Lapine rotaviruses of the genotype P[22] are widespread in Italian rabbitries

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.

Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit

Group A rotaviruses (RVAs) are important gastroenteric pathogens that infect humans and animals. This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Rab1404 possessed the following genotype constellation: G3-P[22]-I2-R3-C3-M3-A9-N2-T3-E3-H3. The P[22] genotype was found to originate from rabbits and was for the first time identified in the ROK. Phylogenetic analysis showed that Rab1404 possessed VP1-3 and VP7 genes, which were closely related to those of the bat strain LZHP2; NSP1-4 genes, which were closely related to those of the simian strain RRV; and VP4, VP6, and NSP5 genes, which were closely related to the genes obtained from other rabbits. Interestingly, a close relationship between Rab1404 and simian RVA strain RVA/Simian-tc/USA/RRV/1975/G3P[3] for 8 gene segments was observed. RRV is believed to be a reassortant between bovine-like RVA strain and canine/feline RVA strains. Rab1404 and canine/feline RVAs shared the genes encoding VP1, VP3, VP7, NSP3, and NSP4. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. These results indicate that Rab1404 could be a result of interspecies transmission, possibly through multiple reassortment events in the strains of various animal species and the subsequent transmission of the virus to a rabbit. Additional studies are required to determine the evolutionary source and to identify possible reservoirs of RVAs in nature.

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This is the first report to describe the complete genome sequence of a rabbit rotavirus (Rab1404) detected in the ROK.

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The 11 genome segments of Rab1404 were determined; G3-P[22]-I2-R3-C3-M3-A9-N2-T3-E3-H3.

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G3P[22] identified in this study is found to originate from rabbit and may have more species specificity.

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Rab1404 could be a result of multiple reassortment events from strains originating from various animal species and transmitted to the rabbit.

Molecular methods in detection and epidemiologic studies of rabbit and hare viruses: a review

Various PCR-based assays for rabbit viruses have gradually replaced traditional virologic assays, such as virus isolation, because they offer high-throughput analysis, better test sensitivity and specificity, and allow vaccine and wild-type virus strains to be fully typed and differentiated. In addition, PCR is irreplaceable in the detection of uncultivable or fastidious rabbit pathogens or those occurring in low quantity in a tested sample. We provide herein an overview of the current state of the art in the molecular detection of lagomorph viral pathogens along with details of their targeted gene or nucleic acid sequence and recommendations for their application. Apart from the nucleic acids-based methods used for identification and comprehensive typing of rabbit viruses, novel methods such as microarray, next-generation sequencing, and mass spectrometry (MALDI-TOF MS) could also be employed given that they offer greater throughput in sample screening for viral pathogens. Molecular methods should be provided with an appropriate set of controls, including an internal amplification control, to confirm the validity of the results obtained.

Rapid detection of three rabbit pathogens by use of the Luminex x-TAG assay

Background

Domestic rabbits especially New Zealand white rabbits play an important role in biological research. The disease surveillance and quality control are essential to guarantee the results of animal experiments performed on rabbits. Rabbit hemorrhagic disease virus, rabbit rotavirus and Sendai virus are the important pathogens that needed to be eliminated. Rapid and sensitive method focus on these three viruses should be established for routine monitoring. The Luminex x-TAG assay based on multiplex PCR and fluorescent microsphere is a fast developing technology applied in high throughput detection. Specific primers modified with oligonucleotide sequence/biotin were used to amplify target fragments. The conjugation between oligonucleotide sequence of the PCR products and the MagPlex-TAG microspheres was specific without any cross-reaction, and the hybridization products could be analyzed using the Luminex 200 analyzer instrument. Recombinant plasmids were constructed to estimate the detection limit of the viruses. Furthermore, 40 clinical samples were used to evaluate the efficiency of this multiplex PCR based Luminex x-TAG assay.

