Complete sequence of the genome of avian paramyxovirus type 9 and comparison with other paramyxoviruses

Abstract

The complete genome consensus sequence was determined for avian paramyxovirus (APMV) serotype 9 prototype strain PMV-9/domestic Duck/New York/22/78. The genome is 15,438 nucleotides (nt) long and encodes six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5' with intergenic regions of 0-30 nt. The genome length follows the "rule of six" and contains a 55-nt leader sequence at the 3' end and a 47-nt trailer sequence at the 5' end. The cleavage site of the F protein is I-R-E-G-R-I downward arrowF, which does not conform to the conventional cleavage site of the ubiquitous cellular protease furin. The virus required exogenous protease for in vitro replication and grew only in a few established cell lines, indicating a restricted host range. Alignment and phylogenetic analysis of the predicted amino acid sequences of APMV-9 proteins with the cognate proteins of viruses of all five genera of family Paramyxoviridae showed that APMV-9 is more closely related to APMV-1 than to other APMVs. The mean death time in embryonated chicken eggs was found to be more than 120h, indicating APMV-9 to be avirulent for chickens.

Fig. 1

Sequences of the APMV-9 3′ leader and 5′ trailer regions. (a) Alignment of the 3′ leader and N gene start sequences of APMV-9 with those of selected paramyxoviruses. Dots indicate identity with the assignment in APMV-9. (b) Comparison of the 5′ trailer region of APMV-9 with those of other APMVs. Bold underlined letters indicate dissimilarity of nt assignments among APMVs. (c) Complementarity between the 3′ leader and 5′ trailer regions of APMV-9. All sequences are in negative-sense. Abbreviations; SV5, Simian virus 5; APMV, Avian paramyxovirus; HPIV, Human parainfluenza virus; TiV, Tioman virus; SeV, Sendai virus; NiV, Nipah virus; HeV, Hendra virus; MeV, Measles virus; CDV, Canine distemper virus.

Fig. 2

APMV-9 gene order, putative transcription signals, and IGS. (a) Schematic representation of the APMV-9 genome with the nt coordinates of the genes shown above the line and the lengths of the 3′ leader, 5′ trailer, and IGS shown below the line. (b) APMV-9 gene-start and gene-end sequence motifs. (c) APMV-9 IGS. All sequences are in negative-sense.

Fig. 3

Comparison of the RNA editing site in the P gene of APMV-9 with those of selected members of subfamily Paramyxovirinae. Sequences are in positive (mRNA) sense.

Fig. 4

Alignment of the amino acid sequence of the C-terminal end of the V protein of APMV-9 with those of different members of subfamily Paramyxovirinae. Conserved cysteine and tryptophan residues are indicated by stars. Numbers on either side of the sequence indicate the amino acid position.

Fig. 5

Comparison of the F protein cleavage site of APMV-9 with those of different members of genus Avulavirus. Basic amino acid residues (R-Arginine, K-lysine) are indicated in bold.

Fig. 6

Phylogenic analysis of the amino acid sequences of the F and HN proteins of APMV-9 and selected members of subfamily Paramyxovirinae. The numbers in branches represent the divergence of APMV-9 with other members of family Paramyxoviridae.