Isolation of a bovine rotavirus with a "super-short" RNA electrophoretic pattern from a calf with diarrhea

Changing profile of the bovine rotavirus G6 population in the south of Ireland from 2002 to 2009

Bovine group A rotavirus is one of the main causes of neonatal diarrhoea in calves. This study examined the different G and P genotypes circulating in the bovine population, from 2002-2009, in the south of Ireland. Rotavirus positive bovine faecal samples (n=332) were collected from the Cork Regional Veterinary Laboratory, between 2002 and 2009 and subjected to RNA extraction, PAGE analysis, and G and P genotyping. Genotyping analysis identified G6, G10, P[5], and P[11] to be the predominant G and P genotypes in the present study, with G6 rotavirus responsible for 70-80% of rotavirus infections. The highest combination of G and P types found was G6 P[5], followed by G6 P[5+11] mixed infection. The prevalence of G6 and G10 has shifted over the years, with an increase in the amount of G10 P[11] being detected. Novel combinations (G6+G10P[11], G6+G10P[5+11] and G10P[5+11]) were also detected for the first time. In addition to this, sequence analysis of the VP7 RT-PCR amplicons has revealed that Irish G6 strains are falling within three different lineages, III-V. During this study, two samples, initially genotyped as G8P[11] were identified through sequence analysis as being true G6, lineage III with a high nucleotide identity to Hun4, a G6 human sample from Hungary. The increase in novel G and P type combinations, as well as changes seen in G6 samples could have an impact on rotavirus vaccination programmes, as the current vaccine available may not offer protection against all of these circulating types.

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.

A novel genomic constellation (G10P[3]) of group A rotavirus detected from buffalo calves in northern India

Group A bovine rotaviruses cause gastroenteritis and calf mortality leading to significant economic losses to dairy farmers in India. Due to segmented nature of the RNA genome and wide host range, vast genetic and antigenic diversity exists among different isolates of rotavirus. Molecular characterization of locally prevalent group A rotavirus strains in buffalo population in north India was undertaken. Out of a total of 455 faecal samples, 21 samples (4.61%) were positive for bovine rota virus (BRV) as determined by PAGE and ELISA, whereas of these only 15 isolates yielded specific products for VP4 and VP7 genes by RT-PCR. Genotyping by nested PCR typed G6, G10 and P[11] genotypes but VP4 genes of 11 isolates remained untyped. The phylogenetic and evolutionary analysis of nucleotide and predicted amino acid sequences of the cloned products of VP4 and VP7 genes confirmed typing results obtained by nested PCR for G6, G10 and P[11] and classified the untyped isolates as P[3] genotypes. In this study, it was observed that G6P[11] (26.66%) and G10P[3] (73.34%) group A rotaviruses are circulating in buffalo herds of organized farms in north India. Unusual reassortants G10P[3] of group A rotaviruses isolated from buffalo calves show novel genomic constellations indicative of interspecies reassortment.

Loop model: mechanism to explain partial gene duplications in segmented dsRNA viruses

Gene rearrangements in a head-to-tail fashion have been described several times for gene segments of the rota-, phytoreo-, and orbiviruses. Several mechanisms have been proposed to explain the occurrence of partial duplications, however, none of these models has been fully satisfactory to explain the occurrence of all the observed duplicated genes. Based on recently available structural data about the lambda3 RNA-dependent-RNA-polymerase of reoviruses, we propose the 'loop model' as a plausible explanation for the occurrence of partial gene duplications in dsRNA viruses.

The VP4 and VP7 of bovine rotavirus VMRI are antigenically and genetically closely related to P-type 5, G-type 6 strains

We have previously reported the isolation of a bovine rotavirus, designated VMRI, with a super-short electropherotype. We have characterized this strain further as it has shown antigenic differences with the prototype G6 strain NCDV-Lincoln. In this communication, we report the antigenic and molecular characterization and the nucleotide sequence of the VP4 and VP7 genes of this strain. Virus neutralization tests indicated 2- to 13-fold differences in the titers between NCDV-Lincoln, B641 and VMRI strains. Northern blot hybridization results indicated a degree of heterogeneity in the VP4 gene of these strains which can be detected under conditions of high stringency. The VP4 and VP7 genes of the VMRI strain were cloned and sequenced and compared with the published sequences of other bovine rotavirus strains. The VP4 gene of VMRI had a high degree of homology with that of UK and B641 strains but differed significantly from that of both NCDV-Lincoln and B223 strains. Sequence analysis of the VP7 gene of VMRI and other strains indicated a high degree of conservation and the amino acid identity between the different strains was 96%. Sequence information regarding these strains and field isolates will assist in the generation of effective vaccination strategies for control of neonatal calf diarrhea.

