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In this study, we undertook the genomic characterization of 54 pseudorabies virus (PRV) strains isolated in Italy during 1984-2010. The characterization was based on partial sequencing of the UL44 (gC) and US8 (gE) genes; 44 strains (38 for gene gE and 36 for gC) were isolated on pig farms; 9 originated from dogs and 1 from cattle. These porcine PRV strains, which were closely related to those isolated in Europe and America in the last 20 years, and the bovine strain bovine/It/2441/1992 belong to cluster B in both phylogenetic trees. Six porcine strains that do not belong to cluster B are related in both gE and gC phylogenetic trees to the 'old' porcine PRV strains isolated in the 1970s and 1980s. In the last two decades, the presence of these strains in domestic pig populations has been reduced drastically, whereas they are prevalent in wild boar. The two remaining strains have an interesting genomic profile, characterized by the gC gene being closely related to the old porcine PRV strains, and the gE gene being similar to that of recently isolated strains. Three strains originating from working dogs on pig farms are located in cluster B in both phylogenetic trees. Five strains isolated from hunting dogs have a high degree of correlation with PRV strains circulating in wild boar. The last isolate has a gC gene similar to that in the two porcine strains mentioned previously, and the gE gene is correlated with the strains isolated from hunting dogs. These results provide interesting insight into the genomic characterization of PRV strains and reveal a clear differentiation between the strains isolated from hunting dogs that are related to the wild boar strains and those originating from domestic pigs.

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Astroviruses (AstVs) are nonenveloped RNA small round viruses (SRVs) with a genome of 6.8-7.9 kb. Known avian AstVs are spread worldwide; they have been associated with poult enteritis and mortality syndrome in the United States and reported in Italy in intensive turkey and guinea fowl flocks. Nevertheless, their real prevalence and their pathogenic role in avian enteritis affecting Italian flocks is far from clear. Negative staining electron microscopy (nsEM) is used for the routine diagnosis of avian enteric SRVs, although it cannot distinguish morphologically similar particles. Enzyme-linked immunosorbent assay (ELISA), reverse-transcription PCR (RT-PCR), and genomic sequencing are now used for this specific purpose. We analyzed 329 samples of chicken, turkey, and guinea fowl intestinal contents from Italian poultry flocks. Most samples were from enteritis outbreaks, but we also included samples from three longitudinal studies (one on 11 broiler flocks and the other two on a guinea fowl flock). We first examined the samples with nsEM. SRVs, including AstVs, are often associated with rotaviruses and were the most commonly detected morphotypes in avian enteric diseases. We then analyzed 124 of the samples with an RT-PCR targeting the open reading frame (ORF)-1b of AstV. This gene codes for an RNA-dependent polymerase. We then sequenced and genetically analyzed the RT-PCR positive samples. Phylogenetic analysis distinguished three defined clusters: the first included guinea fowl AstVs and turkey AstVs-2; the second, chicken AstVs; and the third was formed by avian nephritis viruses (ANVs). No strains clustered with turkey AstVs-1. The results indicate that ORF-1b presents certain genetic variability, even among AstVs from the same species. In longitudinal studies, samples retrieved from the same shed were homogeneous, with some exceptions suggesting possible coexistence of different genetic types in the same unit. The finding of ANV-like viruses in commercial guinea fowls underlines the genetic variability of AstVs and strengthens the hypothesis of a varied intraherd situation.