A novel gyrovirus in a common pheasant (Phasianus colchicus) with poult enteritis and mortality syndrome.

A novel gyrovirus was detected in an intestinal specimen of a common pheasant that died due to poult enteritis and mortality syndrome. The genome of the pheasant-associated gyrovirus (PAGyV) is 2353 nucleotides (nt) long and contains putative genes for the VP1, VP2, and VP3 proteins in an arrangement that is typical for gyroviruses. Gyrovirus-specific motifs were identified in both the coding region and the intergenic region of the PAGyV genome. The VP1 of PAGyV shares up to 67.6% pairwise nt sequence identity with reference sequences and forms a distinct branch in the phylogenetic tree. Thus, according to the recently described species demarcation criteria, PAGyV belongs to a novel species in the genus Gyrovirus, family Anelloviridae, for which we propose the name "Gyrovirus phaco 1".

Genetic characterisation of a novel reptarenavirus detected in a dead pet red-tailed boa (Boa constrictor).

Boid inclusion body disease (BIBD) is a severe and transmissible disease of snakes worldwide. Reptarenaviruses have been identified as the aetiological agents of BIBD. We determined the almost complete genome sequence of an arenavirus detected in a female red-tailed boa that had succumbed in a private collection in Hungary. We used a combination of next generation sequencing and Sanger sequencing methods. Based on the analysis of the obtained sequence data, the virus, tentatively named Coldvalley virus, seemed to belong to the Reptarenavirus genus of the Arenaviridae family. This classification was confirmed by the genome structure (bisegmented single-stranded RNA) characteristic of the genera Mammarenavirus and Reptarenavirus. The pairwise comparison of the nucleotide and amino acid sequences, as well as the topology of the maximum likelihood phylogenetic trees, suggested that the newly-characterised Coldvalley virus can be classified into the species Rotterdam reptarenavirus.

Isolation and complete genome characterization of novel reassortant orthoreovirus from common vole (Microtus arvalis).

A novel mammalian orthoreovirus (MRV) strain was isolated from the lung tissue of a common vole (Microtus arvalis) with Tula hantavirus infection. Seven segments (L1-L3, M2-M3, S2, and S4) of the Hungarian MRV isolate MORV/47Ma/06 revealed a high similarity with an MRV strain detected in bank vole (Myodes glareolus) in Germany. The M1 and S3 segment of the Hungarian isolate showed the closest relationship with the sequence of a Slovenian human and a French murine isolate, respectively. The highest nucleotide and amino acid identity values were above 90 and 95% in all of the comparisons to the reference sequences in GenBank, except for the S1 with a maximum of 69.6% nucleotide and 75.4% amino acid identity. As wild rodents are among the main sources of zoonotic infections, the reservoir role of these animals and zoonotic potential of rodent origin MRVs need to be further investigated.

Taxonomy of the order Mononegavirales: update 2016.

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

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.

Sequencing and phylogenetic analysis identifies candidate members of a new picornavirus genus in terrestrial tortoise species.

Near-complete genome sequences of seven picornavirus (PV) strains isolated from different terrestrial tortoise species were determined and characterized. The genome organization of the strains proved to be similar and displayed a typical PV layout, and the polyprotein-encoding regions showed low similarity to those of other PVs. The predicted regions of the tortoise PV genomes were related to the corresponding genome parts of viruses belonging to distinct genera, implying modular evolution of these novel viruses. Our results suggest that these tortoise PVs belong to a prototype species in a separate proposed genus in the family Picornaviridae, tentatively called Topivirus (Tortoise picornavirus).

Coding-complete sequencing classifies parrot bornavirus 5 into a novel virus species.

In this study, we determined the sequence of the coding region of an avian bornavirus detected in a blue-and-yellow macaw (Ara ararauna) with pathological/histopathological changes characteristic of proventricular dilatation disease. The genomic organization of the macaw bornavirus is similar to that of other bornaviruses, and its nucleotide sequence is nearly identical to the available partial parrot bornavirus 5 (PaBV-5) sequences. Phylogenetic analysis showed that these strains formed a monophyletic group distinct from other mammalian and avian bornaviruses and in calculations performed with matrix protein coding sequences, the PaBV-5 and PaBV-6 genotypes formed a common cluster, suggesting that according to the recently accepted classification system for bornaviruses, these two genotypes may belong to a new species, provisionally named Psittaciform 2 bornavirus.

Complete genome analysis identifies Tvärminne avian virus as a candidate new species within the genus Orthoreovirus.

Orthoreoviruses have been associated with a variety of diseases in domesticated poultry and wild-living birds. In 2002, a reovirus strain named Tvärminne avian virus (TVAV), was identified in Finland in a crow showing neurological disorders. The objective of this study was the molecular characterization of this novel reovirus strain. Genome sequencing was performed by combining semiconductor sequencing and traditional capillary sequencing. Sequence and phylogenetic analyses showed that TVAV shares low nucleotide sequence identity with other reoviruses (range for each gene, 31-72 %) including strains belonging to the species Avian orthoreovirus. The most closely related reovirus strain was an isolate identified in Steller sea lion. Our data indicate that TVAV is a divergent reovirus of avian origin that may be the first representative of a distinct virus species within the genus Orthoreovirus.

