Clinicopathological characterization and genomic sequence differences observed in a highly virulent fowl Aviadenovirus serotype 4

Highly virulent fowl aviadenoviruses (genus: Aviadenovirus) represent a significant risk in poultry farming that may contribute to increased mortality rates and may adversely affect the growth performance of poultry flocks. In this study, we performed the clinicopathological characterization of a FAdV strain SHP95 isolated from a commercial farm and its whole genome sequencing. The study revealed that the isolated strain is a highly virulent serotype 4 FAdV that can cause 100% mortality in day-old specific pathogen free (SPF) chickens with a dose of 2.5?×?10⁵ TCID₅₀. At a lower viral dose (1.5?×?10⁴ TCID₅₀), the infection in day-old SPF chickens caused 40% mortality and lesions characteristic for Hepatitis-hydropericardium syndrome (HHS). The viral strain was detectable by real time PCR in chicken organs, including the lymphoid organs until day 28 after infection. The whole genome assembly of strain SHP95 revealed a size of 45,641?bp, which encodes for 42 viral open reading frame (ORF). The comparative analysis in the genome shows 98.1% similarity between strain SHP95 and other FAdV-4 genomes reported. The major differences in the genome sequence between pathogenic and non-pathogenic fowl Adenovirus were identified in the right arm of the genome.     

Genomic characterization of a novel bat-associated Circovirus detected in European Miniopterus schreibersii bats

Circoviruses are small circular DNA viruses causing severe pig and poultry disease, recently identified in various bat species worldwide. We report the detection and full-genome molecular characterization of a novel bat-associated Circovirus identified in faecal samples of Miniopterus schreibersii bats (Schreiber’s bent-winged bats) from Sardinia, Italy. Full-genomic sequencing revealed a new putative member of Circoviridae family, with a genome size of 2063 nt. Sequencing allowed the characterization of the two major ORFs, inversely arranged, encoding replicase and capsid proteins, as well as the finding of a polythymidine tract within the genome, and highlighted phylogenetic relationships of the novel virus. This is the first report of circovirus in European bats. Giving the high level of genetic diversity of bat circoviruses, it is paramount to further investigate the relationships between these viruses and bats.

     

Characterization of a new bunyavirus and its derived small RNAs in the brown citrus aphid,Aphis citricidus

High-throughput sequencing is widely used for virus discovery, and many RNA viruses have been discovered and identified. A new negative-sense single-stranded RNA virus was identified in the brown citrus aphid and named Aphis citricidus bunyavirus. The genome consists of large (7037 nt), medium (3462 nt), and small (1163 nt) segments. Phylogenetic analysis and amino acid sequences identities of this virus with other bunyaviruses suggest that it is a new species belonging to the family Phenuiviridae. The small interfering RNA pathway could be involved against the infection of this virus in brown citrus aphid as supported by the viral derived small RNAs. The discovery of this virus illustrates the diversity of RNA viruses and contributes to the classification of bunyaviruses.

     

Fatal necrotic tracheitis by Aviadenovirus in captive Alagoas curassows (Pauxi mitu) extinct from the wild

Extinct from nature, captive young Alagoas curassows (Pauxi mitu) were found agonizing or dead with respiratory disease. Intranuclear inclusion bodies were found in the epithelia of the trachea, associated with marked necrotic tracheitis. An Aviadenovirus was isolated in chicken eggs and characterized genetically with 99% identity to the fowl Aviadenovirus A, as based on the hexon protein gene. This is the first report of respiratory disease caused by Aviadenovirus in any cracid species in Brazil, recommending for stricter biosecurity in the conservation premises.

RESEARCH HIGHLIGHTS

• Fatal tracheitis in curassows extinct from nature was associated with Aviadenovirus A.

• Seven-month-old Alagoas curassows (Aves: Cracidae) died with haemorrhagic tracheitis.

• Aviadenovirus A with 99% identity to fowl adenovirus 1 was detected in dead curassows.

