Analysis of the N protein present in Feline Coronavirus strains in Italy

The N protein is a structural component of the helical nucleocapsid and plays an important role in viral pathogenesis, replication and RNA packaging. Antigenic studies have showed that the N protein is one of immunodominant antigens among coronaviruses species and can induce protective immune response against infection. Aminoacid sequences of the N protein from virulent and avirulent feline coronaviruses strains detected in a shelter were analysed. Computational analysis of antigenic sites were done using the method of Kolaskar and Tongaonkar. Prediction of the immunodominat helper T-lymphocyte antigenic sites from primary sequence data, was carried out analysing the occurrence of amphipatic fragments by using AMPHI algorithm; the identification of antigenic sites which interact with mouse MHC II haplotype d was performed using SETTE algorithm (4). Phylogenetic analysis showed an evident separation among avirulent strains producting intestinal infection and virulent strains responsible for FIP; this could be due to the increase of the virulence produced by the genomic mutations visible in the alignment. Comparative analysis of N protein sequences showed the presence of several functional domains that are conserved between the several Coronavirus species, confirming the primary role of N protein in the viral packaging and replication. Antigenic analysis of N proteins showed different putative epitopes recognized by helper T cells and peptide antigenic sites confirming a possible involvement of the nucleocaspid protein in the protective immune response. Our analysis demonstrated a substantial difference between virulent and avirulent strains in the mapping of antigenic sites. On the basis of these results we suppose that virulent strains could elude the immune surveillance removing the immunodominant motifs from the N protein sequences.