Prediction Of T Cell Cross-reactivity Between Hepatitis C Virus And Dengue Virus Utilizing Bioinformatics Approaches

Objectives:This study uses the analysis of the gene structure,geographic distribution,and infected population of the two Flaviviridae viruses of hepatitis C virus(HCV)and dengue virus(DENV)as clues,utilizing bioinformatics methods to test whether there are similar amino acid sequences between the two viruses,whether these sequences can induce virus-specific T cell cross-reactivity,and whether the T cell cross-reactivity differs in different HCV genotypes.Methods:The amino acid sequences of different genotypes and serotypes of the two viruses were retrieved from GenBank database.Protein alignment database Blastp and bioinformatics software DNAMAN 8.0 were used to analyze the amino acid sequences of DENV and HCV.Five or more identical and continuous amino acid sequences between DENV and HCV were defined as candidate sequences,and the corresponding sequences were represented by lowercase letters a,b,c,etc.According to the original frequencies of two viruses,the two ends of the selected candidate sequences were extended by 10 amino acids respectively,and the corresponding sequences were represented by capital letters A,B,C,etc.Referring to DENV 1 amino acid sequence,the amino acid conservatism of corresponding positions between HCV and DENV was compared by BioEdit.Finally,referring to the two virus representative sequences,the extended candidate sequences were imported into bioinformatics software(SSYFPEITHI,NetMHCpan4.1,and NetMHCIIpan4.0)to predict the epitopes of CD4~+and CD8~+ T cells.The predicted values of the corresponding extended candidate sequences were evaluated,and the differences on the predicted scores of HCV genotype 1 and HCV genotype 3 were compared.Results:By sequence alignment,two relatively conservative and more than 5 consecutive amino acid sequences were found between NS3 region of DENV and NS3 region of HCV,which were candidate Sequence-a(TATPPGSV)and candidate Sequence-b(GRRQR).The amino acid sequences of DENV was more similar to HCV than other flaviviruses in terms of candidate Sequence-a.In candidate Sequence-a,there were 1-2 amino acid loci variation among different DENV serotypes.In the analysis of the variation candidate Sequence-a,three HCV subgenotype 1a sequences were identical to DENV 1,while two of HCV subgenotype 1b sequences were identical to DENV 1,and only one was different from DENV 1 by one amino acid(TATPPGSI).All HCV genotype 3 has one amino acid that is different from DENV1,and all of them are V to I variants(TATPPGSI).Candidate Sequence-b was identical across all the genotypes and serotypes of both viruses.In order to compare the variation between DENV and HCV sequences furtherly,more HCV amino acid sequences was included,and we found that the results were consistent with the above results.Noticedly,HCV genotype 3 showed more significant V to I variation(TATPPGSI).In the prediction CD4~+T cell epitopes of the extended Sequence-A,six DENV epitopes were predicted by SYFPEITHI software that might have potential cross-reactivity with HCV.The allele HLA-DRB1*0101 corresponding to xxxxxxxTATPPGSx(The same amino acid of DENV and HCV at the same site were represented by the abbreviated symbol of the amino acid,and the rest by character x.)had a higher predicted score in HCV genotype 1 than in HCV genotype 3(27 vs.19),and there was no difference in the predicted scores between HCV genotype 1 and HCV genotype 3 in the other predicted epitopes.The potential DENV 1-4 epitopes of Sequence-A were mainly concentrated in xxxxxxxxTATPPGS,xxxxxxxTATPPGSx,xxxxxxTATPPGSxx and xxxxxTATPPGSxxx by using the online software NetMHC?pan4.0.The four potential epitopes corresponding to DENV and HCV were analyzed,and the predicted scores of allele HLA-DRB 1*04,DRB4*01,DQA10103-DQB10603 in HCV genotype 1 were higher than those of HCV genotype 3.By predicting the CD8~+T cells epitopes of extended Sequence-A,11 epitopes with potential cross-reactivity between DENV and HCV were predicted using SYFPEITHI online software.Among them,6 potential epitopes predicting values of HCV genotype 1 was higher than those of HCV genotype 3,and only 1 potential epitope of HCV genotype 3 was higher than that of HCV genotype 1.A total of 17 potential epitopes were predicted when the immune epitopes of DENV were predicted by NetMHCpan4.1,but there were no potential epitopes corresponding to HCV.The CD8~+ T cells epitope prediction of the extended Sequence-B showed that 12 epitopes with potential cross-reactivity between DENV and HCV were predicted by SYFPEITHI online software,of which 2 epitopes of HCV genotype 1 had higher prediction scores than that of HCV genotype 3.One CD8~+T cell epitope with potential cross-reactivity between DENV and HCV was predicted by NetMHCpan4.1,and the predicted score of HCV genotype 1 was higher than that of HCV genotype 3(0.429 vs.0.421).CD4~+T cells epitope prediction of DENV and HCV by SYFPEITHI and NetMHCIIpan4.0 online software showed that there was no corresponding potential epitope between the two viruses.Conclusions:There were relatively conserved amino acid sequences in NS3 region between HCV and DENV,and the potential CD4~+T cell epitopes and CD8~+T cell epitopes were predicted between the two viruses in corresponding sequences.The score of potential epitopes corresponding to HCV genotype 1 was significantly higher than those of genotype 3.This suggests that there may be potential T cell cross-reactivity between HCV and DENV,and DENV specific immune response may be the cause of influencing the geographical distribution of HCV genotype 3.In addition,these potential epitopes can also provide a theoretical basis for the future development and design of HCV and DENV combined vaccines.