Complete genome sequence of avian paramyxovirus type 3 reveals an unusually long trailer region

The complete genome sequence was determined for prototype parakeet/Netherlands/449/75 strain of avian paramyxovirus (APMV) serotype 3. The genome is 16,272 nucleotides (nt) in length, consisting of six non-overlapping genes in the order of 3′-N-P/V/W-M-F-HN-L-5′, with intergenic regions of 31–63 nt. APMV-3 genome follows the “rule of six” and is the largest among the avian paramyxoviruses reported to date, with a trailer region of 707 nt, the longest in the family Paramyxoviridae. The cleavage site of F protein, A-R-P-R-G-R↓L, does not conform to the preferred cleavage site of the ubiquitous cellular protease furin. Therefore, exogenous protease was needed for replication in vitro. Alignment and phylogenetic analysis of the predicted amino acid sequences of strain Netherlands proteins with the cognate proteins of viruses of all of the five genera of family Paramyxoviridae showed that APMV-3 strain Netherlands is more closely related to APMV-1 than APMV-6.