• Fatal tracheitis by Aviadenovirus was described in Pauxi mitu (Aves: Cracidae).

     

Molecular characterization of Blastocystis species in Oregon identifies multiple subtypes

The association of Blastocystis species infections with gastrointestinal symptoms in humans is clouded by the variable presentation of disease and multiple lineages of the parasite that can infect humans and other animals. It has long been suspected that certain subtypes of Blastocystis may be more or less pathogenic, be restricted to certain hosts, or have limits to their geographic distribution. In the state of Oregon, USA, Blastocystis spp. are the most commonly encountered parasites in fecal specimens submitted for diagnostic evaluation, yet the diversity of subtypes is unknown. In this study, fecal samples were collected from individuals experiencing symptoms associated with blastocystosis and analyzed by polymerase chain reaction for presence of the parasite and DNA sequenced for subtyping. Five of 19 individuals tested positive for the parasite, all of which were also positive by previous ova and parasitology examination. DNA sequencing of the small subunit ribosomal DNA and elongation factor 1 alpha gene followed by phylogenetic subtyping identified five unique subtypes, representing Blastocystis subtypes 1, 2, 3, 4, and 8. No symptoms were consistently associated with presence or absence of infection, although abdominal pain and fatigue were reported by all infected individuals. Multiple subtypes are indicative of multiple sources of infection, suggesting more extensive surveys are required to understand the transmission of this parasite.     

Molecular characterization and complete genome of alstroemeria mosaic virus (AlMV)

Even though alstroemeria mosaic virus (AlMV) is one of the most important viruses affecting alstroemeria plants, its genome is only partially available in public sequence databases. High throughput sequencing (HTS) of RNA from alstroemeria plants with symptoms of mosaic and streaking, collected in Lasso-Ecuador, indicated the presence of AlMV and lily symptomless virus. In this study, we aimed to assemble and characterize the complete genome sequence of AlMV. Reads from Illumina sequencing of ribosomal RNA-depleted total RNA were assembled into contigs that were mapped to the sunflower chlorotic mottle virus genome, revealing the 9974 bp complete genome sequence of AlMV. Multiple sequence alignment of the AlMV polyprotein with close homologs allowed the identification of ten mature proteins P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP. Furthermore, several potyvirus motifs were identified in the AlMV polyprotein including those related to potyvirus aphid transmission ³³⁴KMTC³³⁷, ⁵⁹²PTK⁵⁹⁴ and ²⁸⁰⁰DAG²⁸⁰². Phylogenetic analysis based in the polyprotein showed that AlMV belongs to the potato virus Y clade and its closest relative is sunflower ring blotch virus. This study describes the first complete genome of AlMV and its placement within the genus Potyvirus, providing valuable information for future studies on this economically important virus.

     

Genomic sequences of blackberry chlorotic ringspot virus and strawberry necrotic shock virus and the phylogeny of viruses in subgroup 1 of the genus Ilarvirus

Three members of subgroup 1 of the genus Ilarvirus: blackberry chlorotic ringspot (BCRV), strawberry necrotic shock (SNSV), and tobacco streak viruses (TSV), may infect Rubus and Fragaria species. All cause symptoms similar to those previously attributed to infection by TSV alone. Although similarities exist among the genomic sequences of the three, phylogenetic analysis shows them to be distinct viruses. These viruses and Parietaria mottle virus, the other currently accepted member of subgroup 1, appear to have evolved from a common ancestral virus, share conserved motifs in the products of the genomic RNAs, and constitute a distinct subgroup within the genus.     

Trichomonasvirus: a new genus of protozoan viruses in the family Totiviridae

The family Totiviridae includes a number of viruses with monosegmented dsRNA genomes and isometric virions that infect either fungi or a number of medically important protozoan parasites such as Leishmania and Giardia. A new genus, Trichomonasvirus, was recently approved for this family. Its name is based on the genus of its host organism, Trichomonas vaginalis, a protozoan parasite that colonizes the human genitourinary mucosa and is the most common non-viral sexually transmitted infection in the world. The type species of this new genus is Trichomonas vaginalis virus 1. Distinguishing characteristics of the new genus include infection of a human sexually transmitted parasite, stable mixed infection with more than one distinct Trichomonasvirus species, and sequence-based phylogenetic divergence that distinguishes it from all other family members.     

