Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius

Stenglein, Mark D.; Jacobson, Elliott R.; Wozniak, Edward J.; Wellehan, James F. X.; Kincaid, Anne; Gordon, Marcus; Porter, Brian F.; Baumgartner, Wes; Stahl, Scott; Kelley, Karen; Towner, Jonathan S.; DeRisi, Joseph L.

Nidoviruses are characterized in part by the presence and organization of a set of functional subunits within their pp1ab replicase polyproteins (1, 5, 9, 10, 38, 39) . We first queried the snake virus pp1ab sequence against the NCBI nr database using the BLASTp tool. The best alignments produced were to pp1ab sequences from viruses in the Torovirinae subfamily, with bafinivirus sequences producing slightly higher scoring alignments than did torovirus sequences. The best alignment was to the pp1ab sequence of fathead minnow nidovirus (FHMNV) (see Fig. S3 in the supplemental material) (40) . This alignment covered nearly the entire second half of pp1ab in 2 contiguous pieces from residues 3973 to 5060 and 5429 to 8029 of snake virus pp1ab. In these regions, the polyproteins shared 22% and 29% pairwise identities, respectively. Thus, the overall organization and domain content of the second half of the snake virus's pp1ab protein resembled most closely those of bafinivirus replicase polyproteins (see Fig. S3 ).