Owing to the huge quantity of GP5 sequence data (8344 sequences) available for the PRRSV-NA plot, the formal P values for this analysis are extremely small for the conserved 5вЂІ region. Scores below the dashed line correspond to more conserved regions and are indicative of overlapping functional elements, either coding or non-coding. The top and middle panels illustrate the degree of conservation at synonymous sites within the GP5 CDS: the top panel depicts the probability that the degree of conservation within a given window could be obtained under a null model of neutral evolution at synonymous sites, while the middle panel depicts the absolute amount of conservation as represented by the ratio of the observed number of substitutions within a given window to the number expected under the null model.

For EAV and the two PRRSV genotypes, plots are shown for several coding-potential statistics in a 15-codon sliding window.

(b) Maps of the ORF5a/ORF5 region of the genomes of representative arterivirus sequences (see Fig. Small grey boxes indicate the positions of the TRS that direct sg RNA synthesis and serve as junction sequences for the 5вЂІ common leader sequence of arterivirus mRNAs. ORF5a slightly overlaps with the GP4 gene and largely overlaps with the GP5 gene. The positions of the ORFs encoding the seven known structural proteins and the newly discovered ORF5a are indicated. (a) EAV genome organization and expression. These defects, which could be partially complemented in ORF5a-expressing cells, indicate that the novel protein, which may be the eighth structural protein of arteriviruses, is expressed and important for arterivirus infection. Inactivation of ORF5a expression by reverse genetics yielded a severely crippled EAV mutant, which displayed lower titres and a tiny plaque phenotype. The 43-64 aa ORF5a protein and GP5 are probably expressed from the same subgenomic mRNA, via a translation initiation mechanism involving leaky ribosomal scanning. The pattern of substitutions across sequence alignments indicated that ORF5a is subject to functional constraints at the amino acid level, while an analysis of substitutions at synonymous sites in ORF5 revealed a greatly reduced frequency of substitution in the portion of ORF5 that is overlapped by ORF5a. However, an in-depth computational analysis now reveals the arterivirus-wide conservation of an additional AUG-initiated ORF, here termed ORF5a, that overlaps the 5' end of ORF5. ORF5, which encodes the major glycoprotein GP5, has been used extensively for phylogenetic analyses. The latter are expressed via synthesis of a set of subgenomic mRNAs that, in general, are functionally monocistronic (except for a bicistronic mRNA encoding the E and GP2 proteins). Their replicative enzymes are translated from their genomic RNA, while their seven structural proteins are encoded by a set of small, partially overlapping genes in the genomic 3'-proximal region. The arterivirus family (order Nidovirales) of single-stranded, positive-sense RNA viruses includes porcine respiratory and reproductive syndrome virus and equine arteritis virus (EAV).

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