The virome of the white-winged vampire bat Diaemus youngi is rich in circular DNA viruses

In the Neotropical region, the white-winged vampire bat (Diaemus youngi) is the rarest of the three species of vampire bats. This bat species feeds preferentially on bird blood, and there is limited information on the viruses infecting D. youngi. Hence, this study aimed to expand the knowledge about the viral diversity associated with D. youngi by sampling and pooling the lungs, liver, kidneys, heart, and intestines of all animals using high-throughput sequencing (HTS) on the Illumina MiSeq platform. A total of three complete and 10 nearly complete circular virus genomes were closely related to gemykrogvirus (Genomoviridae family), smacovirus (Smacoviridae family), and torque teno viruses (TTVs) (Anelloviridae family). In addition, three sequences of bat paramyxovirus were detected and found to be closely related to viruses reported in Pomona roundleaf bats and rodents. The present study provides a snapshot of the viral diversity associated with white-winged vampire bats and provides a baseline for comparison to viruses detected in future outbreaks.

     

Detection and phylogenetic characterization of Columbid circoviruses in Chaharmahal va Bakhtiari province,Iran

The virus genus Circovirus belongs to the family Circoviridae and contains virus species with circular single-stranded DNA genomes. The viruses are known to infect vertebrate species, including pigs, dogs, pigeons and ducks. In this study a nested polymerase chain reaction (PCR) was applied to investigate prevalence of circoviruses in pigeons in the Chaharmahal va Bakhtiari province, Iran. A total of 50 faecal samples were subjected to nucleic acid extraction, PCR amplification and DNA sequencing. Nested PCR primers were designed to amplify a 508 base pair segment of the pigeon circovirus (PiCV) capsid gene. Of the 50 faecal samples examined, 12 (24%) produced the expected DNA amplicons with identical DNA sequences. Phylogenetic analysis has grouped the viruses with those classified as group A circoviruses. The viruses were closely related to PiCVs found in Poland, Northern Ireland, the USA, Nigeria and Hungary. To the authors' knowledge, this is the first report of molecular detection and genomic characterization of PiCV from Iran.     

The grapevine-infecting vitiviruses, with particular reference to grapevine virus A

A number of vitiviruses infect grapevine, arguably the most important fruit crop, and the host from which they derive their genus name. In contrast to most grapevine viruses, the etiological role of these viruses is unclear, albeit that they are associated with several well-known – and a number of emerging – diseases of grapevine. Here, we review the genus Vitivirus, with special reference to its most omnipresent member, grapevine virus A. We discuss the latest taxonomic status of the genus, as well as the genome and genomic organisation, replication mechanism, and genetic variability of GVA, and we also present the latest research progress with vitivirus-based vectors; the identification of a new vitivirus, GVE, the discovery of VIGG, a unique GVA-induced host protein, the molecular characterisation of hitherto unknown or puzzling genetic elements in the GVA genome, and the latest developments in vitivirus diagnostics.     

Molecular characterization of Hop latent virus and phylogenetic relationships among viruses closely related to carlaviruses

