The first complete genome sequence of a chicken group A rotavirus indicates independent evolution of mammalian and avian strains

Molecular characterization of an avian rotavirus a strain detected from a large-billed crow (Corvus macrorhynchos) in Japan

Avian rotaviruses A (RVAs) are occasionally transmitted to animals other than the original hosts across species barriers. Information on RVAs carried by various bird species is important for identifying the origin of such interspecies transmission. In this study, to facilitate an understanding of the ecology of RVAs from wild birds, we characterized all of the genes of an RVA strain, JC-105, that was detected in a fecal sample of a large-billed crow (Corvus macrorhynchos) in Japan. All of the genes of this strain except for the VP4 and VP7 genes, which were classified as novel genotypes (P[56] and G40, respectively), were closely related to those of the avian-like RVA strain detected from a raccoon, indicating the possibility that crows had been involved in the transmission of avian RVAs to raccoons. Our findings highlight the need for further viral investigations in wild birds and mammals to understand the mechanisms of avian-to-mammal RVA transmission.

Rotavirus A and D circulating in commercial chicken flocks in southeastern Brazil

Rotavirus (RV) outbreaks can cause significant economic losses in the livestock and poultry industries. Stool samples were collected from asymptomatic laying and broiler chickens from commercial poultry farms in the states of Rio de Janeiro and Espírito Santo in southeastern Brazil for detection of RV species A and D (RVA and RVD, respectively) by reverse transcription polymerase chain reaction. RV was detected in 10.5% (34/325) of samples: 22 (64.7%) were positive for RVA and nine (26.5%) for RVD, while three (8.8%) exhibited coinfections with both viruses. Sequence analysis of a VP6 fragment from seven RVA-positive samples identified the I11 genotype in all samples. Information regarding avian RV epidemiology is still scanty, despite the high prevalence of RV infections in several bird species and subsequent economic impact. Consequently, monitoring infections caused by avian RVs, especially in commercial birds, is essential not only to provide new and relevant information regarding the biology, epidemiology, and evolution of these viruses, but also to facilitate the implementation of preventive measures.

Interspecies transmission of porcine-originated G4P[6] rotavirus A between pigs and humans: a synchronized spatiotemporal approach

As a leading viral cause of acute gastroenteritis in both humans and pigs, rotavirus A (RVA) poses a potential public health concern. Although zoonotic spillover of porcine RVA strains to humans is sporadic, it has been detected worldwide. The origin of chimeric human-animal strains of RVA is closely linked to the crucial role of mixed genotypes in driving reassortment and homologous recombination, which play a major role in shaping the genetic diversity of RVA. To better understand how genetically intertwined porcine and zoonotic human-derived G4P[6] RVA strains are, the present study employed a spatiotemporal approach to whole-genome characterization of RVA strains collected during three consecutive RVA seasons in Croatia (2018-2021). Notably, sampled children under 2 years of age and weanling piglets with diarrhea were included in the study. In addition to samples tested by real-time RT-PCR, genotyping of VP7 and VP4 gene segments was conducted. The unusual genotype combinations detected in the initial screening, including three human and three porcine G4P[6] strains, were subjected to next-generation sequencing, followed by phylogenetic analysis of all gene segments, and intragenic recombination analysis. Results showed a porcine or porcine-like origin for each of the eleven gene segments in all six RVA strains. The G4P[6] RVA strains detected in children most likely resulted from porcine-to-human interspecies transmission. Furthermore, the genetic diversity of Croatian porcine and porcine-like human G4P[6] strains was propelled by reassortment events between porcine and porcine-like human G4P[6] RVA strains, along with homologous intragenotype and intergenotype recombinations in VP4, NSP1, and NSP3 segments. Described concurrent spatiotemporal approach in investigating autochthonous human and animal RVA strains is essential in drawing relevant conclusions about their phylogeographical relationship. Therefore, continuous surveillance of RVA, following the One Health principles, may provide relevant data for assessing the impact on the protectiveness of currently available vaccines.

Zoonotic RVA: State of the Art and Distribution in the Animal World

Rotavirus species A (RVA) is a pathogen mainly affecting children under five years old and young animals. The infection produces acute diarrhea in its hosts and, in intensively reared livestock animals, can cause severe economic losses. In this study, we analyzed all RVA genomic constellations described in animal hosts. This review included animal RVA strains in humans. We compiled detection methods, hosts, genotypes and complete genomes. RVA was described in 86 animal species, with 52% (45/86) described by serology, microscopy or the hybridization method; however, strain sequences were not described. All of these reports were carried out between 1980 and 1990. In 48% (41/86) of them, 9251 strain sequences were reported, with 28% being porcine, 27% bovine, 12% equine and 33% from several other animal species. Genomic constellations were performed in 80% (32/40) of hosts. Typical constellation patterns were observed in groups such as birds, domestic animals and artiodactyls. The analysis of the constellations showed RVA's capacity to infect a broad range of species, because there are RVA genotypes (even entire constellations) from animal species which were described in other studies. This suggests that this virus could generate highly virulent variants through gene reassortments and that these strains could be transmitted to humans as a zoonotic disease, making future surveillance necessary for the prevention of future outbreaks.

Molecular characterisation of a novel avian rotavirus A strain detected from a gull species (Larus sp.)

