Novel Parvovirus Related to Primate Bufaviruses in Dogs.

A novel protoparvovirus species, related genetically to human bufaviruses, was identified in dogs with respiratory signs. The canine bufavirus was distantly related to the well-known canine protoparvovirus, canine parvovirus type 2, sharing low amino acid identities in the nonstructural protein 1 (40.6%) and in the capsid protein 1 (33.4%). By screening collections of fecal, nasal, and oropharyngeal samples obtained from juvenile dogs (<1 year of age), canine bufavirus DNA appeared as a common component of canine virome. The virus was common in the stool samples of dogs with or without enteric disease and in the nasal and oropharyngeal swab samples of dogs with respiratory signs. However, the virus was not detected in nasal and oropharyngeal swab samples from animals without clinical signs.

Candidate new rotavirus species in sheltered dogs, Hungary.

We identified unusual rotavirus strains in fecal specimens from sheltered dogs in Hungary by viral metagenomics. The novel rotavirus species displayed limited genome sequence homology to representatives of the 8 rotavirus species, A-H, and qualifies as a candidate new rotavirus species that we tentatively named Rotavirus I.

Canine rotavirus C strain detected in Hungary shows marked genotype diversity.

Species C rotaviruses (RVC) have been identified in humans and animals, including pigs, cows and ferrets. In dogs, RVC strains have been reported anecdotally on the basis of visualization of rotavirus-like virions by electron microscopy combined with specific electrophoretic migration patterns of the genomic RNA segments. However, no further molecular characterization of these viruses was performed. Here, we report the detection of a canine RVC in the stool of a dog with enteritis. Analysis of the complete viral genome uncovered distinctive genetic features of the identified RVC strain. The genes encoding VP7, VP4 and VP6 were distantly related to those of other RVC strains and were putatively classified as G10, P8 and I8, respectively. The new strain was named RVC/Dog-wt/HUN/KE174/2012/G10P[8]. Phylogenetic analyses revealed that canine RVC was most closely related to bovine RVC strains with the exception of the NSP4 gene, which clustered together with porcine RVC strains. These findings provide further evidence for the genetic diversity of RVC strains.

Genomic Diversity of CRESS DNA Viruses in the Eukaryotic Virome of Swine Feces.

Replication-associated protein (Rep)-encoding single-stranded DNA (CRESS DNA) viruses are a diverse group of viruses, and their persistence in the environment has been studied for over a decade. However, the persistence of CRESS DNA viruses in herds of domestic animals has, in some cases, serious economic consequence. In this study, we describe the diversity of CRESS DNA viruses identified during the metagenomics analysis of fecal samples collected from a single swine herd with apparently healthy animals. A total of nine genome sequences were assembled and classified into two different groups (CRESSV1 and CRESSV2) of the Cirlivirales order (Cressdnaviricota phylum). The novel CRESS DNA viral sequences shared 85.8-96.8% and 38.1-94.3% amino acid sequence identities for the Rep and putative capsid protein sequences compared to their respective counterparts with extant GenBank record. Data presented here show evidence for simultaneous infection of swine herds with multiple novel CRESS DNA viruses, including po-circo-like viruses and fur seal feces-associated circular DNA viruses. Given that viral genomes with similar sequence and structure have been detected in swine fecal viromes from independent studies, investigation of the association between presence of CRESS DNA viruses and swine health conditions seems to be justified.

Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission.