Summary.  The complete nucleotide sequence of the hop latent virus (HpLV) genome was determined. The viral RNA genome is 8,612 nucleotides long, excluding the poly(A) tail, and contains six open reading frames (ORFs), which encode putative proteins of 224-kDa (ORF 1), 25-kDa (ORF 2), 11-kDa (ORF 3), 7-kDa (ORF 4), 34-kDa (ORF 5), and 12-kDa (ORF 6). ORF 5 encodes the coat protein as demonstrated by N-terminal sequencing of three proteolytic peptides derived from the virus particle. The genome organization of HpLV is similar to that of other species in the genus Carlavirus, and the overall sequence of HpLV is more similar to that of Potato virus M than to sequences of other carlaviruses reported to date. The amino acid sequences of the putative methyltransferase, RNA helicase, and RNA-dependent RNA polymerase encoded in ORF 1 and an ‘accessory’ helicase encoded in ORF 2 of the HpLV genome were compared with those of viruses in the ‘tymo’ lineage: the genera Carlavirus, Potexvirus, Allexivirus, Foveavirus, Trichovirus, Capillovirus, Vitivirus, and Tymovirus. The phylogenetic relationships among the viruses in these genera are discussed. This is the first molecular characterization of a carlavirus infecting hop plants. Accepted June 15, 2000 Received January 19, 2000     

Saliviruses—the first knowledge about a newly discovered human picornavirus

The salivirus, first discovered in the year 2009, is a member of the large and growing family Picornaviridae. At present, the genus Salivirus contains 1 species Salivirus A and 2 genotypes, Salivirus A1 and Salivirus A2. Salivirus has been identified in humans and chimpanzees and may cause acute gastroenteritis in humans, having been detected in 0% to 8.7% of fecal samples collected from gastroenteritis in different human populations. Salivirus is ubiquitous in wastewater of human origin and river water specimens worldwide and represents a potential indicator human RNA virus for monitoring of environmental samples. This review summarizes the current knowledge on saliviruses including discovery, taxonomy, genome structure, and genetic diversity; covers all aspects of infection including epidemiology, molecular epidemiology, clinical feature, host species, environmental characteristics, and laboratory diagnosis; and gives a summary of possible future perspectives.     

The complete nucleotide sequence of potato virus T

Potato virus T (PVT), a member of an unassigned species in the family Flexiviridae, has a genome 6,539 nt in size with three ORFs coding for replication-associated proteins (185 kDa, ORF 1), movement protein (40 kDa, ORF 2) and coat protein (24 kDa, ORF 3), respectively. PVT differs from the type members of all genera of the family Flexiviridae with a 30K-type movement protein and is phylogenetically distant from all of these viruses, least so from grapevine virus A (GVA, genus Vitivirus), with which it groups in all trees. The viral genome resembles that of trichoviruses but is smaller and does not contain the 3′ terminal fourth ORF found in some members of this genus. PTV may represent a new genus of plant viruses for which the provisional name of Andesvirus is proposed.     

Discovery and molecular characterization of a novel trichovirus infecting sweet cherry

Contigs with the highest sequence similarity (73%) to Apricot pseudo-chlorotic leaf spot virus (genus Trichovirus, family Betaflexiviridae) were identified by high-throughput sequencing from a symptomless sweet cherry accession. The complete genome sequence of this new virus is 7460 nucleotides, excluding the 3′ poly(A) tail. Its genome organization is very similar to several trichoviruses infecting fruit trees, with three open reading frames encoding putative replicase, movement protein and coat protein (CP). The virus shares amino acid sequence identities of 60–73% at replicase and 53–76% at CP with other trichoviruses. Phylogenetic analyses group it and other trichoviruses in a cluster. These results support that this virus, which is tentatively named cherry latent virus 1, should be considered a new member in the genus Trichovirus.

     