A recent study demonstrated the possibility that migratory birds are responsible for the global spread of avian rotavirus A (RVA). However, little is known about what types of RVAs are retained in migratory birds. In this study, to obtain information on RVA strains in migratory birds, we characterised an RVA strain, Ho374, that was detected in a faecal sample from a gull species (Larus sp.). Genetic analysis revealed that all 11 genes of this strain were classified as new genotypes (G28-P[39]-I21-R14-C14-M13-A24-N14-T16-E21-H16). This clearly indicates that the genetic diversity of avian RVAs is greater than previously recognised. Our findings highlight the need for investigations of RVA strains retained in migratory birds, including gulls.

Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks

The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases.

OUP accepted manuscript

Species A rotaviruses (RVAs) are important aetiological agents of severe diarrhoea in young children. They are also widely distributed in mammals and birds, and increasing evidence indicates the possibility of zoonotic transmission of RVA strains between animals and humans. Moreover, reassortment of the eleven segments of the RVA genome can result in rapid biological changes and may influence pathogenic properties. Here, the nearly complete genome of an RVA strain from a common shrew (Sorex araneus) was sequenced, which showed high nucleotide sequence similarity to additionally determined partial sequences from common shrew RVAs but only very low identity (below 68 per cent) to RVAs from other animal species and humans. New genotypes were assigned to most genome segments of the novel common shrew RVA strain KS14/269, resulting in the genome constellation G39-P[55]-I27-R26-C22-M22-A37-N26-T26-E30-H26. Phylogenetic analyses clustered the common shrew RVAs as ancestral branches of other mammalian and avian RVAs for most of the genome segments, which is in contrast to the phylogeny of the hosts. Nevertheless, conserved sequences typical for all RVAs were identified at the 5ʹ- and 3ʹ- non-coding segment termini. To explore whether the common shrew RVA can exchange genetic material with other mammalian RVAs by reassortment, a reverse genetics system based on the simian RVA strain SA11 was used. However, no viable reassortants could be rescued by exchanging the VP4-, VP6-, or VP7-encoding genome segment alone or in combinations. It can be concluded that highly divergent RVAs are present in common shrews, indicating an evolution of these viruses largely separated from other mammalian and avian RVAs. The zoonotic potential of the virus seems to be low but needs to be further analysed in future.

Ocurrence of rotavirus and picobirnavirus in wild and exotic avian from amazon forest

The present study reports the occurrence of rotavirus A (RVA), rotavirus D (RVD), rotavirus F (RVF), rotavirus G (RVG), and picobirnavirus (PBV) in fecal specimens of wild (n = 22), and exotic birds (n = 1) from different cities of Pará state. These animals were hospitalized at Veterinary Hospital of the Federal University of Pará, Brazil, in a period from January 2018 to June 2019. The animals exhibited different clinical signs, such as diarrhea, malnutrition, dehydration, and fractures. The results showed 39.1% (9/23) of positivity for RVA by RT-qPCR. Among these, one sample (1/9) for the NSP3 gene of T2 genotype was characterized. About 88.9% (8/9) for the VP7 gene belonging to G1, G3 equine like and G6 genotypes, and 55.5% (5/9) for the VP4 gene of P[2] genotype were obtained. In the current study, approximately 4.5% of the samples (1/23) revealed coinfection for the RVA, RVD and RVF groups. Furthermore, picobirnavirus (PBV) was detected in one of the 23 samples tested, and was classified in the Genogroup I. The findings represent the first report of RVA, RVD, RVF, RVG, and PBV genotypes in wild birds in Brazil, and due to wide distribution it can implies potential impacts of RVs, and PBVs on avian health, and other animals contributing to construction of new knowledge, and care perspectives.

Genome constellations of rotavirus a isolated from avian species in Brazil, 2008-2015

Rotaviruses are members of the family Reoviridae and are a common cause of acute diarrhea in many mammalian and avian species. They are non-enveloped icosahedral particles and their genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). Genotypes are defined based upon the diversity found in these genes and viral characterization plays a central role on epidemiological studies and prevention. Here we investigate the distribution of Brazilian RVAs genotypes in 8 chicken samples collected between 2008 and 2015 from different regions by RT-PCR, partial (Sanger) nucleotide sequencing and phylogenetic analysis from all rotavirus genes. Although the identified genotypes were typical from avian host species, when analyzed together, they form novel genetic constellations: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. This study highlights that avian rotaviruses are widespread among commercial farms in Brazil, and the co-circulation of at least two different genomic constellations indicates that may present a way bigger genetic variability, that can be increased by the possible transmission events from other birds, lack of specific preventive measures, as well as the different viral evolution mechanisms.

Whole genome sequence analysis of cell culture-adapted rotavirus A strains from chicken

