks 0.17, 0.39, 0.51 and 0.81, respectively. Twenty-four MHC-II short peptide epitopes are predicted for HLA-DRB. The promiscuous epitope predicted to bind with HLA-DRB*01:01 is VVGEYLVLSPQTVLRS from 20-35 with a lowest percentile rank of 0.01. These predicted epitopes can be effective targets towards development of vaccine against CHIKV. Epitopes predicted in this study displayed good binding affinity, antigenicity and promiscuity for the HLA classes. These predicted epitopes can prove to be translationally important towards the development of CHIKV.
ABSTRACT
Background: Due to the inherently unstable nature of HCV, various genotypes have been identified. Steatosis is a histological feature in the progression of HCV-associated liver disease and has been shown to alter the host lipid metabolism. Objective: Assess the distribution of HCV genotypes in the two provinces of Pakistan, and determine the association of hepatic steatosis with altered clinical and virological factors in chronic HCV patients. Methods: One hundred twenty six chronic HCV patients (steatosis in 49 patients) were enrolled for qualitative analysis by PCR. Out of 126 ELISA and PCR positive samples, 119 (48 with hepatic steatosis) chronic HCV patients (mean age 42.0±13.3 years, mean body mass index (BMI) 24.2±4.1) were proved positive after PCR-based detection. Biochemical and virological factors such as HCV genotype, or glucose, in 119 CHC patients were determined and compared between patients with and without hepatic steatosis. Results: Out of 126 samples, 119 were HCV positive, where 58 (48.7%) were genotype 3a, 24 (20.2%) were 3b, 12 (10.1%) were 1a, eight (6.7%) were 2a, six (5.0%) were 1b, and one (0.8%) was 4. Furthermore, seven (5.9%) had a co-infection and three (2.5%) were untypable. BMI (p=0.004), genotype 3a (p<0.001), and triglycerides (p=0.002) were significantly associated with steatosis. It is noteworthy that cholesterol (p=0.281), glucose (p=0.305), lowdensity lipoprotein (p=0.101), high-density lipoprotein (p=0.129), alanine amino transferase (p=0.099), aspartate transaminase (p=0.177), bilirubin (p= 0.882), and age (p=0.846) showed non-significant association. Conclusion: Genotype 3a is the predominant genotype in Pakistan. Hepatic steatosis is quite frequent feature in HCV patients and strongly correlates with BMI, genotype 3a, and triglyceride contents in patients infected with HCV.