Results

According to the results, this new method showed high specificity and good stability. Assessed by the recombinant plasmids, the detection limit of three viruses was 100copies/μl. Among 40 clinical specimens, 18 specimens were found positive, which was completely concordant with the conventional PCR method.

Conclusions

The new developed Luminex x-TAG assay is an accurate, high throughput method for rapid detection of three important viruses of rabbits.

Multicausal etiology of the enteric syndrome in rabbits from Mexico

Enteropathies in rabbits are difficult to diagnose; their etiology involves pathogens that act synergistically, causing damage to the intestine. The aim of the present study was isolate enteric pathogens from rabbits in Mexico. Using parasitological, bacteriological and molecular analyses, we screened 58 samples of the intestinal content of rabbits having a clinical history of enteric disease from the southeastern part of the State of Mexico. Out of the 58 samples analyzed, a total of 86 identifications were made, Eimeria spp. were found in 77.5%, followed by Aeromonas spp. in 15.5% and Escherichia coli in 8.6%, which were identified as enteropathogenic E. coli (EPEC), and the presence of the following agents was also confirmed: Salmonella spp., Klebsiella spp., Streptococcus spp., Staphylococcus aureus, Enterococcus spp., Mannheimia spp. and Rotavirus. The concurrent presence of Eimeria spp. with Aeromonas was frequent (15.5%); there was statistical significance for the presence of an association between the clinical profiles and Eimeria spp. (p=0.000), Mannheimia spp. (p=0.001), Salmonella spp., Klebsiella spp., Streptococcus spp. and Enterococcus spp. (p=0.006).

Group A rotavirus gastroenteritis: post-vaccine era, genotypes and zoonotic transmission

This article provides a review of immunity, diagnosis, and clinical aspects of rotavirus disease. It also informs about the changes in epidemiology of diarrheal disease and genetic diversity of circulating group A rotavirus strains following the introduction of vaccines. Group A rotavirus is the major pathogen causing gastroenteritis in animals. Its segmented RNA genome can lead to the emergence of new or unusual strains in human populations via interspecies transmission and/or reassortment events.

Complete genome analysis of a rabbit rotavirus causing gastroenteritis in a human infant

Group A rotaviruses (RVA) are responsible for causing infantile diarrhea both in humans and animals. The molecular characteristics of lapine RVA strains are only studied to a limited extent and so far G3P[14] and G3P[22] were found to be the most common G/P-genotypes. During the 2012-2013 rotavirus season in Belgium, a G3P[14] RVA strain was isolated from stool collected from a two-year-old boy. We investigated whether RVA/Human-wt/BEL/BE5028/2012/G3P[14] is completely of lapine origin or the result of reassortment event(s). Phylogenetic analyses of all gene segments revealed the following genotype constellation: G3-P[14]-I2-R2-C2-M3-A9-N2-T6-E5-H3 and indicated that BE5028 probably represents a rabbit to human interspecies transmission able to cause disease in a human child. Interestingly, BE5028 showed a close evolutionary relationship to RVA/Human-wt/BEL/B4106/2000/G3P[14], another lapine-like strain isolated in a Belgian child in 2000. The phylogenetic analysis of the NSP3 segment suggests the introduction of a bovine(-like) NSP3 into the lapine RVA population in the past 12 years. Sequence analysis of NSP5 revealed a head-to-tail partial duplication, combined with two short insertions and a deletion, indicative of the continuous circulation of this RVA lineage within the rabbit population.

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.