Identification of group B rotaviruses with short genome electropherotypes from adult cows with diarrhea

Two field strains (BB-RVLV and KD) of group B rotaviruses from adult dairy cows with diarrhea displayed short genome electropherotypes. Gnotobiotic calves inoculated with fecal filtrates of each group B rotavirus developed diarrhea, and only group B rotaviruses or antigens were detected in the feces by immunoelectron microscopy and in intestinal epithelial cells by immunofluorescent staining, respectively. The feces or intestinal contents of the cows and inoculated calves were negative for group A and C rotaviruses by enzyme-linked immunosorbent assay, immunoelectron microscopy, or cell culture immunofluorescence assays. Comparison of the genome electropherotypes of the calf-passaged BB-RVLV and KD strains with the original samples and reference bovine group A, B, and C rotaviruses revealed conservative of their short-genome electropherotypes and double-stranded RNA migration patterns characteristics of group B rotaviruses. To our knowledge, our previous study (L.J. Saif, K.V. Brock, D.R. Redman, and E.M. Kohler, Vet. Rec. 128:447-449, 1991) and this report are the first description of bovine group B rotaviruses (in a mixed infection with bovine coronavirus or singly in fecal contents) in adult cows with diarrhea and this is the first report of short-genome electropherotypes among group B rotaviruses.

Genome rearrangements of rotaviruses

Rotaviruses (and other members of the Reoviridae family) undergo rearrangements of their genomes. This review describes evidence of rearranged genomes in rotaviruses. Their structure and functions are reviewed. Possible mechanisms of their emergence are discussed, and the significance of genome rearrangements for viral evolution is considered.

Prevalence of group A and group B rotaviruses in the feces of neonatal dairy calves from California

136 fecal samples, collected from 47 dairy calves on a calf ranch and in a dairy herd in California, were tested for the presence of group A and group B rotaviruses by reverse transcription-polymerase chain reaction (RT-PCR). Samples were collected from each calf at days 1, 7 and 14. Within the 14 day period, 44 calves (94%) were positive for group A rotavirus and an unexpectedly high number of calves (38 calves, 81%) were positive for group B rotavirus. When these samples were examined by polyacrylamide gel electrophoresis (PAGE), rotavirus was found in 21 calves and all of them had group A electropherotype. Among 25 PAGE positive samples from 21 calves, 17 (68%) were of short electropherotype, 4 (28%) were of long electropherotype and 4 (28%) contained both short and long electropherotype rotaviruses. Group B and short and long electropherotype group A rotaviruses were found in both normal and diarrheic calves.

Prevalence of P types among porcine rotaviruses using subgenomic VP4 gene probes

Nucleic acid probes were developed to differentiate VP4 (P) types among porcine rotaviruses. These probes were then used to determine the relative prevalence of P types 6 (Gottfried-like) and 7 (OSU-like) in cultivated rotaviruses and field specimens. The variable regions between bases 205-551 of the VP4 gene of rotavirus strains OSU and Gottfried were amplified by the polymerase chain reaction and radiolabeled with 32P by random primer extension. Radiolabeled probes were tested in a dot blot hybridization assay. The subgenomic probes prepared from VP4 gene detected as little as 5 ng oF rotavirus RNA and were specific for differentiating the two porcine rotavirus P types. The probes were used to determine the P type of several reference rotavirus strains and recently cultivated porcine rotavirus strains. Eight of the 10 cultivated, previously untyped, rotaviruses isolates tested were of P type 7 (OSU-like). Two rotavirus strains neither reacted with OSU nor with the Gottfried probe, therefore, their P type could not be determined. Seventeen out of the 26 rotavirus (65.4%) field samples tested had a P type 6 (Gottfried-like) whereas 5 out of 26 (19.2%) had a P type 7 (OSU-like). Four of the 26 samples (15.4%) reacted neither with the OSU nor with the Gottfried probe and possibly represent previously unrecognized P types in swine. Data in this study suggests that (1) rotaviruses with P type 7 are most common among the cultivated rotaviruses, (2) rotaviruses with P type 6 are the most abundant type of rotavirus in natural infections and (3) rotaviruses with additional P types are also associated with diarrheic swine.

