The fecal viral flora of wild rodents

Identification and complete genome analysis of kobuvirus in faecal samples of European roller (Coracias garrulus): for the first time in a bird

The genus Kobuvirus (Picornaviridae) consists of three species, Aichivirus A (e.g., Aichi virus, which infects humans), Aichivirus B and Aichivirus C. Kobuvirus have not been detected in non-mammal species including birds. In this study, a novel kobuvirus was identified in 3 (17 %) out of 18 faecal samples collected from European rollers (Coracias garrulus) in Hungary. The complete genome sequence of strain SZAL6-KoV/2011/HUN (KJ934637), which was determined using a novel 5'/3' RACE method (dsRNA-RACE) involving a double-stranded (ds)RNA intermediate, has a type-V IRES at the 5' end and a cis-acting element (CRE) in the 3C gene and encodes L and 2A(H-box/NC) proteins, but it does not contain the sequence forming a "barbell-like" secondary RNA structure in the 3'UTR. SZAL6-KoV/2011/HUN has 72 %, 73 %, and 81 % amino acid sequence identity to the P1, P2, and P3 protein, respectively, of Aichi virus. Evolutionary analysis showed that SZAL6-KoV/2011/HUN shares a common ancestor with other kobuviruses but belongs to a more ancient lineage in the species Aichivirus A. Investigation of the known kobuviruses in different animals and discovery of novel kobuviruses in potential host species helps to clarify the evolutionary connection and zoonotic potential of kobuviruses.

Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus

Rats are known as reservoirs and vectors for several zoonotic pathogens. However, information on the viruses shed by urban wild rats that could pose a zoonotic risk to human health is scare. Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids. The determined faecal viromes of rats consisted of a variety of known and unknown viruses, and were highly variable among the individuals. Members of the families Parvoviridae and Picobirnaviridae represented the most abundant species. Novel picornaviruses, bocaviruses, sapoviruses and stool-associated circular ssDNA viruses were identified, which showed only low sequence identity to known representatives of the corresponding taxa. In addition, noroviruses and rotaviruses were detected as potential zoonotic gastroenteritis viruses. However, partial-genome sequence analyses indicated that the norovirus was closely related to the recently identified rat norovirus and the rotavirus B was closely related to the rat rotavirus strain IDIR; both viruses clustered separately from respective human virus strains in phylogenetic trees. In contrast, the rotavirus A sequences showed high identity to human and animal strains. Analysis of the nearly complete genome of this virus revealed the known genotypes G3, P[3] and N2 for three of the genome segments, whereas the remaining eight genome segments represented the novel genotypes I20-R11-C11-M10-A22-T14-E18-H13. Our results indicated a high heterogeneity of enteric viruses present in urban wild rats; their ability to be transmitted to humans remains to be assessed in the future.

Faecal virome of cats in an animal shelter

We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.

Epidemiology, phylogeny, and evolution of emerging enteric Picobirnaviruses of animal origin and their relationship to human strains

Picobirnavirus (PBV) which has been included in the list of viruses causing enteric infection in animals is highly versatile because of its broad host range and genetic diversity. PBVs are among the most recent and emerging small, nonenveloped viruses with a bisegmented double-stranded RNA genome, classified under a new family “Picobirnaviridae.” PBVs have also been detected from respiratory tract of pigs, but needs further close investigation for their inhabitant behavior. Though, accretion of genomic data of PBVs from different mammalian species resolved some of the ambiguity, quite a few questions and hypotheses regarding pathogenesis, persistence location, and evolution of PBVs remain unreciprocated. Evolutionary analysis reveals association of PBVs with partitiviruses especially fungi partitiviruses. Although, PBVs may have an ambiguous clinical implication, they do pose a potential public health concern in humans and control of PBVs mainly relies on nonvaccinal approach. Based upon the published data, from 1988 to date, generated from animal PBVs across the globe, this review provides information and discussion with respect to genetic analysis as well as evolution of PBVs of animal origin in relation to human strains.

Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China

To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact co-infected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets.

Feline fecal virome reveals novel and prevalent enteric viruses

Humans keep more than 80 million cats worldwide, ensuring frequent exposure to their viruses. Despite such interactions the enteric virome of cats remains poorly understood. We analyzed a fecal sample from a single healthy cat from Portugal using viral metagenomics and detected five eukaryotic viral genomes. These viruses included a novel picornavirus (proposed genus "Sakobuvirus") and bocavirus (feline bocavirus 2), a variant of feline astrovirus 2 and sequence fragments of a highly divergent feline rotavirus and picobirnavirus. Feline sakobuvirus A represents the prototype species of a proposed new genus in the Picornaviridae family, distantly related to human salivirus and kobuvirus. Feline astroviruses (mamastrovirus 2) are the closest known relatives of the classic human astroviruses (mamastrovirus 1), suggestive of past cross-species transmission. Presence of these viruses by PCR among Portuguese cats was detected in 13% (rotavirus), 7% (astrovirus), 6% (bocavirus), 4% (sakobuvirus), and 4% (picobirnavirus) of 55 feline fecal samples. Co-infections were frequent with 40% (4/10) of infected cats shedding more than one of these five viruses. Our study provides an initial description of the feline fecal virome indicating a high level of asymptomatic infections. Availability of the genome sequences of these viruses will facilitate future tropism and feline disease association studies.

Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection?

Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite of a bloodsucking arthropod. If a virus is able to adapt and replicate in its new human host, human-to-human transmissions may occur, possibly resulting in an epidemic, such as the A/H1N1 flu pandemic in 2009. Thus, predicting emerging zoonotic infections is an important challenge for public health officials in the coming decades. The recent development of viral metagenomics, i.e., the characterization of the complete viral diversity isolated from an organism or an environment using high-throughput sequencing technologies, is promising for the surveillance of such diseases and can be accomplished by analyzing the viromes of selected animals and arthropods that are closely in contact with humans. In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases.

Canine kobuvirus infections in Korean dogs

To investigate canine kobuvirus (CaKoV) infection, fecal samples (n = 59) were collected from dogs with or without diarrhea (n = 21 and 38, respectively) in the Republic of Korea (ROK) in 2012. CaKoV infection was detected in four diarrheic samples (19.0 %) and five non-diarrheic samples (13.2 %). All CaKoV-positive dogs with diarrhea were found to be infected in mixed infections with canine distemper virus and canine parvovirus or canine adenovirus. There was no significant difference in the prevalence of CaKoV in dogs with and without diarrhea. By phylogenetic analysis based on partial 3D genes and complete genome sequences, the Korean isolates were found to be closely related to each other regardless of whether they were associated with diarrhea, and to the canine kobuviruses identified in the USA and UK. This study supports the conclusion that CaKoVs from different countries are not restricted geographically and belong to a single lineage.

The virome in mammalian physiology and disease

The virome contains the most abundant and fastest mutating genetic elements on Earth. The mammalian virome is constituted of viruses that infect host cells, virus-derived elements in our chromosomes, and viruses that infect the broad array of other types of organisms that inhabit us. Virome interactions with the host cannot be encompassed by a monotheistic view of viruses as pathogens. Instead, the genetic and transcriptional identity of mammals is defined in part by our coevolved virome, a concept with profound implications for understanding health and disease.

Viral metagenomic analysis of feces of wild small carnivores

Background

Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans.

Methods

In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae.

Results

A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses.

Conclusions

Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.

Complete genome characterization of mosavirus (family Picornaviridae) identified in droppings of a European roller (Coracias garrulus) in Hungary

Mosavirus (mosavirus A1, M-7/2010/USA, JF973687), a novel picornavirus, was found in a canyon mouse (Peromyscus crinitus) in the USA in 2010. It represents a novel species (Mosavirus A) in a novel genus (Mosavirus) in the family Picornaviridae. In this study, the first complete genome sequence of another mosavirus, SZAL6-MoV/2011/HUN (KF958461), was determined from one out of 18 fecal samples from an Afro-Palearctic migratory bird, the European roller (Coracias garrulus). The complete genome of SZAL6-MoV/2011/HUN is 8385 nt long (from poly(C) tract to poly(A) tail), contains a 646-nt-long 5'UTR that forms a type II IRES, and encodes a potential 2550-aa-long polyprotein precursor including an aphthovirus-like L(pro)-proteinase, a small aphthovirus-like 2A(NPG↓P), and two 3B(VPg) proteins. SZAL6-MoV/2011/HUN has 67 %, 74 %, and 76 % aa sequence identity in the P1, P2, and P3 region, respectively, to M-7/2010/USA and represents a second mosavirus type, mosavirus A2.

Molecular and phylogenetic analysis of a novel turkey-origin picobirnavirus

A previous metagenomic analysis of the turkey gut RNA virus community identified novel enteric viruses that may play roles in poultry enteric diseases or in performance problems noted in the field. As part of the molecular characterization of these novel enteric viruses, a reverse transcriptase-PCR diagnostic assay was developed, targeting a novel turkey-origin picobirnavirus (PBV) initially identified in a pooled intestinal sample from turkey poults in North Carolina. Little detailed molecular information exists regarding the family Picobirnaviridae, particularly for the PBVs that have been described in avian species. This diagnostic assay targets the turkey PBV RNA-dependent RNA polymerase gene and produces an 1135-bp amplicon. This assay was validated using in vitro transcribed RNA and was tested using archived enteric samples collected from turkey flocks in the southeastern United States. Further, a phylogenetic analysis suggests the turkey PBV is unique because it does not group closely with the recognized PBV genogroups circulating in mammalian hosts.

