Molecular Modeling of Major Structural Protein Genes of Avian Coronavirus: Infectious Bronchitis Virus Mass H120 and Italy02 Strains

In Morocco, the epidemiological situation of infectious bronchitis virus (IBV) is very complex, because of the antigenic diversity associated with the emergence of new serotypes/genotypes and variants. The IBV strains circulating in poultry farms are serotypes/genotypes Italy02 and Massachusetts (Mass) identified during 2010–14. The appearance of these variants hinders the prophylactic strategy carried out by the breeders of the Moroccan poultry farm. To solve this problem, we have opted for the rational design of candidate vaccines in order to study the structure of the three-dimensional (3D) S1 spicule protein of serotype Italy02 and Mass H120, through molecular modeling, using the I-TASSER server, then the COACH, and another Meta server to determine and predict the common immunogenic active sites between these two IBV strains circulating in Morocco. The obtained results showed that the two strains studied had identical spatial conformation of the S1 protein structure with a similarity percentage of 81% and an average stability of the modeled sequences. Thus both serotypes share active antigenic sites common in the hypervariable region, located at residues 229, 230, 232, 233, and 235, with a magnesium molecule association around the Alanine 280 region responsible for stimulating immunogenicity. The quality of the 3D conformation, the stability, and the percentage make it possible to have accessibility to the common predicted neutralizing epitopes. Based on these data, we can conclude that it is highly probable that the H120 vaccine strain confers cross-protection against a challenge with new strains Italy02 circulating in Morocco.