Comparative analyses of the nucleocapsid genes of several strains of infectious bronchitis virus and other coronaviruses

The natural sequence variations of the nucleocapsid genes of the Gray, Arkansas99 (Ark99), and Holland52 (Holl52) strains of infectious bronchitis virus (IBV) were determined. These were compared with previously published sequencing data of other IBV strains, as well as other coronaviruses, in order to correlate the serological and evolutionary relationship of coronaviruses. IBV nucleotide sequence alignment shows that overall the sequences are highly conserved, with homologies from 91.1 to 96.5%. However, there are also two regions (730 to 800 and 1138 to 1166) that appear to be even more highly conserved. Overall, the nucleocapsid protein is highly variable both in size and composition between coronavirus major antigenic groups but is conserved within these groups. A phylogenetic tree of the nucleocapsid protein of various coronaviruses indicates that the coronaviruses fall into distinct groups that correspond to the three major antigenic groups; however, a phylogenetic tree of the IBV nucleocapsid shows that this does not hold true for the type specific antigenic groups of IBV.