Complete nucleotide sequences of two RNA segments of human picobirnavirus

Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts

The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests that these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing Picobirnavirus genera that we tentatively name 'Alpha-', 'Beta-', 'Gamma-', 'Delta-', 'Epsilon-', 'Zeta-', and 'Etapicobirnavirus'. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in Picobirnavirus genomes than in the two groups of established RNA bacteriophage-the Leviviricetes and Cystoviridae. Overall, our findings support the hypothesis that the Picobirnaviridae have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.

Circulation of picobirnavirus in Neotropical free-ranging mammals

Picobirnavirus (PBV) is a family of non-enveloped double-stranded RNA viruses with bisegmented genomes. Segment 1 encodes the capsid protein and segment 2 encodes RNA-dependent RNA polymerase. They exhibit high genomic heterogeneity and infect a wide range of vertebrate hosts, including humans. The objective of this study was to expand our knowledge of the circulation of PBV in free-living animals from two regions (Brazil and Argentina) of the Atlantic Forest. Fecal samples were analyzed from free-living animals: tapir, brocket deer, peccary, and different species of rodents and marsupials. A total of 133 samples were collected and analyzed by RT-PCR, of which 44 (33.08%) were PBV-positive. Nine amplicons were sequenced, five species from Argentina and four from Brazil, and phylogenetic analysis was performed. The nucleotide and amino acid identities of the PBV strains detected in animals from Argentina and Brazil were between 66.3% and 82.5% and between 55.3% and 74.2%, respectively. The analysed strains presented conserved nucleotide blocks without distinction of the host species. The phylogenetic tree showed that PBV strains from Atlantic Forest animals belonging to genogroup I were grouped into different clusters, without defining groups according to host species (human or animal) or the geographical area of detection. This is the first study on PBV in free-living animals in the Atlantic Forest. Our analysis suggested that PBV strains can infect different animal species, leading to PBV transmission between animals and humans. This reinforces the hypothesis of previous crossover points in the ecology and evolution of heterologous PBV strains.

RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters

In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.

Picobirnaviruses in animals: a review

Picobirnaviruses (PBVs) are small non enveloped viruses with bi-segmented ds RNA. They have been observed in a wide variety of vertebrates, including mammals and birds with or without diarrhoea, as well as in sewage samples since its discovery (1988). The source of the viruses is uncertain. True hosts of PBVs and their role as primary pathogens or secondary opportunistic agents or innocuous viruses in the gut remains alien. The mechanisms by which they play a role in pathogenicity are still unclear based on the fact that they can be found in both symptomatic and asymptomatic cases. There is a need to determine their tropism since they have not only been associated with viral gastroenteritis but also been reported in the respiratory tracts of pigs. As zoonotic agents with diverse hosts, the importance of epidemiological and surveillance studies cannot be overstated. The segmented genome of PBV might pose a serious public health issue because of the possibility of continuous genetic reassortment. Aware of the growing attention being given to emerging RNA viruses, we reviewed the current knowledge on PBVs and described the current status of PBVs in animals.

Molecular characterization of picobirnaviruses in small ruminants with diarrhea in Turkey

Picobirnaviruses (PBVs), detected in a wide range of host species, are viruses of which limited information is available about their pathogenic potential, ecology, or evolutionary characteristics. In this study, a molecular analysis of segment 2 encoding the PBV RNA-dependent RNA-polymerase (RdRp) in small ruminants with diarrhea in Turkey was undertaken. A total of 66 fecal samples or gut contents from diarrheic small ruminants including 55 sheep and 11 goats were screened. Four samples (6.06%), obtained from sheep in different farms, yielded the expected amplicon size for the genogroup I RdRp gene fragment, whereas no positivity was detected for genogroup II PBVs. Phylogenetic analysis revealed high levels of genetic diversity among the genogroup I PBVs. Additionally, all PBV infected sheep were also positive for rotavirus A. This study, reporting the presence of the PBVs in sheep Turkey for the first time, contributes to the molecular characterization and epidemiology of PBVs.

Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species

Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.

Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness

Picobirnaviruses (PBV) are found in a wide range of hosts and typically associated with gastrointestinal infections in immunocompromised individuals. Here, a divergent PBV genome was assembled from a patient hospitalized for acute respiratory illness (ARI) in Colombia. The RdRp protein branched with sequences previously reported in patients with ARI from Cambodia and China. Sputa from hospitalized individuals (n = 130) were screened by RT-qPCR which enabled detection and subsequent metagenomic characterization of 25 additional PBV infections circulating in Colombia and the US. Phylogenetic analysis of RdRp highlighted the emergence of two dominant lineages linked to the index case and Asian strains, which together clustered as a distinct genotype. Bayesian inference further established capsid and RdRp sequences as both significantly associated with ARI. Various respiratory-tropic pathogens were detected in PBV+ patients, yet no specific bacteria was common among them and four individuals lacked co-infections, suggesting PBV may not be a prokaryotic virus nor exclusively opportunistic, respectively. Competing models for the origin and transmission of this PBV genotype are presented that attempt to reconcile vectoring by a bacterial host with human pathogenicity. A high prevalence in patients with ARI, an ability to reassort, and demonstrated global spread indicate PBV warrant greater public health concern.