The complete genome sequence of a European goose reovirus strain.

The complete genomic sequence of a Hungarian goose orthoreovirus strain (D20/99) is reported in this study. The genome of D20/99 is 22,969 bp in length (range, 3958 bp for L1 to 1124 bp for S4) and encodes 11 putative proteins. Pairwise sequence comparisons and phylogenetic analyses indicated that D20/99 shares genetic signatures with some contemporary Chinese duck and goose reovirus strains, except for the µA, µNS and σA protein coding genes, which represented independent genetic lineages. This study implies a greater genetic diversity among waterfowl-origin orthoreoviruses than hitherto recognized.

Molecular detection and characterization of human gyroviruses identified in the ferret fecal virome.

The recently described novel gyroviruses may infect chickens and/or humans; however, their pathogenic potential is unknown. In our metagenomic investigation, we detected many of the novel gyroviruses in the fecal viromes of ferrets with lymph node and organ enlargement. The complete genomic sequences of selected gyrovirus strains showed 90.7-99.4 % similarity to homologous reference gyrovirus strains. This study did not demonstrate an association between gyrovirus shedding from ferrets and the observed background disease; however, it provides evidence for genetic diversity among gyroviruses and raises the possibility that pet ferrets may transmit gyroviruses to heterologous hosts, e.g., humans.

Whole-genome sequencing of a green bush viper reovirus reveals a shared evolutionary history between reptilian and unusual mammalian orthoreoviruses.

In this study, we sequenced the whole genome of a reovirus isolated from a green bush viper (Atheris squamigera). The bush viper reovirus shared several features with other orthoreoviruses, including its genome organization. In phylogenetic analysis, this strain was monophyletic with Broome virus and baboon orthoreovirus, indicating that these viruses might have originated from a common ancestor. These new molecular data supplement previous information based mainly on biological properties of reptilian reoviruses, confirming their taxonomic position and broadening our knowledge of the evolution of members of the genus Orthoreovirus.

Classification and characterization of a laboratory chicken rotavirus strain carrying G7P[35] neutralization antigens on the genotype 4 backbone gene configuration.

The laboratory rotavirus strain, BRS/115, has been used for more than two decades to monitor rotaviruses in specific pathogen free flocks of laying hens. However, the virus strain has not been characterized in detail. Therefore we aimed at the description of molecular features of BRS115 by using random primed reverse transcription-PCR of the genomic RNA followed by massive parallel sequencing using the semiconductor sequencing technology. Over 64,000 trimmed reads mapped to reference sequences obtained from GenBank. The strain classified into the species Rotavirus A and genotyped G7-P[35]-I4-R4-C4-M4-A16-N4-T4-E11-H4 according to guidelines of the Rotavirus Classification Working Group. Phylogenetic analysis identified shared features with chicken, turkey and pigeon origin rotaviruses. This study demonstrates the robustness of next generation sequencing in the characterization of reference virus materials used in specialized laboratories.

Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants.

A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.

Detection and characterization of a divergent avian reovirus strain from a broiler chicken with central nervous system disease.

Avian orthoreoviruses have been associated with a variety of diseases in chickens, including tenosynovitis, runting-stunting syndrome, hepatitis, myocarditis, osteoporosis, respiratory diseases, and central nervous system disease. The primary objective of our study was the molecular characterization of an avian reovirus strain, T1781, which was isolated from a broiler chicken with a central nervous system disorder in Hungary during 2012. The complete genome sequence was determined using a traditional sequencing method after cell culture adaptation of the strain. Sequence and phylogenetic analyses showed that T1781 shared only moderate nucleic acid sequence identity in several genes to previously analyzed reovirus strains from chickens, and each gene formed separate branches in the corresponding phylogenetic trees. The maximum nucleotide sequence identities of strain T1781 genes to reference avian reovirus strains ranged from 79 % to 90 %. Collectively, our analyses indicated that T1781 is a divergent chicken reovirus strain. The genetic background of this and other avian reoviruses associated with various disease manifestations needs further investigation.

Integrated circoviral rep-like sequences in the genome of cyprinid fish.

Recently a new group of circoviruses have been detected in tissues of Barbel fish and European catfish in Hungary. In our study circovirus genomes were screened in eight additional fish species for the detection and characterization of circoviruses. Two species of these bore circoviral sequences based on conventional PCR assay targeting the replication-associated protein coding gene fragments. Interestingly, the methods successfully used before failed to amplify other parts of the circular viral genome, suggesting the presence of partial, integrated genetic elements in the genome of the host. The successfully sequenced fragments of the Indian rohu (Labeo rohita) encoded mutations which may cause frameshifts or termination in the coding region described previously in other vertebrates. Phylogenetic analyses presumed that integration of the viral genetic elements might have progressed concurrently or following the diversification of cyprinid fish. Further studies on the nature of whole circovirus genomes and integrated elements may help to understand their potential role and evolution in different fish species.