Identification of a novel single-stranded circular DNA virus in pig feces

Porcine stool-associated circular virus 5 (PoSCV5) was detected in the feces of a pig with diarrhea. The complete 3,062-nucleotide genome contains two bidirectionally transcribed open reading frames (ORFs). Phylogenetic analysis of the deduced replication initiator protein (Rep) places PoSCV5 alone on a deep branch among the small circular Rep-encoding single-stranded DNA viruses.

Phylogenetic analysis of astrovirus and kobuvirus in Korean dogs

Astroviruses and kobuviruses are frequently found in mammalian feces, including that of humans. The present study examined fecal samples from 91 Korean dogs suffering from diarrhea. Canine astroviruses (CAstVs) and canine kobuviruses (CKoVs) were identified in 2 (2.1%) and 46 (50.6%) dogs, respectively. Nucleotide sequence analysis coupled with phylogenetic analysis using the neighbor-joining method showed that CAstVs clustered into four genetically diverse groups. Two Korean CAstVs belonged to group 2 alongside strains isolated in Italy and France. Twelve of the Korean CKoVs belonged to a single clade, along with strain UK003 identified in the UK and six CKoVs identified in the USA. Thus, the results suggest that the Korean strain of CAstV is closely related to strains isolated in Europe. Surely, CKoV in South Korea could identify the circulation among dogs population.

Complete sequencing and phylogenetic analysis of porcine kobuvirus in domestic pigs in Northwest China

Porcine kobuvirus, a member of the genus Kobuvirus that is associated with diarrhea, has been reported in many countries. We determined the complete genome sequence and investigated the genetic evolution of the kobuvirus strain swKoV CH441, which was detected in the highland of Gansu province in Northwest China. The viral genome is 8149 nucleotides (nt) long, including a 29-nt poly(A) tail of the 3' end, and is 90 nt shorter in the 2B coding region than those of other kobuvirus strains whose sequences are available in the GenBank database. Phylogenetic analysis showed that swKoV CH441 was most closely related to porcine kobuvirus CH/HNXX-4 but more distantly related to other strains, including the strains GS-1/2012/CH and GS-2/2012/CH, which were detected in Gansu province, indicating that porcine kobuvirus may have geographic and host differences in evolution.

Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm

We have developed a full genome virus detection process that combines sensitive nucleic acid preparation optimised for virus identification in fecal material with Illumina MiSeq sequencing and a novel post-sequencing virus identification algorithm. Enriched viral nucleic acid was converted to double-stranded DNA and subjected to Illumina MiSeq sequencing. The resulting short reads were processed with a novel iterative Python algorithm SLIM for the identification of sequences with homology to known viruses. De novo assembly was then used to generate full viral genomes. The sensitivity of this process was demonstrated with a set of fecal samples from HIV-1 infected patients. A quantitative assessment of the mammalian, plant, and bacterial virus content of this compartment was generated and the deep sequencing data were sufficient to assembly 12 complete viral genomes from 6 virus families. The method detected high levels of enteropathic viruses that are normally controlled in healthy adults, but may be involved in the pathogenesis of HIV-1 infection and will provide a powerful tool for virus detection and for analyzing changes in the fecal virome associated with HIV-1 progression and pathogenesis.

A novel papillomavirus in Adélie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica

Papillomaviruses are epitheliotropic viruses that have circular dsDNA genomes encapsidated in non-enveloped virions. They have been found to infect a variety of mammals, reptiles and birds, but so far they have not been found in amphibians. Using a next-generation sequencing de novo assembly contig-informed recovery, we cloned and Sanger sequenced the complete genome of a novel papillomavirus from the faecal matter of Adélie penguins (Pygoscelis adeliae) nesting on Ross Island, Antarctica. The genome had all the usual features of a papillomavirus and an E9 ORF encoding a protein of unknown function that is found in all avian papillomaviruses to date. This novel papillomavirus genome shared ~60 % pairwise identity with the genomes of the other three known avian papillomaviruses: Fringilla coelebs papillomavirus 1 (FcPV1), Francolinus leucoscepus papillomavirus 1 (FlPV1) and Psittacus erithacus papillomavirus 1. Pairwise identity analysis and phylogenetic analysis of the major capsid protein gene clearly indicated that it represents a novel species, which we named Pygoscelis adeliae papillomavirus 1 (PaCV1). No evidence of recombination was detected in the genome of PaCV1, but we did detect a recombinant region (119 nt) in the E6 gene of FlPV1 with the recombinant region being derived from ancestral FcPV1-like sequences. Previously only paramyxoviruses, orthomyxoviruses and avian pox viruses have been genetically identified in penguins; however, the majority of penguin viral identifications have been based on serology or histology. This is the first report, to our knowledge, of a papillomavirus associated with a penguin species.