Immunogens of rotaviruses

Rotaviruses cause gastroenteritis in neonates of many animal species including cattle, swine, horses, dogs, cats, chickens and turkeys. Rotavirions are nonenveloped, are about 75 nm in diameter, have a double capsid, and contain 11 double-stranded RNA segments as their genome. Several antigenically distinct groups of rotaviruses have been identified and have been alphabetically designated as A through G. Group A rotaviruses were the first group of rotaviruses isolated and are the most commonly detected rotaviruses in diarrheic animals. Group A rotaviruses have two surface proteins, VP4 and VP7, both of which are important in serotype determination and in inducing neutralizing antibodies and protective immunity. Multiple serotypes of group A rotavirus based on glycoprotein VP7 (designated as G types) and based on VP4 (P types) have been identified. The immune response to rotaviruses is essentially serotype specific, however, cross-reactive or heterotypic epitopes have also been identified. Currently acceptable methods for immunogen quantitation include the induction of neutralizing antibody in host or laboratory animals. The in vivo efficacy of vaccines against rotavirus-associated gastroenteritis remains the standard method against which in vitro methods must be compared. Several animal models have been developed which could potentially be used in evaluating the efficacy of candidate vaccines. Monoclonal antibodies to rotavirus immunogens are also currently available and serve as valuable reagents for in vitro quantitation of rotaviral immunogens.

Genomic rearrangements in human rotavirus strain Wa; analysis of rearranged RNA segment 7

Two rotavirus variants containing genomic rearrangements were isolated from human rotavirus strain Wa. In one variant (H5) the rearrangement involves the RNA segment 5, while in the other variant (H57) two genes, 5 and 7 are rearranged. The rearranged genes are composed exclusively of sequences from the genes they substitute. Sequence analysis of the rearranged segment 7 indicated that it is a partial duplication of the wild type gene, in a head-to-tail orientation.

Some infectious causes of diarrhea in young farm animals

Escherichia coli, rotaviruses, and Cryptosporidium parvum are discussed in this review as they relate to enteric disease in calves, lambs, and pigs. These microorganisms are frequently incriminated as causative agents in diarrheas among neonatal food animals, and in some cases different strains or serotypes of the same organism cause diarrhea in humans. E. coli causes diarrhea by mechanisms that include production of heat-labile or heat-stable enterotoxins and synthesis of potent cytotoxins, and some strains cause diarrhea by yet undetermined mechanisms. Rotaviruses and C. parvum induce various degrees of villous atrophy. Rotaviruses infect and replicate within the cytoplasm of enterocytes, whereas C. parvum resides in an intracellular, extracytoplasmic location. E. coli, rotavirus, and C. parvum infections are of concern to producers, veterinarians, and public health officials. These agents are a major cause of economic loss to the producer because of costs associated with therapy, reduced performance, and high morbidity and mortality rates. Moreover, diarrheic animals may harbor, incubate, and act as a source to healthy animals and humans of some of these agents.

Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes

A dot blot hybridization assay is described for the detection and differentiation of porcine rotavirus serotypes. Recombinant complementary DNA (cDNA) representing gene 9 (the gene encoding the neutralization antigens in VP7 glycoprotein) from OSU (porcine rotavirus serotype 1) and Gottfried (porcine rotavirus serotype 2) strains were used to determine the optimal hybridization conditions which allow specific detection of group A porcine rotaviruses. Probes were prepared by excision of the inserts from the recombinant plasmids and radiolabeling of cDNA with 32P by the random primer extension method. Probes were hybridized at various stringencies with viral RNA from different rotavirus serotypes bound to nylon membranes. Hybridization at low stringency (26% base pair mismatch for stable hybrid formation) had high sensitivity but low specificity. Hybridization at high stringency (16% base pair mismatch for stable hybrid formation) produced high specificity but decreased the sensitivity observed at low stringency. Probes were specific for rotavirus at both stringencies and did not hybridize with nucleic acids from other porcine viruses. Subgenomic gene 9 fragments were then tested to provide more specific probes. A 322 bp fragment from OSU gene 9 between nucleotides 382 and 704 and a 266 bp fragment from Gottfried gene 9 between nucleotides 230 and 496 were found to be specific as hybridization probes. These studies demonstrated the feasibility of the dot blot hybridization assay using subgenomic fragments of gene 9 to detect and differentiate serotypes of porcine rotavirus. Additional studies are warranted to further evaluate the sensitivity and the capability of these probes to detect porcine field isolates of the same serotype.

Applications of nucleic acid probes in veterinary infectious diseases

Nucleic acid probe technology is increasingly being used in basic research in veterinary microbiology and in diagnosis of infectious diseases of veterinary importance. This review presents an overview of nucleic acid probe methodology and its applications in veterinary infectious diseases. The major applications of nucleic acid probes include detection of pathogens in clinical samples, especially those organisms which are fastidious and difficult to cultivate, differentiation of virulent from avirulent organisms and vaccine strains from wild type isolates, typing of microorganisms, mapping genes, screening libraries of cloned DNA for specific genes, detection of latently infected or carrier animals, study of mechanisms of pathogenesis, epidemiological studies and food safety.

