Genogroup I picobirnavirus in diarrhoeic foals: can the horse serve as a natural reservoir for human infection?
TL;DR: A PBV strain, PBV/Horse/India/BG-Eq-3/2010, was identified in the faeces of a 10 month old weaned female foal with diarrhoea in January 2010 from Kolkata, India and sequence comparison and phylogenetic analysis revealed close genetic relatedness to a human genogroup IPBV strain detected earlier from the same part of India.
Abstract: Picobirnaviruses (PBV) are small, non-enveloped viruses with a bisegmented double-stranded RNA genome. In this study a PBV strain, PBV/Horse/India/BG-Eq-3/2010, was identified in the faeces of a 10 month old weaned female foal with diarrhoea in January 2010 from Kolkata, India. Surprisingly, sequence comparison and phylogenetic analysis of a short stretch of the RNA dependent RNA polymerase gene revealed close genetic relatedness (> 98% nucleotide identity) to a human genogroup I PBV strain (Hu/GPBV1) detected earlier from the same part of India. Our observations together with earlier findings on genetic relatedness between human and animal PBV warrant further studies on zoonotic potential.
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TL;DR: Recently, 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.
Abstract: 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.
29 citations
TL;DR: The identification of novel RNA viruses and their genetic diversity increases knowledge about viruses that are associated with stools of wild gorillas and contributes to the initiatives in the search for potential emerging zoonotic viruses.
Abstract: Most of the emerging infectious diseases reported so far originated in wildlife. Therefore, virological surveillance of animals and particularly great apes is of great interest to establish the repertory of viruses associated with healthy hosts. This will further help to identify the emergence of new viruses and predict the possibility of interspecies transmission. In this study, we performed shotgun viral metagenomics on stool samples collected from seventeen free-living wild gorillas from the Republic of the Congo. The analysis revealed the presence of novel RNA viruses (picobirnaviruses, partitivirus, and Picornavirales (posa-like and dicistrovirus-like viruses)). Among these, picobirnavirus-related sequences were abundantly covered in the stools. Based on genetic variations both in capsid and RdRp proteins of picobirnaviruses, at least 96 variants were identified and most of them were novel. Among the 96, 22 variants had a nearly complete genome or segment. A comprehensive sequence analysis identified a potential new genogroup/genetic cluster and the presence of a short linear amino acid motif (ExxRxNxxxE) in a hypothetical protein. The sequence analysis of posa-like virus and dicistrovirus showed that these two viruses were novel members in the respective viral families. In conclusion, the identification of novel RNA viruses and their genetic diversity increases our knowledge about viruses that are associated with stools of wild gorillas and contributes to the initiatives in the search for potential emerging zoonotic viruses.
24 citations
TL;DR: 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.
Abstract: 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 5 cattle, 6 monkeys, 17 horses, 9 pigs, 1 rabbit, 1 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 to 89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segments 1 (viral loads 1.7×104 to 5.9×106/ml) and 15 segments 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 to C4). In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1 to 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.
22 citations
TL;DR: 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.
Abstract: A study aimed to determine the infection model that picobirnavirus (PBV) established in birds was conducted in a farm of greater rheas in Cordoba, 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.
21 citations
TL;DR: Three-dimensional modelling of the porcine PBV capsids suggested structural differences in the protruding domain, tentatively involved as antigens in the humoral immune response and represents a mechanism of virus diversification.
Abstract: 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
18 citations
Cites background from "Genogroup I picobirnavirus in diarr..."
...Whilst the list of host species recorded with PBV infections has increased continuously (Fregolente et al., 2009; Gallimore et al., 1995; Ganesh et al., 2011; Ghosh et al., 2009; Gillman et al., 2013; Green et al., 1999; Haga et al., 1999; Malik et al., 2011; Masachessi et al., 2007, 2012; Pereira…...
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...Whilst the list of host species recorded with PBV infections has increased continuously (Fregolente et al., 2009; Gallimore et al., 1995; Ganesh et al., 2011; Ghosh et al., 2009; Gillman et al., 2013; Green et al., 1999; Haga et al., 1999; Malik et al., 2011; Masachessi et al., 2007, 2012; Pereira et al., 1988; Wang et al., 2007; Woo et al., 2012), an association of PBV infection with enteric or respiratory diseases has not formally been demonstrated....
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...Given that PBV is frequently found in wastewater and surface water, a water-borne route of transmission has been also suggested (Ganesh et al., 2011)....
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...Transmission of PBV from one host species to another has been suggested in molecular epidemiological and strain characterization studies, based on very close genetic relatedness between human and porcine or human and equine PBV strains (Bányai et al., 2008; Ganesh et al., 2011; Giordano et al., 2011)....
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...…of PBV from one host species to another has been suggested in molecular epidemiological and strain characterization studies, based on very close genetic relatedness between human and porcine or human and equine PBV strains (Bányai et al., 2008; Ganesh et al., 2011; Giordano et al., 2011)....
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References
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TL;DR: A rapid simple technique based on the sensitive detection of rotavirus double-stranded RNA genome segments separated in polyacrylamide gels, which is comparable with that of electron microscopy or enzyme-linked immunosorbent assay.
