Historical Outbreaks of Simian Hemorrhagic Fever in Captive Macaques Were Caused by Distinct Arteriviruses

Abstract

Simian hemorrhagic fever (SHF) is lethal for macaques. Based on clinical presentation and serological diagnosis, all reported SHF outbreaks were thought to be caused by different strains of the same virus, simian hemorrhagic fever virus (SHFV; Arteriviridae). Here we show that the SHF outbreaks in Sukhumi in 1964 and in Alamogordo in 1989 were caused not by SHFV but by two novel divergent arteriviruses. Our results indicate that multiple divergent simian arteriviruses can cause SHF.

FIG 1

Genomic and amino acid sequence comparisons of SHEV, PBJV, and other arteriviruses. Sliding-window similarity plots of percent amino acid identity of SHEV and PBJV compared to the coding genomes of other simian arteriviruses, i.e., SHFV, KRCV-1, KRCV-2, KRTGV-1, KRTGV-2, MYBV-1, SWBV-1, and “DeBrazza's monkey arterivirus” (“DeMAV”). Simian arteriviruses associated with SHF outbreaks are shown in red. Open reading frame 1a (ORF1a), ORF1b, ORF2a′, ORF3′, ORF4′, ORF2a, ORF2b, and ORF3 to ORF7 were individually aligned with other simian arteriviruses by a codon-based version of the multiple alignment with fast Fourier transform (MAFFT) algorithm (24) implemented in Translator X (25). Individual ORF alignments were then concatenated, and sliding-window plots of inferred amino acid sequence similarity were created with SimPlot v3.5.1 (window size, 200 amino acids; step size, 25 amino acids) (26). Dashed vertical lines represent the start positions of the ORFs. RefSeq/GenBank accession numbers of the sequences used for the analysis: SHEV, KM677927; PBJV, KR139839; SHFV, NC_003092; KRCV-1, HQ845737; KRCV-2, KC787631.1; KRTGV-1, JX473847; KRTGV-2, JX473849; MYBV-1, NC_025112.1; SWBV-1, NC_025113.1; “DeMAV,” NC_026509.

FIG 2

Arterivirus phylogeny based on ORF1b nucleotide sequences. Sequences were aligned by a codon-based version of the MAFFT algorithm with regions of poor alignment removed by the Gblocks method implemented in the computer program Translator X (25). The tree was constructed by Phylogenetic Analysis Using Parsimony (PAUP*) version 4.0b10 (27) from a final alignment of 3,840 positions by the maximum-likelihood method with a best-fit substitution model of the form GTR+I+Γ (general time-reversible model with invariable sites parameter and gamma distribution accounting for rate variation among sites) and parameters identified through jModeltest (28, 29). Numbers beside branches represent bootstrap values (based on 1,000 bootstrap replicates of the data), and branch lengths are proportional to the numbers of nucleotide substitutions per site (scale bar). Silhouettes indicate hosts (see the text), with nonhuman primates associated with SHF outbreaks shown in red, as the natural hosts of those three viruses remain unknown. The virus name abbreviations and GenBank accession numbers shown are identical to those in Fig. 1 plus equine arteritis virus (EAV; accession no. NC_002532), lactate dehydrogenase-elevating virus (LDV; accession no. NC_001639), porcine reproductive and respiratory syndrome viruses 1 (PRRSV-1; accession no. M96262.2), PRRSV-2 (accession no. NC_001961), wobbly possum disease virus (WPDV; accession no. JN116253), and “African pouched rat arterivirus” (“APRAV”; accession no. NC_026439.1).