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.

ORFs longer than 400 nt internal to larger ORFs, which are of unknown significance. The overall pattern of ORFs matches the pattern observed for related viruses (1-3, 9, 10, 29) . There are 2 large (17,412 and 6,966 nt) 5= ORFs that are predicted to encode nonstructural proteins (see below), designated ORF1a and ORF1b. The next ORF, ORF2, is predicted to encode the "S" or spike glycoprotein. Then, there are 5 "3= ORFs," designated ORF3 to ORF6, that are predicted to encode additional structural proteins (see below). The 5= and 3= UTRs are 1,017 and 916 nt, respectively, and RACE analysis corroborated the prediction that the 3= end of the genome is polyadenylated. We used several tools to study the predicted proteome of this ball python virus. We used the BLASTp alignment tool to search for similar sequences in the NCBI nonredundant protein database (nr) (30) . We also used the more sensitive HMMER3 and HH-PRED hidden Markov model-based alignment and structure prediction software tools to detect more distant homologies and identify functional domains within the replicase polyprotein (31, 32) (http://hmmer.org). We used TMHMM to predict transmembrane domains and the NetNGlyc and NetOGlyc tools to predict N-and O-linked glycosylation sites in protein sequences (33, 34) (http://www.cbs.dtu.dk/services/NetNGlyc/).