High Prevalence of Genogroup I and Genogroup II Picobirnaviruses in Dromedary Camels

Picobirnaviruses (PBVs) are small non-enveloped bisegmented double-stranded RNA viruses found in humans, mammals, and birds. Increasing molecular epidemiology studies suggest a high sequence diversity of PBVs in numerous hosts and the environment. In this study, using 229 fecal samples from dromedary camels in Dubai, 52.8% were positive for PBVs, of which 77.7% and 41.3% were positive for genogroup I and II, respectively, and 19.0% were positive for both genotypes. Phylogenetic analysis showed high diversity among the sequences of genogroup I and II dromedary PBVs. Marked nucleotide polymorphisms were observed in 75.5% and 46.0% of genogroup I and II RNA-dependent RNA polymerase (RdRp) sequences, respectively, suggesting the co-existence of multiple strains in the same specimen. Both high genetic diversity and prevalence of genogroup I and II PBV in dromedaries were observed. In fact, the prevalence of genogroup II PBV in dromedaries is the highest among all animals to date. The complete/near-complete core genomes of five genogroup I and one genogroup II dromedary PBVs and partial segment 1 and 2 of both genotypes were also sequenced. The dromedary PBV genome organizations were similar to those of other animals. Genetic reassortment and mutation are both important in the ecology and evolution of PBVs.

The True Host/s of Picobirnaviruses

Picobirnaviruses (PBVs) are bisegmented double-stranded RNA viruses that have been detected in a wide variety of animal species including invertebrates and in environmental samples. Since PBVs are ubiquitous in feces/gut contents of humans and other animals with or without diarrhea, they were considered as opportunistic enteric pathogens of mammals and avian species. However, the virus remains to be propagated in animal cell cultures, or in gnotobiotic animals. Recently, the classically defined prokaryotic motif, the ribosomal binding site sequence, has been identified upstream of putative open reading frame/s in PBV and PBV-like sequences from humans, various animals, and environmental samples, suggesting that PBVs might be prokaryotic viruses. On the other hand, based on the detection of some novel PBV-like RNA-dependent RNA polymerase sequences that use the alternative mitochondrial genetic code (that of mold or invertebrates) for translation, and principal component analysis of codon usage bias for these sequences, it has been proposed that PBVs might be fungal viruses with a lifestyle reminiscent of mitoviruses. These contradicting observations warrant further studies to ascertain the true host/s of PBVs, which still remains controversial. In this minireview, we have focused on the various findings that have raised a debate on the true host/s of PBVs.

Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus

Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and replication. This ubiquitous capsid remains structurally undisturbed throughout the viral cycle, isolating the genome to avoid triggering host defense mechanisms. Human picobirnavirus (hPBV) is a dsRNA virus frequently associated with gastroenteritis, although its pathogenicity is yet undefined. Here, we report the cryo-electron microscopy (cryo-EM) structure of hPBV at 2.6-Å resolution. The capsid protein (CP) is arranged in a single-shelled, ∼380-Å-diameter T=1 capsid with a rough outer surface similar to that of dsRNA mycoviruses. The hPBV capsid is built of 60 quasisymmetric CP dimers (A and B) stabilized by domain swapping, and only the CP-A N-terminal basic region interacts with the packaged nucleic acids. hPBV CP has an α-helical domain with a fold similar to that of fungal partitivirus CP, with many domain insertions in its C-terminal half. In contrast to dsRNA mycoviruses, hPBV has an extracellular life cycle phase like complex reoviruses, which indicates that its own CP probably participates in cell entry. Using an in vitro reversible assembly/disassembly system of hPBV, we isolated tetramers as possible assembly intermediates. We used atomic force microscopy to characterize the biophysical properties of hPBV capsids with different cargos (host nucleic acids or proteins) and found that the CP N-terminal segment not only is involved in nucleic acid interaction/packaging but also modulates the mechanical behavior of the capsid in conjunction with the cargo.IMPORTANCE Despite intensive study, human virus sampling is still sparse, especially for viruses that cause mild or asymptomatic disease. Human picobirnavirus (hPBV) is a double-stranded-RNA virus, broadly dispersed in the human population, but its pathogenicity is uncertain. Here, we report the hPBV structure derived from cryo-electron microscopy (cryo-EM) and reconstruction methods using three capsid protein variants (of different lengths and N-terminal amino acid compositions) that assemble as virus-like particles with distinct properties. The hPBV near-atomic structure reveals a quasisymmetric dimer as the structural subunit and tetramers as possible assembly intermediates that coassemble with nucleic acids. Our structural studies and atomic force microscopy analyses indicate that hPBV capsids are potentially excellent nanocages for gene therapy and targeted drug delivery in humans.