Comparison of polyacrylamide gel electrophoresis, an enzyme-linked-immunosorbent assay, and an agglutination test for the direct identification of bovine rotavirus from feces and coelectrophoresis of viral RNAs

The dsRNA concentrated polyacrylamide gel electrophoresis (CPAGE) detected rotavirus directly from 19% of 77 stool specimens from diarrheic calves. A commercial enzyme-linked immunosorbent assay (ELISA) detected 25%, latex agglutination test, 23%, and polyacrylamide gel electrophoresis (PAGE), 19%. Establishing CPAGE as the "standard," the commercial ELISA and the latex agglutination test both had higher sensitivity (84%) than PAGE (79%). However, PAGE produced the highest specificity (100%), followed by agglutination (88%) and ELISA (84%). The commercial ELISA had a slightly higher sensitivity than agglutination, PAGE, and CPAGE, but the ELISA specificity was generally lower. The latex agglutination test had a lower sensitivity than ELISA, but specificity was higher. Agglutination had similar negative predictive values (94%), compared with agglutination and PAGe, but had the lowest positive predictive value (a measure of accuracy) (70%). Agreement with CPAGE was highest for PAGE (94.8%), followed by agglutination (87%) and ELISA (84.4%). The calculated percentages of total disagreement with all other tests indicated that ELISA differed from the other rotavirus detection assays in 10.4% of the cases, agglutination in 7.8%, PAGE in 2.6%, and CPAGE in 1.3%. The 2 PAGE assays allowed the detection of atypical rotaviruses from feces based on the characteristic "super-short" migration pattern of the 11 genomic segments of rotaviruses and of other members of the Reoviridae.

Molecular characterization by RNA-RNA hybridization of a serotype 8 human rotavirus with "super-short" RNA electropherotype

A human rotavirus isolate (the 69M strain) with a "super-short" RNA electropherotype has been classified as serotype 8, a new human serotype [Matsuno et al., 1985]RNA-RNA hybridization using 32P-labeled transcription probes was used to assess the genetic relatedness of the 69M strain to a panel of human and animal rotaviruses. The 69M strain showed a medium level of homology with subgroup 1, serotype 2 human rotaviruses with short RNA electropherotypes. However, the 69M strain was not significantly related to any other human rotavirus strains tested in this study, including recently identified serotype 9 strains (represented by the WI61 strain) and subgroup 1 human rotaviruses with long RNA electropherotypes (represented by the AU-1 strain) that are shown to be genetically distinct from other human rotavirus strains. Unexpectedly, a medium level of homology was also found between the 69M probe and the double-stranded RNAs from bovine rotavirus strains (represented by the NCDV strain).

Sequence analysis of gene 11 equivalents from "short" and "super short" strains of rotavirus

The molecular basis for the aberrant migration pattern of the gene 11 equivalent in rotaviruses with "short" (human DS-1) and "super short" (human 69M and bovine VMRI) electropherotypes was investigated. The mRNAs of these viruses were synthesized in vitro, and the entire gene 11 equivalent of each of these viruses was sequenced with specific synthetic oligonucleotide primers. These sequences were compared with previously published sequences of "long" pattern rotavirus gene 11 segments. The increased lengths of the gene 11 equivalents of DS-1, 69M, and VMRI are due to a prolonged, 3' untranslated region in this gene segment. The 3' untranslated region of the VMRI gene 11 equivalent contains a clear duplication of a portion of its coding sequence. A stretch of 18 consecutive nucleotides within the 330-nucleotide, 3' untranslated region of 69M is identical to a section of UK coding sequence. The DS-1 and the remainder of the 69M 3'-end additional sequences are similar to each other, but neither is similar to any other currently available rotavirus gene sequence. This finding suggests that a process other than homologous duplication is involved in the evolution of these sequences. The widespread occurrence of human and animal rotaviruses with short and super short electropherotypes provides evidence that intragenic and possibly intergenic recombinational events associated with an error-prone viral RNA polymerase may play a role in increasing the genetic repertoire of rotaviruses.

Antigenic and molecular characterization of bovine rotaviruses isolated in Japan

Japanese bovine rotavirus isolates, which fall into two different serotypes, were shown to belong to subgroup I and to have long RNA electrophoretypes. This study confirmed the distinction of two serotypes on the basis of a greater than 20-fold difference in neutralization titres between the homologous and heterologous reactions; however, significant one-way cross-neutralization was observed between one of the strains with bovine serotype 2 and antisera to strains with bovine serotype 1 (serotype 6 according to the unified serotyping system). When 32P-labelled transcription probes prepared from Japanese strains as well as a prototype NCDV strain were hybridized with genomic double-stranded RNA from these bovine strains and from prototype human strains, a high level of homology was observed among bovine rotavirus strains; but this level of homology was not found between bovine strains and any of the prototype human strains. These results suggest that bovine rotavirus strains belong to a single genogroup that is distinct from any of the human genogroups previously identified by RNA-RNA hybridization.