Putative papain‐related thiol proteases of positive‐strand RNA viruses Identification of rubi‐ and aphthovirus proteases and delineation of a novel conserved domain associated with proteases of rubi‐, α‐ and coronaviruses

A computer‐assisted comparative analysis of the amino acid sequences of (putative) thiol proteases encoded by the genomes of several diverse groups or positive‐stranded RNA viruses and distantly related to the family of cellular papain‐like proteases is presented. A high level of similarity was detected between the leader protease of foot‐and‐mouth‐disease virus and the protease of murine hepatitis coronavirus which cleaves the N‐terminal p28 protein from the polyprotein. Statistically significant alignment of a portion of the rubella virus polyprotein with cellular papain‐like proteases was obtained, leading to tentative identification of the papain‐like protease as the enzyme mediating processing of the non‐structural proteins of this virus. Specific grouping between the sequences of the proteases of α‐viruses, and poty‐ and bymoviruses was revealed. It was noted that papain‐like proteases of positive‐stranded RNA viruses are much more variable both in their sequences and in genomic locations than chymotrypsin‐related proteases found in the same virus class. A novel conserved domain of unknown function has also been identified which flanks the papain‐like proteases of α‐, rubi‐ and coronaviruses.