Whole genome analysis of sierra nevada virus, a novel mononegavirus in the family nyamiviridae

Abstract

A novel mononegavirus was isolated in 1975 from ticks (Ornithodoros coriaceus) collected during investigation of an outbreak of epizootic bovine abortion (EBA) in northern California. It was originally designated "bovine abortion-tick virus" (BA-T virus). The EBA is now known to be associated with a deltaproteobacterium infection, and not a virus. The BA-T virus had remained uncharacterized until now. We have determined by electron microscopy, serology, and genome sequencing that the BA-T virus is a fourth member of the newly proposed family Nyamiviridae, and we have renamed it Sierra Nevada virus (SNVV). Although antigenically distinct, phylogenetically SNVV is basal to Nyamanini virus (NYMV) and Midway virus (MIDWV), two other tick-borne agents. Although NYMV was found to infect land birds, and MIDWV seabirds, it is presently unknown whether SNVV naturally infects birds or mammals.

Figure 1.

Transmission electron microscopy of Vero cells infected with Sierra Nevada (BA-T) virus. (A) Virions forming at the cell surface. N = nuclei of adjacent cells. Bar = 1 μm. (B) High power of a portion of an infected Vero cell with budding (thick arrowheads) virions (v). Thin arrows indicate cell membranes of adjacent cells. Bar = 100 nm.

Figure 2.

Coverage plot in log scale showing the number of mapped reads across the genomic assembly. Low coverage regions were polymerase chain reaction (PCR) amplified and sequenced by Sanger.

Figure 3.

Schematic of the annotated Sierra Nevada virus (SNVV) genome, in comparison to Nyamanini virus (NYMV), and Midway virus (MIDWV). Coordinates of interpro domains are annotated on each genome. i = site of transcription initiation motif; t = site of transcription termination motif; CC = putative coiled-coil domains (see Figure 4C).

Figure 4.

(A) Phylogenetic tree of RdRP sequences of the order Mononegavirales. The order Mononegavirales comprises five families, within which the family Paramyxoviridae is split into two subfamilies: Pneumovirinae and Paramyxovirinae. The Sierra Nevada virus (SNVV) branches within a clade of Nyamiviridae and branches closely, but as sister to Nyamanini virus (NYWV) and Midway virus (MIDWV). In comparison, the soybean cyst nematode virus 1 (SbCNV) is a distant, deep branching member of the Nyamiviridae. The accession numbers and full names of all the viruses in the tree are listed in Supplemental Table 1. (B) Coiled-coil domain prediction for open-reading frame (ORF) III in SNVV, NYMV, and MIDWV. The coiled-coil domain prediction was done based on a 28-residue window using the program of COILS; there are two peaks shown along the curves, and both of them partially overlap with each other across the three viruses, suggesting a similar pattern of the coiled-coil domain distribution in their genomes. (C) Sequence alignment for the putative coiled-coil regions of ORF III in SNVV, NYMV, and MIDWV. Alignment of the sequences of N- and C- terminal coiled-coil domain across SNVV, NYMV, and MIDWV shows that 39% of the residues are conserved in the N-terminal domains, whereas 63% of the residues are conserved in the C-terminal domains.