First detection and analysis of a fish circovirus.

Circoviruses are present worldwide in birds and pigs but their occurrence in fish has not yet been reported. Recently, increased mortality was observed in barbel fry (Barbus barbus) in Hungary. This paper reports the detection of previously unknown circular viral DNA genomes in barbels by the use of a circovirus-specific wide-range nested PCR. The analysis of two complete genomes (Barbel circovirus, BaCV1 and BaCV2) indicated that they belonged into a new genetic group within the family Circoviridae, distinct from known circoviruses and circovirus-like genomes. Their genome size was 1957 bases and contained two major ORFs similar to the capsid and replication-associated protein genes of circoviruses. A connection between the presence of the virus and clinical manifestations of the infection could not be proved.

Genomic characterization of avian and neoavian orthoreoviruses detected in pheasants.

Avian reoviruses are well-known pathogens seriously affecting the productivity of poultry industry. Game birds represent a small segment of the agricultural sector and much remained to be learnt about factors affecting productivity. Here we show that reovirus infections might occur in pheasants and demonstrate that reoviruses of pheasants are of diverse origin. The complete or coding-complete genomic sequences of two Hungarian reovirus strains, D1996/2/1 and Reo/HUN/Pheasant/216/2015, have been determined in this study. The strain D1996/2/1 was isolated in 2012 from birds with gizzard erosion, whereas the other strain was isolated in 2015 from diarrheic pheasant poults. Phylogenetic analyses showed that none of the Hungarian isolates shared common origin with a pheasant reovirus detected recently in the United States. Additionally, we found that Reo/HUN/Pheasant/216/2015 is a multi-reassortant reovirus within the species Avian orthoreovirus that shared genetic relationship with turkey reoviruses (σC), partridge reoviruses (λA, σB), and chicken reoviruses (λB, λC, µA, σA, and σNS), in the respective gene phylogenies, whereas two genes (µB and µNS) did not reveal any possible common ancestors. The other isolate, D1996/2/1, was found to be distantly related to previously described reoviruses raising the possibility that it might represent a novel orthoreovirus species or a new genogroup within the newly accepted species, Neoavian orthoreovirus. The genetic diversity among pheasant reoviruses could raise challenges for virus classification as well as for development of molecular diagnostic tools and vaccine based prevention and control measures.

Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus.

Genome sequencing and analysis of snake adenovirus type 1 (SnAdV-1), originating from corn snake, were completed. This is the first full genomic sequence of an adenovirus from reptilian hosts. The presence of characteristic genus-common genes and transcription units, showed that SnAdV-1 shares similar genome organisation with members of the recently established genus Atadenovirus. Three novel open reading frames of yet unknown functions were found. One of these seemed to be related to a putative gene, the so-called 105R that has recently been described from the genome of the tree shrew adenovirus. The other two putative genes were found to be unique for SnAdV-1. On phylogenetic trees, SnAdV-1 clustered within the atadenovirus clade. Thereby the hypothesis on the reptilian origin of atadenoviruses was further strengthened. Interestingly, however, one of the most striking features of atadenoviruses, namely the base content heavily biased towards A+T, is not characteristic for SnAdV-1 having a genome of balanced composition with a G+C value of 50.21%.

Genomic sequence and phylogenetic analyses of two novel orthoreovirus strains isolated from Pekin ducks in 2014 in Germany.

Complete genomic sequences of two orthoreovirus strains, D2533/4/1-10 and D2533/6/1-10, isolated from Pekin ducklings in Germany have been determined. Pairwise sequence comparisons and phylogenetic analyses indicated that strain D2533/4/1-10 might have acquired its genomic segments from three different origins, from classical and novel waterfowl reoviruses, and a yet unknown orthoreovirus strain. D2533/6/1-10 proved to be only distantly related to previously described orthoreoviruses. Reassortment, host species transmission events, and successful adaptation of novel variants may signify a challenge for animal health and maintenance of economic production.

Novel adenovirus detected in kowari (Dasyuroides byrnei) with pneumonia.

A male kowari (Dasyuroides byrnei) originating from a zoo facility was delivered for post mortem evaluation in Hungary. Acute lobar pneumonia with histopathologic changes resembling an adenovirus (AdV) infection was detected by light microscopic examination. The presence of an AdV was confirmed by obtaining partial sequence data from the adenoviral DNA-dependent DNA-polymerase. Although the exact taxonomic position of this novel marsupial origin virus could not be determined, pairwise identity analyses and phylogenetic calculations revealed that it is distantly related to other members in the family Adenoviridae.