Complete genome sequence of Nariva virus, a rodent paramyxovirus

Abstract

Nariva virus (NarPV) was isolated from forest rodents (Zygodontomys b. brevicauda) in eastern Trinidad in the early 1960s. Initial classification within the family Paramyxoviridae was based mainly on morphological observations including the structure of nucleocapsids and virion surface projections. Here, we report the characterization of the complete genome sequence of NarPV. The genome is 15,276 nucleotides in length, conforming to the rule-of-six, and has a genome organization typical of most members of the family, with six transcriptional units in the order 3'-N-P-M-F-H-L-5'. The gene junctions contain highly conserved gene start and stop signals and a tri-nucleotide intergenic sequence present in most members of the subfamily Paramyxovirinae. Sequence comparison studies indicate that NarPV is most closely related to Mossman virus, which was isolated from wild rats (Rattus leucopus) in Queensland, Australia, in 1970. This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km.

Fig. 1

Schematic diagram of NarPV (a) and MosPV (b) genomes. The shaded boxes represent the coding regions for each of the six genes, whereas the lines indicate non-translated regions. The genome size scale is given at the bottom

Fig. 2

Alignment of genome terminal sequences. See “Materials and methods” for full virus names and database accession numbers. a Alignment of the 3′ leader and 5′ trailer sequences of NarPV. The 3′ leader is represented as anti-genome written in the 5′ → 3′ sense, and the 5′ trailer is represented as genome written in the 5′ → 3′ sense. The conserved residues are shaded. b Alignment of 3′ leader sequences of selected members of the subfamily Paramyxovirinae. The asterisk indicates the unique 5th C residue present only in the NarPV genome

Fig. 3

Alignment of deduced amino acid sequences for proteins encoded by the P/V/C genes of NarPV and MosPV. a Alignment of the full-length P protein sequences with identical residues shaded. The overlapping coding regions for the C proteins and V-specific polypeptide are indicated by the light grey letters C and V above. b Alignment of the full-length C protein sequences. c Alignment of the V-specific protein sequences

Fig. 4

Sequence alignment of the NarPV F cleavage site and fusion peptide with selected members of the Paramyxovirinae. A gap has been introduced at the predicted cleavage site. Amino acid residue numbers for each protein are shown to the left of each sequence. Conserved residues are shaded. See “Materials and methods” for full virus names and database accession numbers

Fig. 5

Phylogenetic trees based on complete protein sequences of the N proteins of viruses in the subfamily Paramyxovirinae. Numbers at nodes indicate levels of bootstrap support calculated from 1,000 trees. Branch lengths represent relative genetic distances. Full virus names and database accession numbers are provided in “Materials and methods”