Comparative complete genome analysis of chicken and Turkey megriviruses (family picornaviridae): long 3' untranslated regions with a potential second open reading frame and evidence for possible recombination

Members of the family Picornaviridae consist of small positive-sense single-stranded RNA (+ssRNA) viruses capable of infecting various vertebrate species, including birds. One of the recently identified avian picornaviruses, with a remarkably long (>9,040-nucleotide) but still incompletely sequenced genome, is turkey hepatitis virus 1 (THV-1; species Melegrivirus A, genus Megrivirus), a virus associated with liver necrosis and enteritis in commercial turkeys (Meleagris gallopavo). This report presents the results of the genetic analysis of three complete genomes of megriviruses from fecal samples of chickens (chicken/B21-CHV/2012/HUN, GenBank accession no. KF961186, and chicken/CHK-IV-CHV/2013/HUN, GenBank accession no. KF961187) (Gallus gallus domesticus) and turkey (turkey/B407-THV/2011/HUN, GenBank accession no. KF961188) (Meleagris gallopavo) with the largest picornavirus genome (up to 9,739 nucleotides) so far described. The close phylogenetic relationship to THV-1 in the nonstructural protein-coding genome region and possession of the same internal ribosomal entry site type (IVB-like) suggest that the study strains belong to the genus Megrivirus. However, the genome comparisons revealed numerous unique variations (e.g., different numbers of potential 2A peptides, unusually long 3' genome parts with various lengths of a potential second open reading frame, and multiple repeating sequence motifs in the 3' untranslated region) and heterogeneous sequence relationships between the structural and nonstructural genome regions. These differences suggest the classification of chicken megrivirus-like viruses into a candidate novel species in the genus Megrivirus. Based on the different phylogenetic positions of chicken megrivirus-like viruses at the structural and nonstructural genome regions, the recombinant nature of these viruses is plausible.

IMPORTANCE

The comparative genome analysis of turkey and novel chicken megriviruses revealed numerous unique genome features, e.g., up to four potential 2A peptides, unusually long 3' genome parts with various lengths containing a potential second open reading frame, multiple repeating sequence motifs, and heterogeneous sequence relationships (possibly due to a recombination event) between the structural and nonstructural genome regions. Our results could help us to better understand the evolution and diversity (in terms of sequence and genome layout) of picornaviruses.

Human oral viruses are personal, persistent and gender-consistent

Viruses are the most abundant members of the human oral microbiome, yet relatively little is known about their biodiversity in humans. To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. Each subject was examined at 11 time points to characterize longitudinal differences in human oral viruses. Our primary goals were to determine whether oral viruses were specific to individuals and whether viral genotypes persisted over time. We found a subset of homologous viral genotypes across all subjects and time points studied, suggesting that certain genotypes may be ubiquitous among healthy human subjects. We also found significant associations between viral genotypes and individual subjects, indicating that viruses are a highly personalized feature of the healthy human oral microbiome. Many of these oral viruses were not transient members of the oral ecosystem, as demonstrated by the persistence of certain viruses throughout the entire 60-day study period. As has previously been demonstrated for bacteria and fungi, membership in the oral viral community was significantly associated with the sex of each subject. Similar characteristics of personalized, sex-specific microflora could not be identified for oral bacterial communities based on 16S rRNA. Our findings that many viruses are stable and individual-specific members of the oral ecosystem suggest that viruses have an important role in the human oral ecosystem.

Simultaneous rapid sequencing of multiple RNA virus genomes

Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines. However, the difficulty, time and expense of generating full-length sequences individually from each archived sample have hampered these studies. Next generation sequencing technologies have been utilized for analysis of clinical and environmental samples to identify viral pathogens that may be present. This has led to the discovery of many new, uncharacterized viruses from a number of viral families. Use of these sequencing technologies would be advantageous in examining viral evolution. In this study, a sequencing procedure was used to sequence simultaneously and rapidly multiple archived samples using a single standard protocol. This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3'-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. This conferred sequence independence by random priming both first and second strand cDNA synthesis. Viral stocks were treated with a nuclease cocktail to reduce the presence of host nucleic acids. Viral RNA was extracted, followed by single tube random-primed double-stranded cDNA synthesis. The resultant cDNAs were amplified by primer-specific PCR, pooled, size fractionated and sequenced on the Ion Torrent PGM platform. The individual virus genomes were readily assembled by both de novo and template-assisted assembly methods. This procedure consistently resulted in near full length, if not full-length, genomic sequences and was used to sequence multiple bovine pestivirus and coronavirus isolates simultaneously.