Picobirnaviruses: prevalence, genetic diversity, detection methods

This article presents a general overview of the prevalence, genetic diversity and detection methods of picobirnaviruses (PBVs), which are small, non-enveloped icosahedral viruses with a segmented double-stranded RNA genome consisting of two segments taxonomically related to the genus Picobirnavirus of the family Picobirnaviridae. This review of scientific papers published in 1988-2019 provides data on the PBV distribution in the nature and a broad host range. PBV infection is characterized as opportunistic, the lack of understanding of the etiological role of PBVs in diarrhea is emphasized, since these viruses are detected both in symptomatic and asymptomatic cases. The concept of PBV infection as a chronic disease caused by a long-lasting persistence of the virus in the host is considered. Such factors as stress syndrome, physiological conditions, immune status and host age at the time of primary PBV infection influence the virus detection rate in humans and animals. The possible zoonotic nature of human PBV infection is noted due to the capacity for interspecies PBV transmission acquired during evolution as a result of the reassortment of the genome segments of different viruses infecting the same host. Data providing evidence that PBVs belong to eukaryotes and a challenging hypothesis stating that PBVs are bacterial viruses are presented. The need to intensify work on PBV detection because of their wide distribution, despite the complexity due to the lack of the cultivation system, is emphasized. Two strategies of RT-PCR as main PBV detection methods are considered. The genomes of individual representatives of the genus isolated from different hosts are characterized. Emphasis is placed on the feasibility of developing primers with broader specificity for expanding the range of identifiable representatives of the genus PBV due to a huge variety of their genotypes. The importance of effective monitoring of PBV prevalence for studying the zoonotic and anthroponotic potential using metagenomic analysis is highlighted, and so is the possibility of using PBV as a marker for environmental monitoring.

Detection and Molecular Characterization of Picobirnaviruses (PBVs) in the Mongoose: Identification of a Novel PBV Using an Alternative Genetic Code

We report high rates of detection (35.36%, 29/82) of genogroup-I (GI) picobirnaviruses (PBVs) in non-diarrheic fecal samples from the small Indian mongoose (Urva auropunctata). In addition, we identified a novel PBV-like RNA-dependent RNA polymerase (RdRp) gene sequence that uses an alternative mitochondrial genetic code (that of mold or invertebrate) for translation. The complete/nearly complete gene segment-2/RdRp gene sequences of seven mongoose PBV GI strains and the novel PBV-like strain were obtained by combining a modified non-specific primer-based amplification method with conventional RT-PCRs, facilitated by the inclusion of a new primer targeting the 3′-untranslated region (UTR) of PBV gene segment-2. The mongoose PBV and PBV-like strains retained the various features that are conserved in gene segment-2/RdRps of other PBVs. However, high genetic diversity was observed among the mongoose PBVs within and between host species. This is the first report on detection of PBVs in the mongoose. Molecular characterization of the PBV and PBV-like strains from a new animal species provided important insights into the various features and complex diversity of PBV gene segment-2/putative RdRps. The presence of the prokaryotic ribosomal binding site in the mongoose PBV genomes, and analysis of the novel PBV-like RdRp gene sequence that uses an alternative mitochondrial genetic code (especially that of mold) for translation corroborated recent speculations that PBVs may actually infect prokaryotic or fungal host cells.

Waterborne Transmission of Enteric Viruses and Their Impact on Public Health

Viruses of human or animal origin can spread in the environment and infect people via water and food. These viruses are released into the environment by various routes including water runoffs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters.

Viruses are emerging pathogens and are able to adapt by mutation, recombination, and reassortment and can thus become able to infect new hosts and to adjust to new environments. Enteric viruses are among the commonest and most hazardous waterborne pathogens, causing both sporadic and outbreak-related illness.

While considerable research has documented the risk of enteric viruses to human health from contact with contaminated water, the current bacterial indicator-based methods for the evaluation of water quality are often ineffectual proxies for pathogenic viruses, but no correlation was established between the enteric bacteria and viruses studied.

The present chapter will focus on viral pathogens shown to be transmitted through water. It will also provide an overview of viruses that had not been a concern for waterborne transmission in the past, but that may represent potentially emerging waterborne pathogens due to their occurrence and persistence in water environments.

Monitoring effluents from wastewater treatment plants is important to preventing both environmental contamination and the spread of disease.

Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity

Picobirnaviruses (PBVs) are mostly found in animal alimentary samples. In this study, among 576 respiratory specimens from 476 mammals and 100 chickens, genogroup I PBVs were detected in three cattle and three monkeys, and a genogroup II PBV-positive sample was collected from one cattle specimen. More than one PBV sequence type was observed in two and one genogroup I PBV-positive samples from cattle and monkeys, respectively. Twenty-four complete/near-complete segments 2 (nine from respiratory and 15 from alimentary samples) from the cattle and monkey genogroup I PBVs and one complete segment 2 from the cattle genogroup II PBV were sequenced. Similar to other studies, the cattle PBVs also showed a high diversity. In contrast, the monkey PBVs observed in this study were clustered into three distinct clades. Within each clade, all the sequences showed >99% amino acid identities. This unique phenomenon is probably due to the fact that monkeys in our locality reside in separated troops with minimal inter-troop contact.

Epidemiologic Status of Picobirnavirus in India, A Less Explored Viral Disease

Since the unexpected discovery of picobirnaviruses (PBV) in 1988, they have been reported in many animals including mammals and birds, which comprises both terrestrial and marine species. Due to their divergent characteristics to other viral taxa they are classified into a new family Picobirnaviridae. Although their pathogenicity and role in causing diarrhea still remains a question since they have been discovered in symptomatic and asymptomatic cases both. Recent studies employing state-of-art molecular tools have described their presence in various clinical samples, like stool samples from different mammals and birds, respiratory tracts of pigs and humans, sewage water, different foods, etc. Furthermore, their epidemiological status from different parts of the world in different hosts has also increased. Due to their diverse host and irregular host pattern their role in causing diarrhea remains alien. The heterogeneity nature can be ascribed to segmented genome of PBV, which renders them prone to continuous reassortment. Studies have been hampered on PBVs due to their non-adaptability to cell culture system. Here, we describe the molecular epidemiological data on PBVs in India and discusses the overall status of surveillance studies carried out till date in India.