Rotavirus A (RVA) is a major cause of gastroenteritis in humans and mammalian animals, and has also been abundantly detected in avian species. Avian RVA infection is associated with diarrhea, reduced growth and increased mortality, leading to economic losses in the poultry industry. Avian RVA forms a unique genetic clade within the whole RVA species. However, up to now, only a few full-length avian RVA genomes have been published and only a small number of avian RVA strains have been adapted to grow in cell culture for subsequent studies. Here, the four cell culture-adapted chicken RVA strains 02V0002G3, 04V0027G6, 05V0500F6 and 06V0661G1 were characterized in more detail. Transmission electron microscopy of the viruses derived from culture supernatant showed a typical triple-layered morphology of rotavirus particles; in addition, strain 06V0661G1 showed a high proportion of double-layered particles. The (nearly) complete genome sequences of the viruses were determined using next-generation sequencing (NGS). The resulting sequences were compared to full-length or partial sequences of the strains previously determined using Sanger sequencing; and a few nucleotide mismatches, some of them resulting in amino acid substitutions, were identified. The genomes of strains 02V0002G3, 04V0027G6 and 05V0500F6 were closely related to each other showing a G19-P[30]-I11-R6-C6-M7-A16-N6-T8-E10-H8 genotype constellation. Strain 06V0661G1 carries the VP4 genotype P[31] in the same genetic backbone like the other strains. However, further sequence analysis showed that the genes of this strain, especially that encoding NSP3, clustered more separately from the other strains in phylogenetic trees. The characterized cell culture-adapted chicken RVA strains may be useful for future studies investigating genetic diversity and replication of avian rotaviruses, as well as for the development of vaccines and diagnostic tools.

Molecular epidemiology of rotavirus A in Iranian broiler flocks

Avian rotaviruses (RV) are still largely undefined despite being widespread in several avian species and significant economic the impact of rotavirus enteritis in poultry flocks. In this study, the presence of avian RV groups was investigated in 36 commercial poultry flocks with a history of enteric diseases in Iran. Intestinal contents of broiler chickens with diarrhea and stunting syndrome were analyzed by reverse transcription-polymerase chain reaction specific for RVs based on NSP4 gene. Through partial sequencing and BLAST analyses of 11 positive specimens, we identified avian-like RV group A (RVA) strain. There was high prevalence of group A rotaviruses (approximately 30%) in our samples. The phylogenetic analysis also revealed a close genetic relationship between the current isolates and other avian RVAs but located in the separate cluster. This study provides novel data on the prevalence of genetically different avian RVs in Iranian poultry flocks.

The C Terminus of Rotavirus VP4 Protein Contains an Actin Binding Domain Which Requires Cooperation with the Coiled-Coil Domain for Actin Remodeling

The interactions between viruses and actin cytoskeleton have been widely studied. We showed that rotaviruses remodel microfilaments in intestinal cells and demonstrated that this was due to the VP4 spike protein. Microfilaments mainly occur in the apical domain of infected polarized enterocytes and favor the polarized apical exit of viral progeny. The present work aims at the identification of molecular determinants of actin-VP4 interactions. We used various deletion mutants of VP4 that were transfected into Cos-7 cells and analyzed interactions by immunofluorescence confocal microscopy. It has been established that the C-terminal part of VP4 is embedded within viral particles when rotavirus assembles. The use of specific monoclonal antibodies demonstrated that VP4 is expressed in different forms in infected cells: classically as spike on the outer layer of virus particles, but also as free soluble protein in the cytosol. The C terminus of free VP4 was identified as interacting with actin microfilaments. The VP4 actin binding domain is unable to promote microfilament remodeling by itself; the coiled-coil domain is also required in this process. This actin-binding domain was shown to dominate a previously identified peroxisomal targeting signal, located in the three last amino acids of VP4. The newly identified actin-binding domain is highly conserved in rotavirus strains from species A, B, and C, suggesting that actin binding and remodeling is a general strategy for rotavirus exit. This provides a novel mechanism of protein-protein interactions, not involving cell signaling pathways, to facilitate rotavirus exit.IMPORTANCE Rotaviruses are causal agents of acute infantile viral diarrhea. In intestinal cells, in vitro as well as in vivo, virus assembly and exit do not imply cell lysis but rely on an active process in which the cytoskeleton plays a major role. We describe here a novel molecular mechanism by which the rotavirus spike protein VP4 drives actin remodeling. This relies on the fact that VP4 occurs in different forms. Besides its structural function within the virion, a large proportion of VP4 is expressed as free protein. Here, we show that free VP4 possesses a functional actin-binding domain. This domain, in coordination with a coiled-coil domain, promotes actin cytoskeleton remodeling, thereby providing the capacity to destabilize the cell membrane and allow efficient rotavirus exit.

Molecular epidemiology of Avian Rotaviruses Group A and D shed by different bird species in Nigeria

Background

Avian rotaviruses (RVs) cause gastrointestinal diseases of birds worldwide. However, prevalence, diversity, epidemiology and phylogeny of RVs remain largely under-investigated in Africa.

Methods

Fecal samples from 349 birds (158 symptomatic, 107 asymptomatic and 84 birds without recorded health status) were screened by reverse transcription PCR to detect RV groups A and D (RVA and RVD). Partial gene sequences of VP4, VP6, VP7 and NSP4 for RVA, and of VP6 and VP7 for RVD were obtained and analyzed to infer phylogenetic relationship. Fisher’s exact test and logistic regression were applied to identify factors potentially influencing virus shedding in chickens.

Results

A high prevalence of RVA (36.1%; 126/349) and RVD (31.8%; 111/349) shedding was revealed in birds. In chickens, RV shedding was age-dependent and highest RVD shedding rates were found in commercial farms. No negative health effect could be shown, and RVA and RVD shedding was significantly more likely in asymptomatic chickens: RVA/RVD were detected in 51.9/48.1% of the asymptomatic chickens, compared to 18.9/29.7% of the symptomatic chickens (p < 0.001/p = 0.01). First RVA sequences were obtained from mallard ducks (Anas platyrhynchos) and guinea fowls (Numida meleagris). Phylogenetic analyses illustrated the high genetic diversity of RVA and RVD in Nigerian birds and suggested cross-species transmission of RVA, especially at live bird markets. Indeed, RVA strains highly similar to a recently published fox rotavirus (RVA/Fox-tc/ITA/288356/2011/G18P[17]) and distantly related to other avian RVs were detected in different bird species, including pigeons, ducks, guinea fowls, quails and chickens.

