Analysis of mutations in the fusion protein and hemagglutinin-neuraminidase in twelve strains of NDV isolated in Madagascar by bioinformatics methods

Abstract

Many researchers have made efforts to generate genotype-matched and subunit vaccines for Newcastle disease (ND). During the design process, we found that they only considered certain characteristics of the virulent strains. As a result, the resulting vaccines are still poorly effective against new emerging strains of ND virus (NDV). This analysis suggests that consideration of various characteristics of virulent strains in the design is necessary to increase the efficacy of these new vaccines. Thus, analysis of mutations in viral proteins targeted in the design such as fusion proteins (F) and hemagglutinin-neuraminidase (HN) is essential. For this reason, the present study aims to analyze mutations in these two proteins in twelve NDV strains isolated in Madagascar. To achieve this, we employed bioinformatics methods such as sequence alignment, molecular modeling, 3D structure comparison and mutation impact prediction via bioinformatics software and servers. As results, we identified respectively 26 and 41 mutations in the F and HN proteins of the Madagascar isolates. All these mutations have an impact on the stability of the protein. However, only 6 mutations (D344N, G303V, P315S, E347K, P391S and E495S) have an impact on their 3D structures. Finally, the 3 mutations (A477T, G303V and P315S) also affect the functions of these two proteins. In conclusion, we have identified 67 mutations that may affect the stability, structures, and functions of NDV F and HN proteins. Further studies are needed to know their effects on the antigenicity and immunogenicity of these two proteins.