Multiple divergent picobirnaviruses with functional prokaryotic Shine-Dalgarno ribosome binding sites present in cloacal sample of a diarrheic chicken

Picobirnaviruses (PBVs) of family Picobirnaviridae have bisegmented (S1 and S2 segments), double-stranded RNA genomes. In this study a total of N = 12 complete chicken PBVs (ChPBV) segments (N = 5 of S1 and N = 7 of S2, Acc. Nos.: MH425579-90) were determined using viral metagenomic and RT-PCR techniques from a single cloacal sample of a diarrheic chicken. The identified ChPBV segments are unrelated to each other and distant from all of the currently known PBVs. In silico sequence analyses revealed the presence of conserved prokaryotic Shine-Dalgarno-like (SD-like) sequences upstream of the three presumed open reading frames (ORFs) of the S1 and a single presumed ORF of the S2 segments. According to the results of expression analyses in E. coli using 6xHis-tagged recombinant ChPBV segment 1 construct and Western blot these SD-like sequences are functional in vivo suggesting that S1 of study PBVs can contain three ORFs and supporting the bacteriophage-nature of PBVs.

Molecular characterization of a novel picobirnavirus in a chicken

Picobirnaviruses (PBVs) are bisegmented viruses with a wide geographical and host species distribution. The number of novel PBV sequences has been increasing with the help of the viral metagenomics. A novel picobirnavirus strain, pbv/CHK/M3841/HUN/2011, was identified by viral metagenomics; the complete segment 1 (MH327933) and 2 (MH327934) sequences were obtained by RT-PCR from a cloacal sample of a diseased broiler breeder pullet in Hungary. Although the conserved nucleotide (e.g., ribosome binding site) and amino acid motifs (e.g., ExxRxNxxxE, S-domain of the viral capsid and motifs in the RNA-dependent RNA polymerase) were identifiable in the chicken picobirnavirus genome, the putative segment 1 showed low (< 30%) amino acid sequence identity to the corresponding proteins of marmot and dromedary PBVs, while segment 2 showed higher (< 70%) amino acid sequence identity to a wolf PBV protein sequence. This is the first full-genome picobirnavirus sequence from a broiler breeder chicken, but the pathogenicity of this virus is still questionable.

High detection rates of picobirnaviruses in free roaming rats (Rattus spp.): Molecular characterization of complete gene segment-2

We report here high rates of detection (54%, 21/39) of picobirnaviruses (PBVs) in feces/intestinal contents of free roaming, apparently healthy rats (Rattus spp.) on the Caribbean island of St. Kitts. One of the PBV strains, strain PBV/Rat/KNA/Rat9/2017, was molecularly characterized for complete gene segment-2. To determine the nucleotide (nt) sequence of full-length gene segment-2, the 5'- and 3'- portions of gene segment-2 of strain Rat9 containing an overlapping region were amplified using a non-specific primer-based amplification method with modifications. The complete gene segment-2 of PBV strain Rat9 was 1730 bp in length, encoding a putative RNA-dependent RNA polymerase (RdRp) of 535 amino acid (aa). By nt and deduced aa sequence identities and phylogenetic analysis, the complete gene segment-2 of strain Rat9 exhibited high genetic diversity with those of PBVs from other host species. On the other hand, 5'- and 3'- end nt sequences of gene segment-2, and the three domains of putative RdRp that are conserved in PBVs were retained in strain Rat9. To our knowledge, this is the first report on molecular characterization of complete gene segment-2 of a PBV strain from Rattus spp., providing important insights into the putative RdRp, and genetic diversity and evolution of PBV in rats. The high detection rates of PBV in free roaming rats on St. Kitts emphasizes the importance of further studies on epidemiology and genetic makeup of PBVs in Rattus spp.

High detection rate and genetic diversity of picobirnavirus in a sheep flock in Brazil

This study reports the detection by RT-PCR and molecular characterization of partial RdRp gene of picobirnavirus (PBV) dsRNA in fecal samples (n = 100) from a meat sheep flock in southern Brazil. The analysis of the results allowed the identification of two important characteristics of PBV infection. The first was the high frequency of infection in the sheep flock evaluated where 62% of the analyzed fecal samples were PBV-positive. The second was the high genetic variability found in field strains of ovine PBV genogroup I circulating in animals of the same sheep flock.

Marmota himalayana in the Qinghai-Tibetan plateau as a special host for bi-segmented and unsegmented picobirnaviruses

Wildlife has been considered the main source of novel viruses causing emerging infectious diseases. Marmota himalayana is endemic to the Qinghai–Tibetan Plateau, China. Here, based on a high-throughput method using Illumina RNA sequencing, we studied the RNA virome of M. himalayana and discovered multiple novel viruses, especially picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae. A total of 63% of the viral contigs corresponded to PBVs, comprising 274 segment 1 and 56 segment 2 sequences. Unexpectedly, four unsegmented PBV genomes were also detected and confirmed by PCR and resequencing. According to the phylogenetic analysis, the following nine PBV assortment types are proposed: C1:GI, C2:GIV, C4:GI, C4:GV, C5:GI, C7:GI, C8:GIV, C8:GV and C8:GII. We hypothesize a model of segmentation for the PBV genome, mediated by a 6-bp direct repeat sequence, GAAAGG. The model is supported by detection of the segmentation-associated sequence GAAAGG not only in the 5′ untranslated regions of segment 1 (221 in 289) and segment 2 (57 in 80) of bi-segmented PBVs but also in the 5′ untranslated regions and junction sequences between the capsid and RdRp genes of unsegmented PBVs. Therefore, with RNA sequencing, we found an unexpected biodiversity of PBVs in M. himalayana, indicating that M. himalayana is a special host for PBVs. We also proposed a putative model of how bi-segmented PBVs could be converted into unsegmented PBVs, which sheds new light on the processes of RNA virus genome evolution.

Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses

Currently, the Leviviridae and Cystoviridae are the only two recognized families of prokaryotic RNA viruses. Picobirnaviruses, which are bisegmented double-stranded RNA viruses commonly found in animal stool samples, are currently thought to be animal viruses, but have not been propagated in cell culture or in an animal model. We hypothesize that picobirnaviruses are prokaryotic RNA viruses. We identified and analyzed the genomes of 38 novel picobirnaviruses and determined that a classical bacterial sequence motif, the ribosomal binding site (RBS), is present in the 5' untranslated regions (5' UTRs) of all of the novel as well as all previously published picobirnavirus sequences. Among all viruses, enrichment of the RBS motif is only observed in viral families that infect prokaryotes and not in eukaryotic infecting viral families. These results will enable future studies to more accurately understand the biology of picobirnaviruses.

An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus

Advances in Next Generation Sequencing technologies have enabled the generation of millions of sequences from microorganisms. However, distinguishing the sequence of a novel species from sequencing errors remains a technical challenge when the novel species is highly divergent from the closest known species. To solve such a problem, we developed a new method called Optimistic Protein Assembly from Reads (OPAR). This method is based on the assumption that protein sequences could be more conserved than the nucleotide sequences encoding them. By taking advantage of metagenomics, bioinformatics and conventional Sanger sequencing, our method successfully identified all coding regions of the mouse picobirnavirus for the first time. The salvaged sequences indicated that segment 1 of this virus was more divergent from its homologues in other Picobirnaviridae species than segment 2. For this reason, only segment 2 of mouse picobirnavirus has been detected in previous studies. OPAR web tool is available at http://bioinformatics.czc.hokudai.ac.jp/opar/.

Detection of picobirnaviruses in vervet monkeys (Chlorocebus sabaeus): Molecular characterization of complete genomic segment-2

During 2014-2015, 270 fecal samples were collected from non-diarrheic, captive and wild African green monkeys (AGMs) on the island of St. Kitts, Caribbean region. By RNA-PAGE, picobirnaviruses (PBVs) were detected in sixteen captive AGMs. By RT-PCR and sequencing of partial gene segment-2, PBVs in 15 of these 16 samples were assigned to genogroup-I. The full-length nucleotide (nt) sequence of gene segment-2 of one of the genogroup-I PBV strains, strain PBV/African green monkey/KNA/016593/2015, was obtained using a non-specific primer-based amplification method with modifications. Gene segment-2 of strain 016593 was 1707bp long, and encoded a putative RNA-dependent RNA polymerase (RdRp) of 538aa. Furthermore, the nearly complete gene segment-2 sequences of three other AGM PBV strains were determined using primers designed from gene segment-2 sequence of 016593. The gene segment-2 of the 4 AGM PBV strains were almost identical to each other, and exhibited a high degree of genetic diversity (maximum nt and deduced aa sequence identities of 66.4% and 65.3%, respectively) with those of PBVs from other host species. The 5'- and 3'- (except for one mismatch) end nt sequences and the three domains of RdRps were retained in the AGM PBV strains. To our knowledge, this is the first report on detection, and molecular characterization of complete gene segment-2 of PBVs in vervet monkeys. PBVs were detected for the first time from the Caribbean region.

High Diversity of Genogroup I Picobirnaviruses in Mammals

In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs) were positive by RT-PCR targeting the partial RdRp gene in specimens from five cattle, six monkeys, 17 horses, nine pigs, one rabbit, one dog, and 12 California sea lions, with 11, 9, 23, 17, 1, 1, and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4–89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segment 1 (viral loads 1.7 × 10⁴ to 5.9 × 10⁶/ml) and 15 segment 2 (viral loads 4.1 × 10³ to 1.3 × 10⁶/ml) of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1–C4). In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1–R9). In four sea lions, PBVs were detected in two different years, with the same segment 1 clade (C3) present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.

Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus

During the replication cycle of double-stranded (ds) RNA viruses, the viral RNA-dependent RNA polymerase (RdRP) replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 Å resolution structure of an RdRP from the human picobirnavirus (hPBV). In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1) the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2) the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3) RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4) the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP) indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5'-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.

Monthly Distribution of Norovirus and Sapovirus Causing Viral Gastroenteritis in Thailand

A total of 1,141 rotavirus-negative stool specimens collected from diarrheic children in 4 distinct regions under sentinel surveillance in Thailand between 2006 and 2008 were examined by reverse-transcription (RT)-PCR for norovirus (NoV) and sapovirus (SaV). Three hundred 3 specimens (26.6%) were positive for NoV, with 34 and 269 belonging to genogroup I (GI) and genogroup II (GII), respectively. Twelve specimens (1.1%) were positive for SaV. Mixed infections were found in 5 specimens: 3 samples indicated the presence of both NoV GI and GII, and 2 samples indicated the presence of both NoV GII and SaV. Analysis of the monthly distribution of NoV and SaV revealed that NoV GII was clustered between September and February, while NoV GI was detected mainly in June and July; SaV was found in May, June, and July. In addition, 3 outbreaks of acute gastroenteritis at 2 junior high schools in Phichit and Bangkok, and at a university in Phitsanulok, Thailand in 2006 were found to have been caused by NoV infection. Sequence analysis of NoVs from sporadic cases and outbreaks showed them to be genotypes GII.4 and GII.6.