Conclusion

This study provides new insights into epidemiology, diversity and classification of avian RVA and RVD in Nigeria. We show that cross-species transmission of host permissive RV strains occurs when different bird species are mixed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-017-0778-5) contains supplementary material, which is available to authorized users.

Faecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular ssDNA viruses

This study is focused on the identification of the faecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with blastx revealed that 279 contigs (4 %) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes. In addition, a range of circular replication-associated protein encoding DNA viruses were also identified. The characterization of the faecal virome of healthy chickens described here not only provides a description of the viruses encountered in such niche but should also represent a baseline for future studies comparing viral populations in healthy and diseased chicken flocks. Moreover, it may also be relevant for human health, since chickens represent a significant proportion of the animal protein consumed worldwide.

A candidate packaging signal of human rotavirus differentiating Wa-like and DS-1-like genomic constellations

Rotavirus A (RVA) possesses a genome of 11 segmented RNAs. In human RVA, two major genomic constellations are represented by prototype strains Wa and DS-1. Here packaging signals differentiating Wa-like and DS-1-like genomic constellations were searched for by analyzing genomic sequences of Wa-like and DS-1-like strains. One pair of 11 nucleotide sites in the coding regions of viral structural protein (VP) 2 and VP6 was found to be complementary specifically among Wa-like strains. These sites tended to be free from base-pairing in secondary structures of genomic segments, suggesting that they may serve as a packaging signal in Wa-like strains.

Genome Sequences of Rotavirus A Strains Ty-1 and Ty-3, Isolated from Turkeys in Ireland in 1979

To obtain complete genome sequences of turkey rotavirus A strains Ty-1 and Ty-3, we sequenced the gene segments that had not been decoded previously. The genotype constellations of the respective strains were determined to be G17-P[38]-I4-R4-C4-M4-A16-N4-T4-E4-H4 and G7-P[35]-I4-R4-C4-M4-A16-N4-T4-E11-H14. Notably, their VP4 and NSP5 genes were classified into novel genotypes.

Rotavirus NSP6 localizes to mitochondria via a predicted N-terminal α-helix

Specific roles have been ascribed to each of the 12 known rotavirus proteins apart from the non-structural protein 6 (NSP6). However, NSP6 may be present at sites of viral replication within the cytoplasm. Here we report that NSP6 from diverse species of rotavirus A localizes to mitochondria via conserved sequences in a predicted N-terminal α-helix. This suggests that NSP6 may affect mitochondrial functions during rotavirus infection.

Generation of an Avian-Mammalian Rotavirus Reassortant by Using a Helper Virus-Dependent Reverse Genetics System

The genetic diversity of rotavirus A (RVA) strains is facilitated in part by genetic reassortment. Although this process of genome segment exchange has been reported frequently among mammalian RVAs, it remained unknown if mammalian RVAs also could package genome segments from avian RVA strains. We generated a simian RVA strain SA11 reassortant containing the VP4 gene of chicken RVA strain 02V0002G3. To achieve this, we transfected BSR5/T7 cells with a T7 polymerase-driven VP4-encoding plasmid, infected the cells with a temperature-sensitive SA11 VP4 mutant, and selected the recombinant virus by increasing the temperature. The reassortant virus could be stably passaged and exhibited cytopathic effects in MA-104 cells, but it replicated less efficiently than both parental viruses. Our results show that avian and mammalian rotaviruses can exchange genome segments, resulting in replication-competent reassortants with new genomic and antigenic features.

IMPORTANCE

This study shows that rotaviruses of mammals can package genome segments from rotaviruses of birds. The genetic diversity of rotaviruses could be broadened by this process, which might be important for their antigenic variability. The reverse genetics system applied in the study could be useful for targeted generation and subsequent characterization of distinct rotavirus reassortant strains.

A possible packaging signal in the rotavirus genome

Group A rotavirus (RVA), an etiological agent of gastroenteritis in young mammals and birds, possesses a genome of 11 double-stranded RNA segments. Although it is believed that the RVA virion contains one copy of each genomic segment and that the positive-strand RNA (+RNA) is incorporated into the core shell, the packaging mechanisms of RVA are not well understood. Here, packaging signals of RVA were searched for by analyzing genomic sequences of mammalian and avian RVA, which are considered to have evolved independently without reassortment. Assuming that packaging is mediated by direct interaction between +RNA segments via base-pairing, co-evolving complementary nucleotide sites were identified within and between genomic segments. There were two pairs of co-evolving complementary sites within the segment encoding VP7 (the VP7 segment) and one pair between the NSP2 and NSP3 segments. In the VP7 segment, the co-evolving complementary sites appeared to form stem structures in both mammalian and avian RVA, supporting their functionality. In contrast, co-evolving complementary sites between the NSP2 and NSP3 segments tended to be free from base-pairings and constituted loop structures, at least in avian RVA, suggesting that they are involved in a specific interaction between these segments as a packaging signal.