Viral infections of rabbits

Viral diseases of rabbits have been used historically to study oncogenesis (e.g. rabbit fibroma virus, cottontail rabbit papillomavirus) and biologically to control feral rabbit populations (e.g. myxoma virus). However, clinicians seeing pet rabbits in North America infrequently encounter viral diseases although myxomatosis may be seen occasionally. The situation is different in Europe and Australia, where myxomatosis and rabbit hemorrhagic disease are endemic. Advances in epidemiology and virology have led to detection of other lapine viruses that are now recognized as agents of emerging infectious diseases. Rabbit caliciviruses, related to rabbit hemorrhagic disease, are generally avirulent, but lethal variants are being identified in Europe and North America. Enteric viruses including lapine rotavirus, rabbit enteric coronavirus and rabbit astrovirus are being acknowledged as contributors to the multifactorial enteritis complex of juvenile rabbits. Three avirulent leporid herpesviruses are found in domestic rabbits. A fourth highly pathogenic virus designated leporid herpesvirus 4 has been described in Canada and Alaska. This review considers viruses affecting rabbits by their clinical significance. Viruses of major and minor clinical significance are described, and viruses of laboratory significance are mentioned.

Rotavirus disease and vaccination: impact on genotype diversity

Temporal and spatial fluctuations in the genotype distribution of human rotaviruses are continuously observed in surveillance studies. New genotypes, such as G9 and G12, have emerged and spread worldwide in a very short time span. In addition, reassortment events have the potential to contribute substantially to genetic diversity among human and animal rotaviruses. With the recent introduction of the two rotavirus vaccines, RotaTeq and Rotarix, in many countries, it appears that the total number of hospitalizations due to rotavirus infections is being reduced, at least in developed countries that implemented a universal immunization program. However, continued surveillance is warranted, especially regarding the long-term effects of the vaccines. No data analyses are available to clarify whether rotavirus vaccine introduction would allow other rotavirus P and G genotypes, which are not covered by the current vaccines, to emerge into the human population and fill the apparent gap. This kind of data analysis is essential, but its interpretation is hampered by natural and cyclical genotype fluctuations.

Frequent rearrangement may explain the structural heterogeneity in the 11th genome segment of lapine rotaviruses - short communication

In rotaviruses, intragenic recombination or gene rearrangement occurs almost exclusively in the genome segments encoding for non-structural proteins. Rearranged RNA originates by mechanisms of partial sequence duplications and deletions or insertions of non-templated nucleotides. Of interest, epidemiological investigations have pointed out an unusual bias to rearrangements in genome segment 11, notably in rotavirus strains of lapine origin, as evidenced by the detection of numerous lapine strains with super-short genomic electropherotype. The sequence of the full-length genome segment 11 of two lapine strains with super-short electropherotype, LRV-4 and 3489/3, was determined and compared with rearranged and normal cognate genome segments of lapine rotaviruses. The rearranged genome segments contained head-to-tail partial duplications at the 3' end of the main ORF encoding NSP5. Unlike the strains Alabama and B4106, intermingled stretches of non-templated sequences were not present in the accessory RNA of LRV-4 and 3489/3, while multiple deletions were mapped, suggesting the lack of functional constraints. Altogether, these findings suggest that independent rearrangement events have given origin to the various lapine strains that have super-short genome pattern.

Are human P[14] rotavirus strains the result of interspecies transmissions from sheep or other ungulates that belong to the mammalian order Artiodactyla?

A limited number of human G6P[14] rotavirus strains that cause gastroenteritis in humans have been isolated in Europe and Australia. The complete genome sequences were determined for five of these human strains--B10925-97 (isolated in Belgium in 1997), 111/05-27 (Italy, 2005), PA169 (Italy, 1987), MG6 (Australia, 1993), and Hun5 (Hungary, 1997)--and their genetic relatedness to animal rotavirus strains was evaluated by sequencing the complete genome of the sheep rotavirus OVR762 (G8P[14]; Spain, 2002), the guanaco (Lama guanicoe) rotavirus strains Arg/Chubut/99 and Arg/Río Negro/98 (G8P[14] and G8P[1], respectively; Argentina, 1999 and 1998), the sable antelope strain RC-18/08 (G6P[14]; South Africa, 2008), and the bovine rotavirus strain Arg/B383/98 (G15P[11]; Argentina, 1998). These analyses revealed an overall consensus genomic constellation (G6/G8)-P[14]-I2-(R2/R5)-C2-M2-(A3/A11)-N2-T6-(E2/E12)-H3, together with a few gene reassortments, and the phylogenetic analyses confirmed that the P[14] human strains evaluated in this study were closely related to rotavirus strains isolated from sheep, cattle, goats, guanacos, and antelopes and to rabbits (albeit to a lesser extent), suggesting that one (or more) of these animal species might be the source of the human G6P[14] strains. The main feature of the genotype and phylogenetic analyses was the close overall genomic relatedness between the five human G6P[14] rotavirus strains and the ovine and antelope rotavirus strains. Taken together, these data strongly suggest a common origin for the human P[14] strains and those of the even-toed ungulates belonging to the mammalian order Artiodactyla, with sheep probably playing a key role in the interspecies transmission responsible for the introduction of P[14] rotavirus strains into the human population.