Prevalence and complete genome characterization of turkey picobirnaviruses

The "light turkey syndrome" (LTS), in which birds weigh less than their standard breed character at the marketing time, is believed to be a consequence of viral enteritis at an early age (3-5 weeks) from which the birds never fully recover. In a previously published study, we collected fecal pools from 2, 3, 5 and 8 week old turkey poults (80 pools from LTS farms and 40 from non-LTS farms) and examined them for the presence of astro-, rota-, reo-, and coronaviruses. To determine the presence of additional enteric viruses, we analyzed a fecal pool by Illumina sequencing and found picobirnavirus (PBV). Segments 1 and 2 of this virus shared 45.8%aa and 60.9-64.5%aa identity with genogroup I of human PBV, respectively. Primers based on RNA-dependent RNA polymerase and capsid genes were designed for detection and molecular characterization of PBVs in the 120 fecal pools described above. From LTS farms, 39 of 80 (48.8%) pools were PBV positive while 23 of 40 (57.5%) were positive from non-LTS farms. The phylogenetic analysis of 15 randomly selected strains divided them into four subgroups within genogroup I (subgroups 1A-D). Nine strains were in subgroup IA showing 69.9-76.4%nt identity with human PBV GI strainVS111 from the Netherlands. Strains in subgroup IB (n=2) had 91.4-91.7%nt identity with chicken PBV GI strain AVE 42v1 from Brazil. Two strains in subgroup IC had 72.3-74.2%nt identity with chicken PBV strain AVE 71v3 from Brazil. In subgroup ID, two strains showed 72.4-81.8%nt identity with chicken PBV GI strain AVE 57v2 from Brazil. Subgroup IC and ID were the most divergent. Five of the 15 strains were typed using capsid gene primers. They showed 32.6-33.4%nt and 39.5-41.3%aa identity with VS10 human PBV strain. These results indicate co-circulation of divergent strains of PBVs among Minnesota turkeys.

Maintenance of picobirnavirus (PBV) infection in an adult orangutan (Pongo pygmaeus) and genetic diversity of excreted viral strains during a three-year period

The present work provide data about the maintenance of picobirnavirus (PBV) infection during adulthood in a mammalian host. For this purpose PBV infection was studied in an adult orangutan (Pongo pygmaeus) by PAGE/SS, RT-PCR and nucleotide sequencing. PBV infection in the animal was asymptomatic and was characterized by interspaced silent and high/ low active viral excretion periods. The PBV strains excreted by the studied individual were identified as genogroup I and revealed a nucleotide identity among them of 64-81%. The results obtained allowed to arrive to a deeper understanding of the natural history of PBV infection, which seems to be characterized by new-born, juvenile and adult asymptomatic hosts which persistently excrete closely related strains in their feces. Consequently, picobirnaviruses could be considered frequent inhabitants of the gastrointestinal tract, leaving the question open about the molecular mechanisms governing persistent and asymptomatic coexistence within the host and the potential host suitability to maintain this relationship.

Genome sequencing identifies genetic and antigenic divergence of porcine picobirnaviruses

The full-length genome sequence of a porcine picobirnavirus (PBV) detected in Italy in 2004 was determined. The smaller (S) genome segment was 1730 nt, coding for a putative RNA-dependent RNA polymerase. Two distinct subpopulations of larger (L) genome segment (LA and LB) were identified in the sample, with the sizes ranging from 2351 to 2666 nt. The ORF1, coding for a protein of unknown function, contained a variable number of repetitions of the ExxRxNxxxE motif. The capsid protein-coding ORF2 spanned nt 810–2447 in the LB variants and started at nt 734 in the LA variants. However, a termination codon was present only in one of all the LA segment variants. Three-dimensional modelling of the porcine PBV capsids suggested structural differences in the protruding domain, tentatively involved as antigens in the humoral immune response. Altogether, these findings suggest the simultaneous presence of two different PBV strains sharing the same S segment but displaying genetically diverse L segments. In addition, the sample probably contained a mixture of PBVs with aberrant RNA replication products. Altered structure in the L segments could be tolerated and retained in the presence of functionally integer-cognate genes and represents a mechanism of virus diversification.

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.

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.

VP6 genetic diversity, reassortment, intragenic recombination and classification of rotavirus B in American and Japanese pigs

Rotavirus B (RVB) has been identified as a causative agent of diarrhea in rats, humans, cattle, lambs, and swine. Recently, 20 RVB VP7 genotypes were determined based on an 80% nucleotide percent cut-off value. In this study, we sequenced the RVB VP6 gene segment from 80 RVB positive swine samples from the United States and Japan. Phylogenetic analyses, using the 30 available RVB VP6 sequences from GenBank and our 80 novel RVB VP6 sequences, revealed a large genetic diversity of RVB strains, mainly in pigs. For classification purposes, pairwise identity frequency analyses suggested an 81% nucleotide percent cut-off value, resulting in 13 RVB VP6 (I) genotypes. In addition, an intragenic recombinant RVB VP6 segment was identified from Japan. Furthermore, the data indicates frequent reassortment events occurred between the porcine RVB VP7 and VP6 gene segments.