Avian rotavirus enteritis - an updated review

Rotaviruses (RVs) are among the leading causes of enteritis and diarrhea in a number of mammalian and avian species, and impose colossal loss to livestock and poultry industry globally. Subsequent to detection of rotavirus in mammalian hosts in 1973, avian rotavirus (AvRV) was first reported in turkey poults in USA during 1977 and since then RVs of group A (RVA), D (RVD), F (RVF) and G (RVG) have been identified around the globe. Besides RVA, other AvRV groups (RVD, RVF and RVG) may also contribute to disease. However, their significance has yet to be unraveled. Under field conditions, co-infection of AvRVs occurs with other infectious agents such as astroviruses, enteroviruses, reoviruses, paramyxovirus, adenovirus, Salmonella, Escherichia coli, cryptosporidium and Eimeria species prospering severity of disease outcome. Birds surviving to RV disease predominantly succumb to secondary bacterial infections, mostly E. coli and Salmonella spp. Recent developments in molecular tools including state-of-the-art diagnostics and vaccine development have led to advances in our understanding towards AvRVs. Development of new generation vaccines using immunogenic antigens of AvRV has to be explored and given due importance. Till now, no effective vaccines are available. Although specific as well as sensitive approaches are available to identify and characterize AvRVs, there is still need to have point-of-care detection assays to review disease burden, contemplate new directions for adopting vaccination and follow improvements in public health measures. This review discusses AvRVs, their epidemiology, pathology and pathogenesis, immunity, recent trends in diagnostics, vaccines, therapeutics as well as appropriate prevention and control strategies.

Silencing the alarms: Innate immune antagonism by rotavirus NSP1 and VP3

The innate immune response involves a broad array of pathogen sensors that stimulate the production of interferons (IFNs) to induce an antiviral state. Rotavirus, a significant cause of childhood gastroenteritis and a member of the Reoviridae family of segmented, double-stranded RNA viruses, encodes at least two direct antagonists of host innate immunity: NSP1 and VP3. NSP1, a putative E3 ubiquitin ligase, mediates the degradation of cellular factors involved in both IFN induction and downstream signaling. VP3, the viral capping enzyme, utilizes a 2H-phosphodiesterase domain to prevent activation of the cellular oligoadenylate synthase (OAS)/RNase L pathway. Computational, molecular, and biochemical studies have provided key insights into the structural and mechanistic basis of innate immune antagonism by NSP1 and VP3 of group A rotaviruses (RVA). Future studies with non-RVA isolates will be essential to understand how other rotavirus species evade host innate immune responses.

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Rotavirus NSP1 and VP3 directly antagonize host innate immune pathways.

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NSP1, a putative E3 ubiquitin ligase, mediates turnover of multiple immune factors.

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VP3, the viral capping enzyme, has phosphodiesterase activity to block OAS/RNase L.

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

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

Rotavirus inhibits IFN-induced STAT nuclear translocation by a mechanism that acts after STAT binding to importin-α

The importance of innate immunity to rotaviruses is exemplified by the range of strategies evolved by rotaviruses to interfere with the IFN response. We showed previously that rotaviruses block gene expression induced by type I and II IFNs, through a mechanism allowing activation of signal transducer and activator of transcription (STAT) 1 and STAT2 but preventing their nuclear accumulation. This normally occurs through activated STAT1/2 dimerization, enabling an interaction with importin α5 that mediates transport into the nucleus. In rotavirus-infected cells, STAT1/2 inhibition may limit the antiviral actions of IFN produced early in infection. Here we further analysed the block to STAT1/2 nuclear accumulation, showing that activated STAT1 accumulates in the cytoplasm in rotavirus-infected cells. STAT1/2 nuclear accumulation was inhibited by rotavirus even in the presence of the nuclear export inhibitor Leptomycin B, demonstrating that enhanced nuclear export is not involved in STAT1/2 cytoplasmic retention. The ability to inhibit STAT nuclear translocation was completely conserved amongst the group A rotaviruses tested, including a divergent avian strain. Analysis of mutant rotaviruses indicated that residues after amino acid 47 of NSP1 are dispensable for STAT inhibition. Furthermore, expression of any of the 12 Rhesus monkey rotavirus proteins did not inhibit IFN-stimulated STAT1 nuclear translocation. Finally, co-immunoprecipitation experiments from transfected epithelial cells showed that STAT1/2 binds importin α5 normally following rotavirus infection. These findings demonstrate that rotavirus probably employs a novel strategy to inhibit IFN-induced STAT signalling, which acts after STAT activation and binding to the nuclear import machinery.

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.

Exotic rotaviruses in animals and rotaviruses in exotic animals

Group A rotaviruses (RVA) are a major cause of viral diarrhea in the young of mammals and birds. RVA strains with certain genotype constellations or VP7-VP4 (G-P) genotype combinations are commonly found in a particular host species, whilst unusual or exotic RVAs have also been reported. In most cases, these exotic rotaviruses are derived from RVA strains common to other host species, possibly through interspecies transmission coupled with reassortment events, whilst a few other strains exhibit novel genotypes/genetic constellations rarely found in other RVAs. The epidemiology and evolutionary patterns of exotic rotaviruses in humans have been thoroughly reviewed previously. On the other hand, there is no comprehensive review article devoted to exotic rotaviruses in domestic animals and birds so far. The present review focuses on the exotic/unusual rotaviruses detected in livestock (cattle and pigs), horses and companion animals (cats and dogs). Avian rotaviruses (group D, group F and group G strains), including RVAs, which are genetically divergent from mammalian RVAs, are also discussed. Although scattered and limited studies have reported rotaviruses in several exotic animals and birds, including wildlife, these data remain to be reviewed. Therefore, a section entitled "rotaviruses in exotic animals" was included in the present review.