Spotlight on avian pathology: fowlpox virus

Fowlpox virus is the type species of an extensive and poorly-defined group of viruses isolated from more than 200 species of birds, together comprising the avipoxvirus genus of the poxvirus family. Long known as a significant poultry pathogen, vaccines developed in the early and middle years of the twentieth century led to its effective eradication as a problem to commercial production in temperate climes in developed western countries (such that vaccination there is now far less common). Transmitted mechanically by biting insects, it remains problematic, causing significant losses to all forms of production (from backyard, through extensive to intensive commercial flocks), in tropical climes where control of biting insects is difficult. In these regions, vaccination (via intradermal or subcutaneous, and increasingly in ovo, routes) remains necessary. Although there is no evidence that more than a single serotype exists, there are poorly-described reports of outbreaks in vaccinated flocks. Whether this is due to inadequate vaccination or penetrance of novel variants remains unclear. Some such outbreaks have been associated with strains carrying endogenous, infectious proviral copies of the retrovirus reticuloendotheliosis virus (REV), which might represent a pathotypic (if not newly emerging) variant in the field. Until more is known about the phylogenetic structure of the avipoxvirus genus (by more widespread genome sequencing of isolates from different species of birds) it remains difficult to ascertain the risk of novel avipoxviruses emerging from wild birds (and/or by recombination/mutation) to infect farmed poultry.     

A whole genome perspective on the phylogeny of the plant virus family <Emphasis Type="Italic">Tombusviridae</Emphasis>

Summary. Most current classifications of viruses are based on single gene analysis of capsid protein or polymerase. The comparison of entire genomes is a more balanced approach that should provide a more complete picture of relatedness. We have used a singular value decomposition (SVD)-based analysis to generate phylogenetic trees using whole genome protein sequences from a family of single-stranded RNA plant viruses. Our dataset includes the 26 species of the family Tombusviridae, 25 of which have complete genome sequences cataloged in GenBank. The resulting phylogenetic tree agrees well with current taxonomic classifications, but with significant exceptions. One previously unassigned virus within this family, Maize necrotic streak virus, is definitively placed within the genus Tombusvirus by this analysis. In addition, the analysis defines two distinct subsets within the genus Necrovirus. Future datasets will be expanded to include other icosahedral positive strand RNA plant viruses, and then perhaps all positive strand RNA plant viruses.     

Further characterization of two sequiviruses infecting lettuce and development of specific RT-PCR primers

Summary. Lettuce mottle virus (LeMoV) and dandelion yellow mosaic virus (DaYMV) infect lettuce in South America and Europe, respectively. LeMoV and DaYMV possess isometric particles, occur at low concentrations in plants and have narrow host ranges. Partial genome sequences of both viruses were obtained using purified viral preparations and universal primers for members of the family Sequiviridae. DaYMV and LeMoV sequences were analyzed and showed identity with other members of the family. Universal primers that detect both viruses and specific primers for LeMoV and DaYMV were designed and used in RT-PCR-based diagnostic assays. These results provide the first molecular data on the LeMoV and DaYMV genomes and suggest that LeMoV is a member of the genus Sequivirus, probably distinct from DaYMV.     

Sequence analysis of porcine kobuvirus VP1 region detected in pigs in Japan and Thailand

Porcine kobuvirus is a new candidate species of the genus Kobuvirus in the family Picornaviridae, and information is still limited. The identification of porcine kobuvirus has been performed by the sequence analyses of the 3D region of the viruses. Therefore, the purpose of this study was to characterize the molecular properties of VP1 nucleotide sequences of the porcine kobuviruses isolated from porcine stool samples in Japan during 2009 and Thailand between 2006 and 2008. In addition, previous identification of a unique porcine kobuvirus; Japanese H023/2009/JP, which is a bovine kobuvirus-like strain based on sequence analysis of the 3D region, was also included in this study. All of the strains were amplified by the VP1-specific primer pair: the amplicons were subjected to direct sequencing and compared with the VP1 nucleotide sequences of reference strains. The VP1 sequences of strains from the GenBank database revealed high nucleotide sequence identity at 84.3–100%. On the other hand, the nucleotide identities among the 15 porcine kobuvirus strains analyzed in this study ranged from 78.8 to 99.8%. The results revealed that diversity of the strains in this study were higher than those of the strains in previous studies. Furthermore, it was found that the VP1 region of the bovine kobuvirus-like strain, H023/2009/JP, clustered with nine porcine kobuvirus strains that were isolated in Thailand and Japan. Since this strain was previously found to be closely related to bovine kobuviruses in the 3D gene region, it may be a natural recombinant.