Abstract: A rapid simple technique for the diagnosis of rotavirus has been developed based on the sensitive detection of rotavirus double-stranded RNA genome segments separated in polyacrylamide gels. The method utilizes a recently described ultrasensitive silver stain for polypeptides, which can also detect subnanogram amounts of nucleic acid. The sensitivity of the technique is comparable with that of electron microscopy or enzyme-linked immunosorbent assay.
834 citations
"Genogroup I picobirnavirus in diarr..." refers methods in this paper
...From 10% fecal suspensions, total RNA was extracted for PAGE and silver staining [14,31]....
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...The detection of the bisegmented dsRNA genome of PBV by polyacrylamide gel electrophoresis (PAGE) and silver staining [31], is one of the standard and reliable laboratory diagnoses....
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TL;DR: The most abundant fecal virus in this study was pepper mild mottle virus (PMMV), which was found in high concentrations—up to 109 virions per gram of dry weight fecal matter, indicating that this plant virus is prevalent in the human population.
Abstract: The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy humans has not been described. Here, we present a comparative metagenomic analysis of the RNA viruses found in three fecal samples from two healthy human individuals. For this study, uncultured viruses were concentrated by tangential flow filtration, and viral RNA was extracted and cloned into shotgun viral cDNA libraries for sequencing analysis. The vast majority of the 36,769 viral sequences obtained were similar to plant pathogenic RNA viruses. The most abundant fecal virus in this study was pepper mild mottle virus (PMMV), which was found in high concentrations—up to 109 virions per gram of dry weight fecal matter. PMMV was also detected in 12 (66.7%) of 18 fecal samples collected from healthy individuals on two continents, indicating that this plant virus is prevalent in the human population. A number of pepper-based foods tested positive for PMMV, suggesting dietary origins for this virus. Intriguingly, the fecal PMMV was infectious to host plants, suggesting that humans might act as a vehicle for the dissemination of certain plant viruses.
648 citations
"Genogroup I picobirnavirus in diarr..." refers background in this paper
...The lack of a consistent pattern in PBV detection concomitantly in healthy [27] and diarrhoeic individuals and animal species raises questions regarding the pathogenic potential of PBV, albeit they have been often implicated in opportunistic infections in immunocompromised patients [28-30]....
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TL;DR: Methods and oligonucleotide primers are described to overcome failures to type G9, G 10 and P[11] rotavirus strains, and cross-reactivity identified between G10 and G3 rotaviruses.
411 citations
"Genogroup I picobirnavirus in diarr..." refers methods in this paper
...(Similarly, RT-PCR assay using the primers [32] targeting the rotavirus VP4 and VP7 genes failed to detect the group A rotavirus)....
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TL;DR: Novel enteric viruses such as astrovirus and picobirnavirus may be more important etiologic agents of diarrhea in HIV-infected patients than previously recognized and may been more common than either bacterial or parasitic enteropathogens.
Abstract: Background Diarrhea occurs frequently among persons with the acquired immunodeficiency syndrome, but the cause often remains unknown. We used a group of diagnostic assays to determine which viruses were etiologic agents of diarrhea in a group of persons infected with the human immunodeficiency virus (HIV). Methods Stool and serum specimens were obtained from HIV-infected patients enrolled in a longitudinal study in Atlanta. Fecal specimens from patients with diarrhea and from control patients without diarrhea were screened by electron microscopy, polyacrylamide-gel electrophoresis, and enzyme immunoassays for rotaviruses, enteric adenoviruses, caliciviruses, picobirnaviruses, and astroviruses. Paired serum samples were tested for antibody responses to Norwalk virus and picobirnavirus. Results Viruses were detected in 35 percent of 109 fecal specimens from patients with diarrhea but in only 12 percent of 113 specimens from those without diarrhea (P<0.001). Specimens from patients with diarrhea were more li...
278 citations
TL;DR: A baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments, and uncovered previously unknown sequence diversity in human picobirnaviruses.
Abstract: Human fecal matter contains a large number of viruses, and current bacterial indicators used for monitoring water quality do not correlate with the presence of pathogenic viruses. Adenoviruses and enteroviruses have often been used to identify fecal pollution in the environment; however, other viruses shed in fecal matter may more accurately detect fecal pollution. The purpose of this study was to develop a baseline understanding of the types of viruses found in raw sewage. PCR was used to detect adenoviruses, enteroviruses, hepatitis B viruses, herpesviruses, morbilliviruses, noroviruses, papillomaviruses, picobirnaviruses, reoviruses, and rotaviruses in raw sewage collected throughout the United States. Adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples and 25% and 33% of final effluent samples, respectively. Enteroviruses and noroviruses were detected in 75% and 58% of raw sewage samples, respectively, and both viral groups were found in 8% of final effluent samples. This study showed that adenoviruses, enteroviruses, noroviruses, and picobirnaviruses are widespread in raw sewage. Since adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples, they are potential markers of fecal contamination. Additionally, this research uncovered previously unknown sequence diversity in human picobirnaviruses. This baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments.
146 citations
"Genogroup I picobirnavirus in diarr..." refers background in this paper
...PBV are commonly detected in communal sewage and surface waters [33], thus consumption of water contaminated with PBV may provide one way to acquire PBV by different host species....
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