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.

Recombinant monovalent llama-derived antibody fragments (VHH) to rotavirus VP6 protect neonatal gnotobiotic piglets against human rotavirus-induced diarrhea

Group A Rotavirus (RVA) is the leading cause of severe diarrhea in children. The aims of the present study were to determine the neutralizing activity of VP6-specific llama-derived single domain nanoantibodies (VHH nanoAbs) against different RVA strains in vitro and to evaluate the ability of G6P[1] VP6-specific llama-derived single domain nanoantibodies (VHH) to protect against human rotavirus in gnotobiotic (Gn) piglets experimentally inoculated with virulent Wa G1P[8] rotavirus. Supplementation of the daily milk diet with 3B2 VHH clone produced using a baculovirus vector expression system (final ELISA antibody -Ab- titer of 4096; virus neutralization -VN- titer of 256) for 9 days conferred full protection against rotavirus associated diarrhea and significantly reduced virus shedding. The administration of comparable levels of porcine IgG Abs only protected 4 out of 6 of the animals from human RVA diarrhea but significantly reduced virus shedding. In contrast, G6P[1]-VP6 rotavirus-specific IgY Abs purified from eggs of hyperimmunized hens failed to protect piglets against human RVA-induced diarrhea or virus shedding when administering similar quantities of Abs. The oral administration of VHH nanoAb neither interfered with the host's isotype profiles of the Ab secreting cell responses to rotavirus, nor induced detectable host Ab responses to the treatment in serum or intestinal contents. This study shows that the oral administration of rotavirus VP6-VHH nanoAb is a broadly reactive and effective treatment against rotavirus-induced diarrhea in neonatal pigs. Our findings highlight the potential value of a broad neutralizing VP6-specific VHH nanoAb as a treatment that can complement or be used as an alternative to the current strain-specific RVA vaccines. Nanobodies could also be scaled-up to develop pediatric medication or functional food like infant milk formulas that might help treat RVA diarrhea.

Group A rotavirus (RVA) is the most common cause of severe diarrhea in human infants worldwide. Live-attenuated rotavirus vaccines are available to prevent rotavirus diarrhea in children, although their efficacy in impoverished areas has been questioned, in addition to not being suitable for children suffering from immune deficiencies. Since no rotavirus-specific treatments are available as an alternative, we investigated llama-derived single-chain antibody fragments (VHH) as preventive therapy and a potential treatment option. Gnotobiotic piglets were chosen as an animal model because their gastrointestinal physiology and mucosal immune system resemble that of human infants. We evaluated the broad neutralizing activity of a VHH clone (3B2) to different genotypes of RVA circulating in humans, and tested the efficacy of oral administration of 3B2 VHH as a functional milk to prevent the diarrhea induced by one of the most prevalent human RVA strains (G1P[8]). Supplementation of the milk diet with 3B2 twice a day for 9 days conferred full protection against rotavirus-associated diarrhea and significantly reduced virus shedding in gnotobiotic piglets experimentally inoculated with a human RVA. This study demonstrates the potential application of VHH to prevent rotavirus-induced diarrhea, and suggests that VHHs should be further investigated as a suitable treatment for gastroenteritis.

Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses

Group A rotaviruses (RVAs) are an important cause of diarrhoeal illness in humans, as well as in mammalian and avian animal species. Previous sequence analyses indicated that avian RVAs are related only distantly to mammalian RVAs. Here, the complete genomes of RVA strain 03V0002E10 from turkey (Meleagris gallopavo) and RVA strain 10V0112H5 from pheasant (Phasianus colchicus) were analysed using a combination of 454 deep sequencing and Sanger sequencing technologies. An adenine-rich insertion similar to that found in the chicken RVA strain 02V0002G3, but considerably shorter, was found in the 3′ NCR of the NSP1 gene of the pheasant strain. Most genome segments of both strains were related closely to those of avian RVAs. The novel genotype N10 was assigned to the NSP2 gene of the pheasant RVA, which is related most closely to genotype N6 found in avian RVAs. However, this virus contains a VP4 gene of the novel genotype P[37], which is related most closely to RVAs from pigs, dogs and humans. This strain either may represent an avian/mammalian rotavirus reassortant, or it carries an unusual avian rotavirus VP4 gene, thereby broadening the potential genetic and antigenic variability among RVAs.

Detection of substantial porcine group B rotavirus genetic diversity in the United States, resulting in a modified classification proposal for G genotypes

Rotavirus (RV) is an important cause of gastrointestinal disease in animals and humans. In this study, we developed an RT-PCR to detect RV group B (RVB) and characterized the VP7 (G) gene segment detected in porcine samples. One hundred seventy three samples were tested for RV group A (RVA), RVB, and C (RVC) by RT-PCR and examined for RV-like lesion using histopathology. A majority (86.4%) of the samples had mixed RV infections and co-infections of RVA/RVB/RVC were detected at a higher rate (24.3%) than previously reported. RVB was identified in 46.8% of the 173 samples. An adapted VP7 classification was developed using previously published (n=57) and newly sequenced (n=68) RVB strains, resulting in 20 G genotypes based on an 80% nucleotide identity cutoff value. Our results revealed a broad genetic diversity of porcine RVB strains, suggesting RVB has been the cause of common/pre-existing, yet undiagnosed, disease in pigs.