Epidemiology of human and animal kobuviruses

Kobuviruses are member of the family Picornaviridae. Initially, members in Kobuvirus genus were named according to the basis of their host species. The viruses found in humans called "Aichi virus", the viruses from cattle called "bovine kobuvirus", and the viruses isolated from pigs called "porcine kobuvirus". Currently, taxonomy of kobuviruses has been proposed and the virus species have been renamed. The "Aichi virus" has been renamed as "Aichivirus A", "bovine kobuvirus" has been renamed as "Aichivirus B", and "porcine kobuvirus" has been changed to "Aichivirus C". Among Aichivirus A, three distinct members, including Aichi virus 1 (Aichivirus in human), canine kobuvirus 1, and murine kobuvirus 1, have been described. Aichi virus 1 in human is globally distributed and has been identified at low incidence (0-3 %) in sporadic acute gastroenteritis cases. Aichi virus 1 has been reported to be associated with variety types of clinical illnesses including diarrhea, vomiting, fever, purulent conjunctivitis, and respiratory symptoms. The studies from Japan, Spain, Germany, and Tunisia demonstrated that high antibody prevalence against Aichi virus 1 were found in the populations. Aichivirus B or previously known as bovine kobuvirus was first reported in 2003. Since then, Aichivirus B has also been reported from several countries worldwide. An overall prevalence of Aichivirus B varies from 1 to 34.5 %, and the highest prevalence was found in cattle with diarrhea in Korea. Aichivirus C or porcine kobuvirus is widely distributed in pigs. Aichivirus C has been found in both diarrhea and healthy pigs and the positive rate of this virus varies from 3.9 up to 100 %. It was reported that Aichivirus C was found with high prevalence in wild boars in Hungary. The accumulated data of the biological, pathological, as well as epidemiological studies of kobuviruses are still limited. Comprehensive global investigations of the prevalence and diversity are required and will be helpful for providing further insight into pathogenicity, genetic heterogeneity, interspecies transmission, and global distribution of kobuviruses.

Discovery of rosavirus 2, a novel variant of a rodent-associated picornavirus, in children from The Gambia

We describe the identification of a novel picornavirus recovered from the fecal specimen of a child in The Gambia, provisionally named rosavirus 2. Comparison of the rosavirus 2 complete genome demonstrated 71.9% nucleotide identity to its closest relative rosavirus M-7, an unclassified picornavirus identified from rodent fecal material. A unique RNA structure was predicted in the 3' UTR of rosavirus 2 that was conserved with rosavirus M-7 and cadiciviruses. We detected rosavirus 2 in four pediatric fecal specimens (0.55% prevalence) in a Gambian diarrheal case-control cohort, but we did not detect it in a panel of 634 pediatric diarrheal stool specimens from the USA. There was no statistical evidence that rosavirus 2 was associated with diarrheal cases. This study broadens our understanding of unknown viruses present in children in developing country settings.

Molecular detection and nucleotide sequence analysis of a new Aichi virus closely related to canine kobuvirus in sewage samples

Between 2001 and 2005, 207 raw sewage samples were collected at the inflow of a sewage treatment plant in Aichi Prefecture, Japan. Of the 207 sewage samples, 137 (66.2 %) were found to be positive for amplification of Aichi virus (AiV) nucleotide using reverse transcription (RT)-PCR with 10 forward and 10 reverse primers in the 3D region corresponding to the nucleotide sequence of all kobuviruses. AiV genotype A sequences were detected in all 137 samples. New sequences of AiV were detected in nine samples, exhibiting 83 % similarity with AiV A846/88, but 95 % similarity with canine kobuvirus (CKV) US-PC0082 in this region. The nucleotide sequences from the VP3 region to the 3' untranslated region (UTR) of sewage sample Y12/2004 were determined. The number of nucleotides in each region was the same as that of CKV. The similarity of the nucleotide (amino acid) identity of a complete VP1 region was 90.5 % (94.8 %) between Y12/2004 and CKV US-PC0082. The phylogenic analyses based on the nucleotide and the deduced amino acid sequences of VP1 and 3D showed that Y12/2004 was independent from AiV, but closely related to CKV. These results suggested that CKV is present in Aichi Prefecture, Japan.

Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus

In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya.

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.

Molecular evidence of kobuviruses in free-ranging red foxes (Vulpes vulpes)

Red foxes (Vulpes vulpes) are susceptible to viral diseases of domestic carnivores. In this study, by screening rectal swabs collected from 34 red foxes in Italy, we identified kobuvirus RNA in five samples. Based on analysis of partial RdRp and full-length VP1 genes, all of the strains shared the highest identity with canine kobuviruses (CaKVs) recently detected in the US, the UK and Italy. These findings provide the first evidence of the circulation of these novel viruses in foxes.

New insights into mycoviruses and exploration for the biological control of crop fungal diseases

Mycoviruses are viruses that infect fungi. A growing number of novel mycoviruses have expanded our knowledge of virology, particularly in taxonomy, ecology, and evolution. Recent progress in the study of mycoviruses has comprehensively improved our understanding of the properties of mycoviruses and has strengthened our confidence to explore hypovirulence-associated mycoviruses that control crop diseases. In this review, the advantages of using hypovirulence-associated mycoviruses to control crop diseases are discussed, and, as an example, the potential for Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) to control the stem rot of rapeseed (Brassica napus) is also introduced. Fungal vegetative incompatibility is likely to be the key factor that limits the wide utilization of mycoviruses to control crop diseases; however, there are suggested strategies for resolving this problem.

