en 39606685 <p style="text-align:justify"><span style="font-size:11pt"><strong><span style="font-size:10.0pt">Background:</span></strong><span style="font-size:10.0pt"> Despite the success of &quot;direct-acting antivirals&quot; in treating Hepatitis C Virus (HCV) infection, invention of a preventive HCV vaccine is crucial for global elimination of the virus. Recent data indicated the importance of the induction of Pan-genomic neutralizing Antibodies (PnAbs) against heterogenic HCV Envelope 2(E2), the cellular receptor binding antigen, by any HCV vaccine candidate. To overcome HCVE2 heterogeneity, &quot;generation of consensus HCVE2 sequences&quot; is proposed. However, Consensus Sequence (CS) generating algorithms such as &quot;Threshold&quot; and &quot;Majority&quot; have certain limitations including &quot;Threshold-rigidity&quot; which leads to induction of undefined residues and insensitivity of the &quot;Majority&quot; towards the &quot;evolutionary cost of residual substitutions&quot;. </span></span></p> <p style="text-align:justify"><span style="font-size:11pt"><strong><span style="font-size:10.0pt">Methods:</span></strong><span style="font-size:10.0pt"> Herein, first a modification to the &quot;Majority&quot; algorithm was introduced by incorporating BLOSUM matrices. Secondly, the HCVE2 sequences generated by the &quot;Fitness&quot; algorithm (using 1698 sequences from genotypes 1, 2, and 3) was compared with those generated by the &quot;Majority&quot; and &quot;Threshold&quot; algorithms using several <em>in silico </em>tools. </span></span></p> <p style="text-align:justify"><span style="font-size:11pt"><strong><span style="font-size:10.0pt">Results:</span></strong><span style="font-size:10.0pt"> Results indicated that only &quot;Fitness&quot; provided completely defined, gapless HCVE2s for all genotypes/subtypes, while considered the evolutionary cost of amino acid replacements (main &quot;Majority/Threshold&quot; limitations) by substitution of several residues within the generated consensuses. Moreover, &quot;Fitness-generated HCVE2 CSs&quot; were superior for antigenic/immunogenic characteristics as an antigen, while their positions within the phylogenetic trees were still preserved. </span></span></p> <p style="text-align:justify"><span style="font-size:11pt"><strong><span style="font-size:10.0pt">Conclusion:</span></strong><span style="font-size:10.0pt"> &quot;Fitness&quot; algorithm is capable of generating superior/optimum HCVE2 CSs for inclusion in a pan-genomic HCV vaccine and can be similarly used in CS generation for other highly variable antigens from other heterogenic pathogens.</span></span></p> Amino acids, Antibodies, Antiviral Agents, Consensus sequence, Genomics, Genotype, Hepacivirus, Hepatitic C, Inventions, Phylogeny, Vaccines, Virus diseases 268 278 https://www.ajmb.org/En/Article.aspx?id=60594 https://www.ajmb.org/PDF/En/FullText/60594.pdf ReyhanehMohabatiDepartment of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran92259RezaRezaeiSchool of Biology, College of Science, University of Tehran, Tehran, Iran92260NasirMohajelDepartment of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran92261Mohammad MehdiRanjbarDepartment of FMD Vaccine Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran92262KatayounSamimi-RadDepartment of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran92263KayhanAzadmanesh483FarzinRoohvand160