Molecular characterization of bovine rotavirus circulating in beef and dairy herds in Argentina during a 10-year period (1994-2003)

Group A bovine rotavirus (BRV) is one of the main causes of neonatal calf diarrhea. The present study reports the incidence of rotavirus diarrhea and the genotypes of BRV strains circulating in beef and dairy herds from Argentina, during a 10-year period (1994-2003). Group A BRV was detected in 62.5% (250/400) of the total studied cases of diarrhea. Positive cases were analyzed by heminested multiplex RT-PCR for P and G genotypes identification. Sixty percent of them were typed as P[5]G6, 4.4% P[11]G10, 4.4% P[11]G6 and 2.4% P[5]G10. Additionally, 9.2% of the cases were initially typed as G8 combined with P[5] or P[11], but sequence analysis revealed they belonged to genotype G6, lineage Hun4-like. Partial typing was assessed in 12.0% of the cases. One of the partially typed samples was closely related to genotype G15. BRV was detected in 71% and 58% of the outbreaks registered in beef and dairy farms, respectively. A clear differential distribution of G/P types was found according to the herd type. P[5]G6 was the prevalent strain in beef herds, while P[11] was the prevalent P-type in dairy herds (71%), associated in similar proportions with G6 and G10, These findings indicate that BRV genotypes included in the current commercially available rotavirus vaccines (G6, G10, P[5] and P[11]) should protect calves from most Argentinean field strains. Nevertheless, continuous surveillance is necessary to detect the emergence of new variants.

Identification of a novel VP4 genotype carried by a serotype G5 porcine rotavirus strain

Rotavirus genome segment 4, encoding the spike outer capsid VP4 protein, of a porcine rotavirus (PoRV) strain, 134/04-15, identified in Italy was sequenced, and the predicted amino acid (aa) sequence was compared to those of all known VP4 (P) genotypes. The aa sequence of the full-length VP4 protein of the PoRV strain 134/04-15 showed aa identity values ranging from 59.7% (bovine strain KK3, P8[11]) to 86.09% (porcine strain A46, P[13]) with those of the remaining 25 P genotypes. Moreover, aa sequence analysis of the corresponding VP8* trypsin cleavage fragment revealed that the PoRV strain 134/04-15 shared low identity, ranging from 37.52% (bovine strain 993/83, P[17]) to 73.6% (porcine strain MDR-13, P[13]), with those of the remaining 25 P genotypes. Phylogenetic relationships showed that the VP4 of the PoRV strain 134/04-15 shares a common evolutionary origin with porcine P[13] and lapine P[22] rotavirus strains. Additional sequence analyses of the VP7, VP6, and NSP4 genes of the PoRV strain 134/04-15 revealed the highest VP7 aa identity (95.9%) to G5 porcine strains, a porcine-like VP6 within VP6 genogroup I, and a Wa-like (genotype B) NSP4, respectively. Altogether, these results indicate that the PoRV strain 134/04-15 should be considered as prototype of a new VP4 genotype, P[26], and provide further evidence for the vast genetic and antigenic diversity of group A rotaviruses.