Prevalence and genetic diversity of bovine kobuvirus in China

A total of 166 faecal specimens from diarrheic cattle were collected in China for detection of bovine kobuvirus (BKV) by reverse transcription PCR (RT-PCR) targeting the region a portion of the 3D nonstructural protein, with an amplicon size of 631 bp. The RNA corresponding to the BKV 3D region was detected in 34.9 % of faecal samples (58/166) in four major dairy-cattle-production areas in China, and sequence analysis based on the partial 3D sequences (35/58) indicated that the Chinese BKVs shared 88.9-96.2 % nucleotide sequence identity to BKV reference strains. Further phylogenetic analysis based on the complete VP1-encoding sequences (17/35) revealed that the Chinese BKVs shared 81-83.4 % nucleotide sequence identity to the U-1 strain, and these Chinese BKV strains, together with the U-1 strain, are apparently divided into four lineages, representing four genotypes of BKV, designated as A, B, C and D. Our results show that BKV infection is widely distributed, with high genetic diversity in China.

Discovery of urchin-associated densoviruses (family Parvoviridae) in coastal waters of the Big Island, Hawaii

Echinoderms are important constituents of marine ecosystems, where they may influence the recruitment success of benthic flora and fauna, and are important consumers of detritus and plant materials. There are currently no described viruses of echinoderms. We used a viral metagenomic approach to examine viral consortia within three urchins - Colobocentrotus atratus, Tripneustes gratilla and Echinometra mathaei - which are common constituents of reef communities in the Hawaiian archipelago. Metagenomic libraries revealed the presence of bacteriophages and densoviruses (family Parvoviridae) in tissues of all three urchins. Densoviruses are known typically to infect terrestrial and aquatic arthropods. Urchin-associated densoviruses were detected by quantitative PCR in all tissues tested, and were also detected in filtered suspended matter (>0.2 µm) from plankton and in sediments at several locations near to where the urchins were collected for metagenomic analysis. To the best of our knowledge, this is the first report of echinoderm-associated viruses, which extends the known host range of parvoviruses.

New single-stranded DNA virus with a unique genomic structure that infects marine diatom Chaetoceros setoensis

Diatoms are among the most abundant organisms in nature; however, their relationships with single-stranded DNA (ssDNA) viruses have not yet been defined in detail. We report the isolation and characterisation of a virus (CsetDNAV) that lytically infects the bloom-forming diatom Chaetoceros setoensis. The virion is 33 nm in diameter and accumulates in the nucleus of its host. CsetDNAV harbours a covalently closed-circular ssDNA genome comprising 5836 nucleotides and eight different short-complementary fragments (67–145 nucleotides), which have not been reported in other diatom viruses. Phylogenetic analysis based on the putative replicase-related protein showed that CsetDNAV was not included in the monophyly of the recently established genus Bacilladnavirus. This discovery of CsetDNAV, which harbours a genome with a structure that is unique among known viruses that infect diatoms, suggests that other such undiscovered viruses possess diverse genomic architectures.

Characterization of a novel picornavirus isolate from a diseased European eel (Anguilla anguilla)

A novel picornavirus was isolated from specimens of a diseased European eel (Anguilla anguilla). This virus induced a cytopathic effect in eel embryonic kidney cells and high mortality in a controlled transmission study using elvers. Eel picornavirus has a genome of 7,496 nucleotides that encodes a polyprotein of 2,259 amino acids. It has a typical picornavirus genome layout, but its low similarity to known viral proteins suggests a novel species in the family Picornaviridae.

Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China

East Lake (Lake Donghu), located in Wuhan, China, is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years. Marine and fresh water are considered to contain a large number of viruses. However, little is known about their genetic diversity because of the limited techniques for culturing viruses. In this study, we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring, Summer, Autumn, and Winter. The libraries from four samples each generated 234,669, 71,837, 12,820, and 34,236 contigs (> 90 bp each), respectively. The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families, with the majority of contigs homologous to DNA viruses, including members of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and Microviridae, which infect bacteria or algae, and members of Circoviridae, which infect invertebrates and vertebrates. The highest viral genetic diversity occurred in samples collected in August, then December and June, and the least diversity in March. Most contigs have low-sequence identities with known viruses. PCR detection targeting the conserved sequences of genes (g20, psbA, psbD, and DNApol) of cyanophages further confirmed that there are novel cyanophages in the East Lake. Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.

Metagenomics for pathogen detection in public health

Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals.

Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis

The application of viral metagenomic techniques and a series of PCRs in a human fecal sample enabled the detection of two novel circular unisense DNA viral genomes with 92% nucleotide similarity. The viruses were tentatively named circo-like virus-Brazil (CLV-BR) strains hs1 and hs2 and have genome lengths of 2526 and 2533 nucleotides, respectively. Four major open reading frames (ORFs) were identified in each of the genomes, and differences between the two genomes were primarily observed in ORF 2. Only ORF 3 showed significant amino acid similarities to a putative rolling circle replication initiator protein (Rep), although with low identity (36%). Our phylogenetic analysis, based on the Rep protein, demonstrated that the CLV-BRs do not cluster with members of the Circoviridae, Nanoviridae or Geminiviridae families and are more closely related to circo-like genomes previously identified in reclaimed water and feces of a wild rodent and of a bat. The CLV-BRs are members of a putative new family of circular Rep-encoding ssDNA viruses. Electron microscopy revealed icosahedral (~23 nm) structures, likely reflecting the novel viruses, and rod-shaped viral particles (~65-460 × 21 × 10 nm in length, diameter, and axial canal, respectively). Circo-like viruses have been detected in stool samples from humans and other mammals (bats, rodents, chimpanzees and bovines), cerebrospinal fluid and sera from humans, as well as samples from many other sources, e.g., insects, meat and the environment. Further studies are needed to classify all novel circular DNA viruses and elucidate their hosts, pathogenicity and evolutionary history.

Molecular and phylogenetic analysis of the porcine kobuvirus VP1 region using infected pigs from Sichuan Province, China

BACKGROUND

Porcine kobuvirus (PKoV) is a member of the Kobuvirus genus within the Picornaviridae family. PKoV is distributed worldwide with high prevalence in clinically healthy pigs and those with diarrhea.

METHODS

Fecal and intestinal samples (n = 163) from pig farms in Sichuan Province, China were obtained to determine the presence of PKoV using reverse transcription polymerase chain reaction assays. Specific primers were used for the amplification of the gene encoding the PKoV VP1 protein sequence. Sequence and phylogenetic analyses were conducted to clarify evolutionary relationships with other PKoV strains.

RESULTS

Approximately 53% (87/163) of pigs tested positive for PKoV. PKoV was widespread in asymptomatic pigs and those with diarrhea. A high prevalence of PKoV was observed in pigs younger than 4 weeks and in pigs with diarrhea. Phylogenetic analysis of 36 PKoV VP1 protein sequences showed that Sichuan PKoV strains formed four distinct clusters. Two pigs with diarrhea were found to be co-infected with multiple PKoV strains. Sequence and phylogenetic analyses revealed diversity within the same host and between different hosts. Significant recombination breakpoints were observed between the CHN/SC/31-A1 and CHN/SC/31-A3 strains in the VP1 region, which were isolated from the same sample.

CONCLUSION

PKoV was endemic in Sichuan Province regardless of whether pigs were healthy or suffering from diarrhea. Based on our statistical analyses, we suggest that PKoV was the likely causative agent of high-mortality diarrhea in China from 2010. For the first time, we provide evidence for the co-existence of multiple PKoV strains in one pig, and possible recombination events in the VP1 region. Our findings provide further insights into the molecular properties of PKoV, along with its epidemiology.

The viruses of wild pigeon droppings

Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initial assessment of the enteric virome in the droppings of pigeons, a feral urban species with frequent human contact.

Novel myco-like DNA viruses discovered in the faecal matter of various animals

A wide variety of novel single-stranded DNA (ssDNA) viruses have been found in faecal matter of chimpanzees, cows, rodents, bats, badgers, foxes and pigs over the last few years. Using a combination of rolling circle amplification coupled with restriction enzyme digests based approach as well as a next generation sequencing informed approach, we have recovered fourteen full genomes of ssDNA viruses which exhibit genomic features described for members of the recently proposed gemycircularvirus group from a wide variety of mammal and bird faecal samples across New Zealand. The fourteen novel ssDNA viruses (2122-2290nt) encode two major proteins, a replication associated protein (Rep) and a capsid protein (Cp) which are bi-directionally transcribed. Interestingly, the Rep of these novel viruses are similar to gemycircularviruses detected in insects, cassava leaves, and badger faecal matter, the novel viruses share sequence similarities with the mycovirus sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and Rep-like sequences found in fungal genomes. Pairwise sequence similarities between the 14 novel genomes with other related viral isolates (gemycircularviruses) indicated that they share greater than 55.8% genome-wide identity. Additionally, they share between 55% and 59% pairwise identity with putative novel ssDNA virus genomes recently isolated from sewage baminivirus, niminivirus and nephavirus. Based on the similarities to SsHADV-1 and Rep-like sequences found in fungal genomes, these novel gemycircularviruses may infect fungi.

Detection and genetic characterization of feline kobuviruses

In order to survey for feline kobuviruses infection, fecal samples (n = 39) of cats with diarrhea were collected during 2011–2012. Six (14.5 %) of the fecal samples tested were positive for feline kobuviruses. The partial nucleotide sequences of feline kobuviruses based on the RNA-dependent RNA polymerase gene were compared to those of other species. Feline kobuviruses were most closely related to canine kobuvirus in terms of their amino acid and nucleotide levels. In a phylogenetic tree, feline kobuviruses were also closely clustered with canine kobuvirus, Aichi virus (human), and mouse kobuvirus. This is the first report of the detection and genetic characterization of feline kobuviruses.