Canine astrovirus RNA was detected in the stools of 17/63 (26.9%) samples, using either a broadly reactive consensus RT-PCR for astroviruses or random RT-PCR coupled with massive deep sequencing. The complete or nearly complete genome sequence of five canine astroviruses was reconstructed that allowed mapping the genome organization and to investigate the genetic diversity of these viruses. The genome was about 6.6kb in length and contained three open reading frames (ORFs) flanked by a 5' UTR, and a 3' UTR plus a poly-A tail. ORF1a and ORF1b overlapped by 43 nucleotides while the ORF2 overlapped by 8 nucleotides with the 3' end of ORF1b. Upon genome comparison, four strains (HUN/2012/2, HUN/2012/6, HUN/2012/115, and HUN/2012/135) were more related genetically to each other and to UK canine astroviruses (88-96% nt identity), whilst strain HUN/2012/126 was more divergent (75-76% nt identity). In the ORF1b and ORF2, strains HUN/2012/2, HUN/2012/6, and HUN/2012/135 were related genetically to other canine astroviruses identified formerly in Europe and China, whereas strain HUN/2012/126 was related genetically to a divergent canine astrovirus strain, ITA/2010/Zoid. For one canine astrovirus, HUN/2012/8, only a 3.2kb portion of the genome, at the 3' end, could be determined. Interestingly, this strain possessed unique genetic signatures (including a longer ORF1b/ORF2 overlap and a longer 3'UTR) and it was divergent in both ORF1b and ORF2 from all other canine astroviruses, with the highest nucleotide sequence identity (68% and 63%, respectively) to a mink astrovirus, thus suggesting a possible event of interspecies transmission. The genetic heterogeneity of canine astroviruses may pose a challenge for the diagnostics and for future prophylaxis strategies.

The fecal virome of domesticated animals.

Next-generation sequencing is a new research tool in our hands helping us to explore still unknown fields of human and veterinary virology. Metagenomic analysis has enabled the discovery of putative novel pathogens and the identification of the etiologic agents of several diseases, solving long-standing mysteries caused by divergent viruses. This approach has been used in several studies investigating fecal samples of livestock, and companion animal species, providing information on the diversity of animal fecal virome, helping the elucidation of the etiology of diarrheal disease in animals and identifying potential zoonotic and emerging viruses.

Large-scale whole genome sequencing identifies country-wide spread of an emerging G9P[8] rotavirus strain in Hungary, 2012.

With the availability of rotavirus vaccines routine strain surveillance has been launched or continued in many countries worldwide. In this study relevant information is provided from Hungary in order to extend knowledge about circulating rotavirus strains. Direct sequencing of the RT-PCR products obtained by VP7 and VP4 genes specific primer sets was utilized as routine laboratory method. In addition we explored the advantage of random primed RT-PCR and semiconductor sequencing of the whole genome of selected strains. During the study year, 2012, we identified an increase in the prevalence of G9P[8] strains across the country. This genotype combination predominated in seven out of nine study sites (detection rates, 45-83%). In addition to G9P[8]s, epidemiologically major strains included genotypes G1P[8] (34.2%), G2P[4] (13.5%), and G4P[8] (7.4%), whereas unusual and rare strains were G3P[8] (1%), G2P[8] (0.5%), G1P[4] (0.2%), G3P[4] (0.2%), and G3P[9] (0.2%). Whole genome analysis of 125 Hungarian human rotaviruses identified nine major genotype constellations and uncovered both intra- and intergenogroup reassortment events in circulating strains. Intergenogroup reassortment resulted in several unusual genotype constellations, including mono-reassortant G1P[8] and G9P[8] strains whose genotype 1 (Wa-like) backbone gene constellations contained DS1-like NSP2 and VP3 genes, respectively, as well as, a putative bovine-feline G3P[9] reassortant strain. The conserved genomic constellations of epidemiologically major genotypes suggested the clonal spread of the re-emerging G9P[8] genotype and several co-circulating strains (e.g., G1P[8] and G2P[4]) in many study sites during 2012. Of interest, medically important G2P[4] strains carried bovine-like VP1 and VP6 genes in their genotype constellation. No evidence for vaccine associated selection, or, interaction between wild-type and vaccine strains was obtained. In conclusion, this study reports the reemergence of G9P[8] strains across the country and indicates the robustness of whole genome sequencing in routine rotavirus strain surveillance.