Rotavirus RNA polymerases resolve into two phylogenetically distinct classes that differ in their mechanism of template recognition

Rotaviruses (RVs) are segmented double-stranded RNA viruses that cause gastroenteritis in mammals and birds. Within the RV genus, eight species (RVA-RVH) have been proposed. Here, we report the first RVF and RVG sequences for the viral RNA polymerase (VP1)-encoding segments and compare them to those of other RV species. Phylogenetic analyses indicate that the VP1 RNA segments and proteins resolve into two major clades, with RVA, RVC, RVD and RVF in clade A, and RVB, RVG and RVH in clade B. Plus-strand RNA of clade A viruses, and not clade B viruses, contain a 3'-proximal UGUG cassette that serves as the VP1 recognition signal. VP1 structures for a representative of each RV species were predicted using homology modeling. Structural elements involved in interactions with the UGUG cassette were conserved among VP1 of clade A, suggesting a conserved mechanism of viral RNA recognition for these viruses.

Detection of avian group D rotavirus using the polymerase chain reaction for the VP6 gene

Group D rotaviruses (RVs-D) have been documented in birds and, while they may be common in these animals, few molecular studies are available for this specific group. In this study, specific primers for the gene that encodes for the RVs-D VP6 protein were designed and used in a reverse transcription polymerase chain reaction (RT-PCR). Thirty pools of samples were tested by polyacrylamide gel electrophoresis (PAGE) yielding a 30% (9/30) positivity. These pools were subjected subsequently to RT-PCR, with a 53% (16/30) positivity rate. The sensitivity of the PCR assay was demonstrated up to a dilution of 5 × 10(-4)ng/μL (0.5 pg/μL) of the cloned VP6 gene. The four samples were sequenced and showed 90.8-91.1% similarity with regards to the RVs-D VP6 gene. To assess for specificity our RT-PCR was applied to nine samples known to contain enteric viral agents other than group D rotaviruses including picobirnavirus, rotavirus group A, and reovirus with negative results. Overall, the data confirm the specificity of the primers used for detecting the RVs-D by RT-PCR, suggesting that this assay can be used for diagnostic purposes.

Detection of avian rotaviruses of groups A, D, F and G in diseased chickens and turkeys from Europe and Bangladesh

Avian rotaviruses (AvRVs) represent a diverse group of intestinal viruses, which are suspected as the cause of several diseases in poultry with symptoms of diarrhoea, growth retardation or runting and stunting syndrome (RSS). To assess the distribution of AvRVs in chickens and turkeys, we have developed specific PCR protocols. These protocols were applied in two field studies investigating faecal samples or intestinal contents of diseased birds derived from several European countries and Bangladesh. In the first study, samples of 166 chickens and 33 turkeys collected between 2005 and 2008 were tested by PAGE and conventional RT-PCR and AvRVs were detected in 46.2%. In detail, 16.1% and 39.2% were positive for AvRVs of groups A or D, respectively. 11.1% of the samples contained both of them and only four samples (2.0%) contained rotaviruses showing a PAGE pattern typical for groups F and G. In the second study, samples from 375 chickens and 18 turkeys collected between 2009 and 2010 were analyzed using a more sensitive group A-specific and a new group D-specific real-time RT-PCR. In this survey, 85.0% were AvRV-positive, 58.8% for group A AvRVs, 65.9% for group D AvRVs and 38.9% for both of them. Although geographical differences exist, the results generally indicate a very high prevalence of group A and D rotaviruses in chicken and turkey flocks with cases of diarrhoea, growth retardation or RSS. The newly developed diagnostic tools will help to investigate the epidemiology and clinical significance of AvRV infections in poultry.

Molecular characterization of G and P-types bovine rotavirus strains from Goiás, Brazil: high frequency of mixed P-type infections

In this study, 331 samples from calves less than one month old from a dairy herd in the district of Piracanjuba, state of Goiás, Brazil were tested for rotavirus. Thirty-three samples (9.9%) tested positive for rotavirus. Out of those, 31 were submitted to G and P characterization by reverse transcription followed by semi-nested polymerase chain reaction. Two samples were characterized as G6P[1], three as G10P[11] and five as G6P[11]. The majority of the samples (51.6%) displayed multiple P genotypes (P-genotype mixtures), including typical human genotypes P[4] and P[6M], suggesting the occurrence of co-infections and genetic reassortment. Also, the detection of human genotypes in bovine samples may be considered evidence of the zoonotic potential of rotaviruses. To our knowledge, this is the first report of such a high frequency of P genotype mixtures in bovine rotavirus samples. It also increases data on G and P rotavirus genotypes circulating in dairy herds in Brazil and can help in the development of more efficient immunization approaches, thereby controlling infection and reducing economical losses.

Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)

In April 2008, a nucleotide-sequence-based, complete genome classification system was developed for group A rotaviruses (RVs). This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff values. Using this approach, the genome of individual RV strains are given the complete descriptor of Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus Classification Working Group (RCWG) was formed by scientists in the field to maintain, evaluate and develop the RV genotype classification system, in particular to aid in the designation of new genotypes. Since its conception, the group has ratified 51 new genotypes: as of April 2011, new genotypes for VP7 (G20-G27), VP4 (P[28]-P[35]), VP6 (I12-I16), VP1 (R5-R9), VP2 (C6-C9), VP3 (M7-M8), NSP1 (A15-A16), NSP2 (N6-N9), NSP3 (T8-T12), NSP4 (E12-E14) and NSP5/6 (H7-H11) have been defined for RV strains recovered from humans, cows, pigs, horses, mice, South American camelids (guanaco), chickens, turkeys, pheasants, bats and a sugar glider. With increasing numbers of complete RV genome sequences becoming available, a standardized RV strain nomenclature system is needed, and the RCWG proposes that individual RV strains are named as follows: RV group/species of origin/country of identification/common name/year of identification/G- and P-type. In collaboration with the National Center for Biotechnology Information (NCBI), the RCWG is also working on developing a RV-specific resource for the deposition of nucleotide sequences. This resource will provide useful information regarding RV strains, including, but not limited to, the individual gene genotypes and epidemiological and clinical information. Together, the proposed nomenclature system and the NCBI RV resource will offer highly useful tools for investigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.

Genetic characterization of Bulgarian rotavirus isolates and detection of rotavirus variants: challenges for the rotavirus vaccine program?

Annually 20-70% of all hospital admissions and 20% of fatal diarrhea cases among children less than 5 years of age occur due to severe rotavirus diarrhea. Universal immunization is the major strategy aimed at controlling rotavirus infection. The main objective of the present study was to elucidate the evolutionary relationships of the most common rotavirus strains co-circulating in Bulgaria. The sequence and phylogenetic analysis revealed strain diversity and circulation of different rotavirus variants belonging to a single genotype. A mutated G4P[8] strain with the insertion of an asparagine residue in position 76; G2, G9, and G1 variants with amino acid substitutions in the antigenic regions A, B, and/or C were all identified in this study in the absence of an immunization program. Rotavirus strain surveillance in both the pre- and post-vaccine eras is of increasing importance in order to assess the effectiveness of the rotavirus vaccines for protection against disease associated with a diverse population of rotavirus strains.

Sequence analysis of the VP6-encoding genome segment of avian group F and G rotaviruses

Rotavirus groups A to E are mainly defined by antibody reactivity to the capsid protein VP6. Additionally, two putative rotavirus groups (F and G) have been identified in birds. Here, the first nucleotide sequences of the VP6-encoding genome segment of group F (strain 03V0568) and group G (strain 03V0567) rotaviruses, both derived from chickens, are presented. The group F rotavirus is most closely related to avian group A and D rotaviruses, with 49.9-52.3% nucleotide and 36.5-39.0% amino acid sequence identity. The group G rotavirus is most closely related to mammalian group B rotaviruses, with 55.3-57.5% nucleotide and 48.2-49-9% amino acid sequence identity. The terminal sequences of the genome segment were similar in groups A, D and F, and in groups B and G. The findings indicate a long-term evolution of rotavirus groups in two separated clades and support the development of a sequence-based classification system for rotavirus groups.

Full genomic analyses of human rotavirus G4P[4], G4P[6], G9P[19] and G10P[6] strains from North-eastern India: evidence for interspecies transmission and complex reassortment events

In hospitalized patients with acute gastroenteritis in Manipur, India, four rotavirus strains were found to possess VP7 and/or VP4 genes with porcine or bovine characteristics. Considering the animal-like nature of these strains, the remaining eight gene segments were analysed to decipher their exact origin. Analyses of full genome of these strains exhibited their origin from porcine/bovine rotaviruses. This study suggests single or multiple events of reassortment involving multiple gene segments of more than one host type among the strains and emphasizes the significance of complete genetic characterization of unusual strains in regions with high incidence and mortality rates.

Correlation between rotavirus A genotypes detected in hospitalized children and sewage samples in 2006, Córdoba, Argentina

Routine rotavirus A (RV-A) surveillance is based on clinical cases, so only symptomatic infections are reported. The objective of this study was to determine whether the RV-A genotypes and cold seasonal pattern described in patients with diarrhea is reflected by sewage surveillance, which could be representative of the RV-A genotypes circulating in the population. The genotype distribution of RV-A in effluent samples from a local sewage treatment plant was compared to those from local clinical cases. A total of 52 sewage samples and 70 stool specimens from children with acute non-bacterial diarrhea were collected from January to December 2006. The effluent specimens were concentrated and RNA extracts from concentrated sewage and clinical samples were genotyped for the rotavirus VP7 gene. The proportional distribution of the RV-A G-genotypes in sewage and clinical samples during the cold season was similar: G1 accounted for 26.6% of the typed sewage isolates and 28.8% of the clinical infections; G3 type accounted for 21.9% and 25.8%; G2 type 15.6% and 10.6%; G4 type 17.2% and 21.2%; G8 type 1.6% and 0%; and the G9 type 17.2% and 13.6%, respectively. A similar picture of RV-A genotype detection was obtained in sewage samples collected during the cold and warm seasons. The results indicate that there is a correlation between genotypes of RV-A isolates from human diarrheic patients and of those from sewage samples. In addition, sewage monitoring highlighted the uniform all-year RV-A circulation, which was in contrast to the peak incidence of RV-A infection in the community.