Knowledge of porcine astrovirus diversity and epidemiology remains limited. We used a broad range PCR approach to investigate the presence and diversity of astroviruses in healthy pigs of different ages on 20 farms and in 3 slaughterhouses situated in the province of Quebec, Canada between 2005 and 2007. Our study unexpectedly revealed remarkable levels of genetic diversity and high prevalence of astroviruses in pigs of this province. Astroviruses were detected on every farm investigated and in all age groups of pigs, from suckling piglets to adults. In addition, we found that nearly 80% of healthy finisher pigs harbour astroviruses in their intestine at slaughter. Phylogenetic evidence based on partial polymerase and complete capsid sequences, suggests that porcine astroviruses do not form a monophyletic group but are rather found on separate branches across the mamastrovirus tree. In addition to type species strains, we found highly divergent strains that form two additional lineages, one of which falls outside existing taxonomic groups. The presence of diverse astroviruses in a majority of healthy pigs likely represents a continuous source of infection to piglets and possibly to other animal species including humans. Porcine astrovirus strains appeared phylogenetically related not only to prototypical human astroviruses, as was already known, but also to novel human strains recently discovered suggesting multiple cross species transmission events between these hosts and other animal species. Overall, the findings reported in this study suggest an active role of pigs in the evolution and ecology of the Astroviridae.

The family Caliciviridae includes viruses with single-stranded, positive-sense RNA genomes of 7.4–8.3 kb. The most clinically important representatives are human noroviruses, which are a leading cause of acute gastroenteritis in humans. Virions are non-enveloped with icosahedral symmetry. Members of seven genera infect mammals ( Lagovirus , Norovirus , Nebovirus , Recovirus , Sapovirus , Valovirus and Vesivirus ), members of two genera infect birds ( Bavovirus and Nacovirus ), and members of two genera infect fish ( Minovirus and Salovirus ). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caliciviridae , which is available at ictv.global/report/caliciviridae .

This study reports the molecular characterization of novel caliciviruses, the St-Valérien-like viruses, which were isolated from pig feces in the province of Quebec, Canada between 2005 and 2007. The genomes of St-Valérien-like viruses contain 6409 nucleotides and include two main open reading frames (ORFs). ORF1 encodes the non structural (NS) polyprotein and the major capsid protein (VP1) while ORF2 encodes the putative basic minor capsid protein. Typical conserved amino acid motifs predict a gene order reminiscent of calicivirus genomes. Phylogenetic, pairwise homology, and distance analyses performed on complete genomic sequences and partial amino acid sequences from the NTPase, polymerase, and major capsid protein segregated the St-Valérien-like viruses in a unique cluster sharing a common root with the Tulane virus and the noroviruses. Based on the genomic analyses presented, the St-Valérien-like viruses are members of a new genus of Caliciviridae for which we propose the name Valovirus.

Two different cytoplasmic male-sterility (CMS) systems, nap and pol, are found in the oilseed rape (canola) species Brassica napus. Physical mapping studies have previously shown that organizational differences between the sterile pol and fertile cam mitochondrial genomes are restricted to a relatively small region immediately upstream of the atp6 gene. An approximately 4.5-kb pol mtDNA segment containing a chimeric open reading frame (orf224) co-transcribed with atp6 is missing from cam mtDNA and located at a different site on nap mtDNA; expression of the orf224/atp6 gene region is highly correlated with the pol CMS trait. Sequence analysis now shows that the transposed nap segment contains an open reading frame (ORF) related to, but distinct from, pol orf224. This open reading frame (orf222) potentially encodes a protein of 222 amino acids possessing 79% sequence similarity to the predicted product of the pol orf224 gene. nap orf222 is co-transcribed with the third exon of the trans-spliced nad5 gene and another ORF. orf222 transcripts are several times more abundant in nap CMS than in fertility restored nap-cytoplasm plants and qualitative transcript differences for the region between CMS and restored plants are found as well. Expression of the orf222/nad5c/orf139 region is specifically correlated with nap CMS: of 21 mitochondrial gene regions examined, including all the sites of rearrangement between the nap and fertile cam mitochondrial genomes and 22 known genes, only the orf222/nad5c/orf139 region detected transcript differences between maintainer cam cytoplasm, nap CMS- and fertility restored nap cytoplasm-plants. Our results suggest that expression of the orf222/nad5c/orf139 region may be associated with nap CMS, and, more generally, that different forms of CMS may be associated with genes encoding structurally similar proteins.

Emerging viruses represent a continuous threat to human health and to farmed animals, as evidenced on multiple occasions by outbreaks of influenza, henipavirus and SARS. Knowledge about the diversity of viromes present in reservoir species can lead to a better understanding of the origin of emerging pathogens. In this study, we extend the knowledge of astrovirus diversity in pigs by reporting the genetic characterization of an unknown astrovirus lineage. Phylogenetic analyses provided evidence that this porcine astrovirus lineage is unique and does not appear to share a recent common ancestor with any known mamastrovirus. The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins.