Reorganization and expansion of the nidoviral family Arteriviridae

Abstract

The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American "types" of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.

Fig. 1

Structure of arterivirions. A) Electron micrograph of simian hemorrhagic fever virus particles inside of cellular vacuoles. B) Cartoon of a generalized simian arterivirus particle depicting all structural proteins. Arteriviruses from non-simian hosts, such as African pouched rat virus 1, equine arterivirus virus, lactate dehydrogenase-elevating viruses, porcine reproductive and respiratory syndrome viruses, or wobbly possum disease virus have a similar particle organization but lack proteins 2a′, 2b′, 3′, and 4′

Fig. 2

Organization of arterivirus genomes. Individual arterivirus open reading frames (ORFs) drawn to scale are shown in colors. ORF1a (green) encodes polyprotein 1a (pp1a). ORF1a and ORF1b (yellow) can be joined through a “-1” programmed ribosomal frameshift to express polyprotein 1ab. pp1a and pp1ab are translated directly from genomic RNA and are subsequently proteolytically cleaved into numerous nonstructural proteins, many of which are part of the replicase complex. Nonstructural protein 2 transframe (nsp2TF) is produced through a “-2” programmed ribosomal frameshift by most, but not all, arteriviruses. The remaining ORFs are translated from subgenomic RNAs. Purple ORFs (four shades) encode minor structural proteins (envelope protein E, glycoproteins 2b, 3 and 4); blue ORFs (three shades) encode the major structural proteins GP5 (glycoprotein 5), M (matrix protein), and N (nucleocapsid protein). Red ORFs (four shades), present only in simian arterivirus (simartevirus) genomes, encode minor structural proteins of unknown function (see also Fig. 1B). Virus genomes are labeled by retained or new virus abbreviations with previous designations in grey in parentheses. Simian arteriviruses (simarteviruses) are: KRTGV-1/2, Kibale red-tailed guenon viruses 1 and 2; DeBMV-1, DeBrazza’s monkey virus 1; PBJV, Pebjah virus; SHFV, simian hemorrhagic fever virus; KKCBV-1, Kafue kinda-chacma baboon virus 1; MYBV-1, Mikumi yellow baboon virus 1; SWBV-1, Southwest baboon virus 1; KRCV-1/2, Kibale red colobus viruses 1 and 2; SHEV, simian hemorrhagic encephalitis virus; DMVV-1; Drakensberg Mountain vervet virus 1. Murine and porcine arteriviruses (rodarteviruses) are: LaDV-1/2, lactate dehydrogenase-elevating viruses 1 and 2; PRRSV-1/2, and porcine reproductive and respiratory syndrome viruses 1 and 2. Nesomyid arteriviruses (nesarteviruses) contain: APRAV-1, African pouched rat virus 1. Equine arteriviruses (equarteviruses) contain: EAV, equine arteritis virus. Possum arterviruses (diparteviruses) include: WPDV, wobbly possum disease virus. For GenBank accession numbers used for the analyses, see Table 2 (color figure online)

Fig. 3

Pairwise sequence comparison of the arterivirus proteomes. Coding regions from each arterivirus genome (Fig. 2) were aligned in CLC Genomics Workbench version 6, and a pairwise comparison matrix was constructed. Only orthologous genes common to all known arteriviruses were used (i.e., simian arterivirus-/simartevirus-specific ORFs were ignored). Numbers represent the percent nucleotide identity between two viruses, with red highlighting virus pairs with relatively high degrees of similarity and white showing virus pairs with lower similarity. Virus abbreviations and sequences sources for the analyses are identical to those outlined in Fig. 2 and Table 2

Fig. 4

Phylogenetic relationships among classified and unclassified arteriviruses based on ORF1b amino acid sequences (see Fig. 2 for genomes and virus abbreviations). Silhouettes represent mammals in which each virus was found, with question marks indicating uncertain natural hosts (viruses discovered in captive macaques). Sequences were compiled from Table 2. ORF1b nucleotide sequences were aligned using a codon-guided version of the multiple alignment using fast fourier transform (MAFFT) method [29] implemented in the computer program TranslatorX [1]. Poorly aligned sites were removed using the Gblocks alignment cleaning method [17] and the resulting sequence was translated into amino acid sequences. Phylogenetic analyses were then conducted on aligned sequences (final alignment length of 1,055 positions) using the Neighbor-Joining method [45] with the Poisson distance correction method [60]. Robustness of phylogenetic groupings was assessed using 1,000 bootstrap replicates of the data [25]; only bootstrap values >50 % are shown. The scale bar represents amino acid substitutions per site. Analyses were conducted in MEGA7. The topology of the tree shown is identical to that of trees constructed using maximum likelihood analyses of nucleic acid sequences (not shown)

Fig. 5

PAirwise Sequence Comparison (PASC) analysis using a modified basic local alignment search tool (BLAST) algorithm [11]. The resulting histograms, visualizing the distribution of the number of arterivirus pairs at each identity percentage, confirm results shown in Figure 3. The x-axis shows percent identity (0–100 %) and the y-axis shows the number of compared arterivirus sequence pairs. A) original color coding assigned by the NCBI PASC tool, showing disarray. B) reassigned color coding after implementation of the arterivirus taxonomy proposed herein (color figure online)