Divergent picobirnaviruses in human feces

The near-complete genomes of two picobirnaviruses (PBVs) in diarrheal stool samples, human picobirnaviruses D and E (HuPBV-D and -E), were genetically characterized. Their RNA-dependent RNA polymerase (RdRp) protein sequences had <66% identities to known PBVs. Due to a single nucleotide insertion, the open reading frame 2 (ORF2) in segment 1 of HuPBV-D was interrupted by a stop codon. A small stem-loop structure overlying the stop codon may result in translational readthrough into the rest of ORF2.

Animal picobirnavirus

Picobirnavirus (PBV) is a small, non-enveloped, bisegmented double-stranded RNA (dsRNA) virus of vertebrate hosts. The name 'Picobirnavirus' derives from the prefix 'pico' (latin for 'small') in reference to the small virion size, plus the prefix 'bi' (latin for 'two') and the word 'RNA' to indicate the nature of the viral genome. The serendipitous discovery of PBV dates back to 1988 from Brazil, when human fecal samples collected during the acute gastroenteritis outbreaks were subjected for routine rotavirus surveillance by polyacrylamide gel electrophoresis (PAGE) and silver straining (S/S). The PAGE gels after silver staining showed a typical 'two RNA band' pattern, and it was identified as Picobirnavirus. Likewise, the feces of wild black-footed pigmy rice rats (Oryzomys nigripes) subjected for PAGE assay by the same research group in Brazil reported the presence of PBV (Pereira et al., J Gen Virol 69:2749-2754, 1988). PBVs have been detected in faeces of humans and wide range of animal species with or without diarrhoea, worldwide. The probable role of PBV as either a 'primary diarrhoeal agent' in 'immunocompetent children'; or a 'potential pathogen' in 'immunocompromised individuals' or an 'innocuous virus' in the intestine remains elusive and needs to be investigated despite the numerous reports of the presence of PBV in fecal samples of various species of domestic mammals, wild animals, birds and snakes; our current knowledge of their biology, etiology, pathogenicity or their transmission characteristics remains subtle. This review aims to analyse the veterinary and zoonotic aspects of animal Picobirnavirus infections since its discovery.

Novel seadornavirus (family Reoviridae) related to Banna virus in Europe

Banna virus, whose genome is composed of 12 segments of double-stranded RNA, is a member of the genus Seadornavirus in the family Reoviridae and is thought to be an emerging mosquito-transmitted human pathogen in Southeast Asia. A novel phylogenetic relative of Banna virus (Balaton virus, BALV, JX947843-JX947850 and KC522611-KC522612) was identified using viral metagenomics in the intestinal contents of freshwater carp (Cyprinus carpio) in Hungary. The amino acid sequence identity of Balaton virus to homologous proteins of Banna viruses was 25-26 % for segment 12 (VP12) and 61-62 % for segment 1 (VP1), indicating that Balaton virus potentially represents a novel seadornavirus species. This study demonstrates that seadornaviruses are genetically diverse, not restricted geographically to Southeast Asia and present in an aquatic environment.

Detection and molecular characterization of porcine picobirnavirus in feces of domestic pigs from kolkata, India

Picobirnaviruses (PBVs) are small, non-enveloped, 35-41 nm virion with bisegmented double-stranded RNA genome. PBVs are widespread and were detected in feces of humans and a wide variety of animals. Domestic pig, one of the ubiquitous farm animal reported incessant association with a variety of viral zoonoses. The objective of our study is to find out the incidence of PBV infection in healthy domestic pigs. The study was conducted by collecting feces of healthy/asymptomatic pigs from a piggery located in an urban slum at Kolkata, India to detect PBV infections. All the 11 fecal samples were tested by polyacrylamide gel electrophoresis and reverse transcription-polymerase chain reaction assay. In this study, we report the first incidence of detection and molecular characterization of porcine PBV (BG-Por-2/2010 and BG-Por-7/2010) in feces of domestic pigs from India using the human PBV genogroup I specific primer pair: PicoB25(+) and PicoB43(-). Sequence comparison and phylogenetic analysis of partial RNA-dependent RNA polymerase gene of genome segment 2 revealed genetic relatedness to hitherto reported porcine, murine and human genogroup I PBVs from different geographical regions. This warrants a stringent global surveillance to study the potential zoonotic and emerging PBV infections.

Nearly constant shedding of diverse enteric viruses by two healthy infants

Stool samples from two healthy infant siblings collected at about weekly intervals during their first year of life were analyzed by PCR for 15 different enteric viral genera. Adenovirus, Aichi virus, Anellovirus, Astrovirus, Bocavirus, Enterovirus, Parechovirus, Picobirnavirus, and Rotavirus were detected. Not detected were Coronavirus, Cardiovirus, Cosavirus, Salivirus, Sapovirus, and Norovirus. Long-term virus shedding, lasting from one to 12 months, was observed for adenoviruses, anelloviruses, bocaviruses, enteroviruses, parechoviruses, and picobirnaviruses. Repeated administration of oral poliovirus vaccine resulted in progressively shorter periods of poliovirus detection. Four nonpolio enterovirus genotypes were also detected. An average of 1.8 distinct human viruses were found per time point. Ninety-two percent (66/72) of the fecal samples tested contained one to five different human viruses. Two British siblings in the mid-1980s showed nearly constant fecal viral shedding. Our results demonstrate that frequent enteric infections with diverse viruses occur during early childhood in the absence of severe clinical symptoms.