Metagenomic analysis of the ferret fecal viral flora

Ferrets are widely used as a small animal model for a number of viral infections, including influenza A virus and SARS coronavirus. To further analyze the microbiological status of ferrets, their fecal viral flora was studied using a metagenomics approach. Novel viruses from the families Picorna-, Papilloma-, and Anelloviridae as well as known viruses from the families Astro-, Corona-, Parvo-, and Hepeviridae were identified in different ferret cohorts. Ferret kobu- and hepatitis E virus were mainly present in human household ferrets, whereas coronaviruses were found both in household as well as farm ferrets. Our studies illuminate the viral diversity found in ferrets and provide tools to prescreen for newly identified viruses that potentially could influence disease outcome of experimental virus infections in ferrets.

Rosavirus: the prototype of a proposed new genus of the Picornaviridae family

We describe a 8,724-nucleotide-long picornavirus genome encoding a single 2,470-aa polyprotein obtained from the feces of a wild mouse. Rosavirus is genetically closest to the double ORF Dicipivirus found in canine feces that is currently the only picornavirus with a second internal ribosome entry site (IRES). Of note, a section of rosavirus' 5'UTR showed strong sequence and structural conservation with the type II IRES from the Parechovirus and Hungarovirus genera possibly reflecting exchange of genetic modules between genera. Based on genetic distance criteria rosavirus qualifies as prototype of a new genus of the Picornaviridae family.

Identification of a Novel Circular DNA Virus in New Zealand Fur Seal (Arctocephalus forsteri) Fecal Matter

Fur seal feces-associated circular DNA virus (FSfaCV) is a novel virus isolated from the fecal matter of New Zealand fur seals. FSfaCV has two main open reading frames in its 2,925-nucleotide (nt) genome. The replication-associated protein (Rep) of FSfaCV has similarity to Rep-like sequences in the Giardia intestinalis genome.

Identification of a novel picornavirus in healthy piglets and seroepidemiological evidence of its presence in humans

In this study, we describe a novel porcine parechovirus-like virus (tentatively named PLV-CHN) from healthy piglets in China using 454 high-throughput sequencing. The complete genome of the virus comprises 6832 bp, encoding a predicted polyprotein of 2132 amino acids that is most similar to Ljungan virus (32% identity). A similar virus that belongs to a novel Picornaviridae genus, named swine pasivirus 1 (SPaV-1), was reported during the preparation of this paper. Sequence analysis revealed that PLV-CHN and SPaV1 shared 82% nucleotide identity and 89% amino acid identity. Further genomic and phylogenetic analyses suggested that both SPaV1 and PLV-CHN shared similar genomic characteristics and belong to the same novel Picornaviridae genus. A total of 36 (20.0%) fecal samples from 180 healthy piglets were positive for PLV-CHN by RT-PCR, while no fecal samples from 100 healthy children and 100 children with diarrhea, and no cerebrospinal fluid samples from 196 children with suspected viral encephalitis, was positive for the virus. However, Western blot and enzyme-linked immunosorbent assays using recombinant PLV-CHN VP1 polypeptide as an antigen showed a high seroprevalence of 63.5% in the healthy population. When grouped by age, the antibody-positivity rates showed that the majority of children under 12 years of age have been infected by the virus. It was suggested that PLV-CHN, SPaV1, or an as-yet-uncharacterized virus can infect humans early in life. Thus, investigation of the role of this novel virus is vital.

Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus

Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.

Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes

Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.

Identification of an astrovirus commonly infecting laboratory mice in the US and Japan

Mice (Mus musculus) are the most commonly used laboratory animals. Viral metagenomics on tissues of immunodeficient mice revealed sequences of a novel mammalian astrovirus. Using PCR, we screened mice from 4 breeders, 4 pharmaceutical companies, 14 research institutes and 30 universities in the US and Japan. Mice from one US breeder tested positive while none from Japanese breeders were positive for MuAstV. Mice in over half of the universities (19/30), institutes (7/14) and pharmaceutical animal facilities (2/4) investigated revealed the presence of MuAstV. Nine mice strains tested positive including both immunodeficient strains (NSG, NOD-SCID, NSG-3GS, C57BL6-Timp-3 (-/-), and uPA-NOG) and immunocompetent strains (B6J, ICR, Bash2, BALB/c). Our data indicates that MuAstV has a wide geographical, institutional and host strain distribution. Comparison of the MuAstV RdRp sequences showed numerous mutations indicating ongoing viral divergence in different facilities. This study demonstrates the need for metagenomic screening of laboratory animals to identify adventitious infections that may affect experimental outcomes.