Establishment and maintenance of persistent infection by picobirnavirus in greater rhea (Rhea Americana)

A study aimed to determine the infection model that picobirnavirus (PBV) established in birds was conducted in a farm of greater rheas in Córdoba, Argentina. Analysis of stools collected during a longitudinal study involving seven birds provided evidence that PBV is acquired very early in life and establishes a persistent infection in the host, which is characterized by intermingled periods of high, low and silent viral activity. Genomic analysis indicated that the rheas excreted virus with nucleotide sequence identity between 90.5-100 % and that more than one PBV strain with different electropherotype profiles could be involve in the infection. This report provides the first evidence of persistent infection of PBV in birds. The natural history of PBV infection has begun to be understood, and it appears that asymptomatic PBV-infected mammals and birds could persistently excrete the virus in stool samples, contributing to wide circulation of the virus in the environment.

Complete genome sequence of a novel picobirnavirus, otarine picobirnavirus, discovered in California sea lions

We discovered a novel otarine picobirnavirus in fecal samples of California sea lions. Its genome contains a large segment with two open reading frames (ORFs), ORF1 encoding a putative protein of 163 amino acids with unknown function and ORF2 encoding capsid protein, and a small segment with one ORF encoding RNA-dependent RNA polymerase.

Picobirnavirus in captive animals from Uruguay: identification of new hosts

The Picobirnaviruses (PBVs) have been detected in several species of animals from different countries worldwide, including in South America. The host range of these viruses has increased in recent years; thus, in order to contribute to the knowledge in this topic we analyzed samples from captivity animals from Uruguay. We found the presence of PBVs in four species of animals, Panthera leo, Panthera onca, Puma concolor and Oncifelis geoffroyi, representing new PBV-susceptible hosts. All strains belonged to genogroup I.

Picobirnavirus infections: viral persistence and zoonotic potential

Picobirnaviruses (PBVs) are small, non-enveloped, bisegmented double-stranded RNA genomic viruses of vertebrate hosts. Since their discovery in the late 1980s in clinical specimens from outbreaks of acute gastroenteritis in children, significant efforts have been made to investigate the role of PBV in diarrheic diseases. PBV has been detected in sporadic episodes of diarrhea as sole pathogen or coinfection as well as in outbreaks of acute gastroenteritis and in immunocompromised patients with diarrhea. However, PBV is frequently detected in non-diarrheic healthy hosts, and prolonged shedding has been observed in some individuals. Of interest, similar patterns of PBV infection have also been observed in pigs and other animal hosts. The increasing amount of PBV sequence data gathered from molecular epidemiological studies has evidenced a great sequence diversity of PBVs in various hosts and environmental samples. Importantly, evidence has been found for genetic relatedness between human and animal PBV strains, suggesting extant crossing points in the ecology and evolution of heterologous PBV strains. At present, no cell culture and animal model exists for PBVs. Well-structured epidemiological studies are still the only alternative to demonstrate the potential etiological role of PBVs in acute gastroenteritis or other diseases. This review aims to analyze the public health aspects of PBV infection, especially its possible association with zoonosis.

Porcine rotavirus closely related to novel group of human rotaviruses

We determined nucleotide sequences and inferred amino acid sequences of viral protein (VP) 4, VP6, VP7, and nonstructural protein 4 genes of a porcine rotavirus strain (SKA-1) from Japan. The strain was closely related to a novel group of human rotavirus strains (B219 and J19).

Genetic divergence and classification of non-structural protein 1 among porcine rotaviruses of species B

Porcine rotavirus B (RVB) has frequently been detected in diarrhoea of suckling and weaned pigs. Moreover, epidemiological studies using ELISA have demonstrated high antibody prevalence in sera from sows, indicating that RVB infections are widespread. Because it is difficult to propagate RVBs serially in cell culture, genetic analysis of RNA segments of porcine RVBs other than those encoding VP7 and NSP2 has been scarcely performed. We conducted sequence and phylogenetic analyses focusing on non-structural protein 1 (NSP1), using 15 porcine RVB strains isolated from diarrhoeic faeces collected around Japan. Sequence analysis showed that the porcine NSP1 gene contains two overlapping ORFs. Especially, peptide 2 of NSP1 retains highly conserved cysteine and histidine residues among RVBs. Comparison of NSP1 nucleotide and deduced amino acid sequences from porcine RVB strains demonstrated low identities to those from other RVB strains. Phylogenetic analysis of RVB NSP1 revealed the presence of murine, human, ovine, bovine and porcine clusters. Furthermore, the NSP1 genes of porcine RVBs were divided into three genotypes, suggesting the possibility that porcine species might be an original host of RVB infection. Of nine strains common to those used in our previous study, only one strain was classified into a different genotype from the others in the analysis of VP7, in contrast to the analysis of NSP1, where all belonged to the same cluster. This fact suggests the occurrence of gene reassortment among porcine RVBs. These findings should provide more beneficent information to understand the evolution and functions of RVBs.