Rapid mapping of functional cis-acting RNA elements by recovery of virus from a degenerate RNA population: application to genome segment 10 of bluetongue virus.

The regulatory elements which control the processes of virus replication and gene expression in the Orbivirus genus are uncharacterized in terms of both their locations within genome segments and their specific functions. The reverse genetics system for the type species, Bluetongue virus, has been used in combination with RNA secondary structure prediction to identify and map the positions of cis-acting regions within genome segment 10. Through the simultaneous introduction of variability at multiple nucleotide positions in the rescue RNA population, the functional contribution of these positions was used to map regions containing cis-acting elements essential for virus viability. Nucleotides that were individually lethal when varied mapped within a region of predicted secondary structure involving base pairing between the 5' and 3' ends of the transcript. An extended region of predicted perfect base pairing located within the 3' untranslated region of the genome segment was also found to be required for virus viability. In contrast to the identification of individually lethal mutations, gross alteration of the composition of this predicted stem region was possible, providing the base-pairing potential between the two strands was maintained, identifying a structural feature predicted to be conserved throughout the Orbivirus genus. The approach of identifying cis-acting sequences through sequencing the recovered virus following the rescue of a degenerate RNA population is broadly applicable to viruses where reverse genetics is available.

Regulation of gene expression by the NSP1 and NSP3 non-structural proteins of rotavirus.

The role of the rotavirus non-structural proteins NSP1 and NSP3 in regulating cellular and viral mRNA translation has been investigated by examining the effect of added recombinant NSP3 on protein translation in a T7-based in vitro coupled transcription-translation system. Addition of purified NSP3 to assays primed solely with cellular mRNA was found to have no effect on the translation efficiency of the mRNA. However, as expected, the addition of viral mRNA to such assays competitively inhibited the synthesis of cellular protein, and interestingly, this inhibition was enhanced by the addition of NSP3. Treatment of NSP3 with antisera raised against the purified protein abrogated its function, but only when used prior to mixing the protein with viral mRNA. Addition of partially purified NSP1 to the coupled system was able to alleviate the enhancement of the inhibition of cellular mRNA translation caused by NSP3. The role of NSP1 in this process appears to be to modulate the impact of the NSP3-based inhibition of cellular translation by binding to the 5' end of viral mRNAs.

A rapid and accurate assay for assessing the cytotoxicity of viral proteins.

A fluorescence-based assay is presented for measuring the cytoxicity of viral proteins added exogenously to cells. The assay is based on the use of two fluorescent dyes, calcein-AM and ethidium homodimer (EtD-1) to specifically stain living and dead cells respectively and employs fluorescence activated cells sorting (FACS) to achieve a rapid and accurate measurement of the cytotoxic capacity of a potential viral toxin. The assay has been developed using the group B homologue (ADRV-NSP4) of the NSP4 enterotoxin encoded by Group A rotaviruses but should be applicable to assaying any viral protein exhibiting cytotoxic activity.

Molecular characterization of the rotavirus NSP4 enterotoxin homologue from group B rotavirus.

The RNA segment (Gene 10) from a human group B rotavirus which encodes the homologue of the rotavirus enterotoxin (NSP4) has been cloned and sequenced. The gene is of the same length (751 nucleotides) as its better-characterized group A rotavirus counterpart but shows minimal homology (approximately 10%) to it at the primary sequence level. Despite this low level of sequence homology, secondary structure predictions for the group B protein (ADRV-NSP4) showed a close similarity of structural features with the group A protein. Full-length ADRV-NSP4 was expressed in Escherichia coli with an amino terminal 6xHis tag that was used to purify it to homogeneity. The cytotoxicity of the purified protein was examined in a rapid dye-uptake assay that assesses membrane permeability and was found to be comparable to its group A counterpart.

Expression of the E2 envelope glycoprotein of bovine viral diarrhoea virus (BVDV) elicits virus-type specific neutralising antibodies.

A region of genome from the NADL strain of BVDV corresponding to the coding sequence for the E2 glycoprotein has been molecularly cloned using RT-PCR. The viral cDNA sequence was used to construct vaccinia virus recombinants that expressed either the entire E2 coding sequence or fragments of it. These recombinants were used to immunise mice of three H-2 haplotypes to investigate their ability to elicit a neutralising antibody response against BVDV. Sera from mice immunised with the recombinant expressing full length E2 contained high levels of virus neutralising antibodies that in addition to giving neutralisation of the homologous NADL strain were also able to neutralise the Oregon C24V reference strain. These sera failed to give any neutralisation of the Osloss reference strain providing evidence for the division of BVDV isolates into at least two distinct E2 serotypes. These results were confirmed in gnotobiotic lambs. Expression of E2 fragments revealed the presence of at least two distinct neutralising epitopes, one of which was localised within the carboxy terminal 90 amino acids of the protein.

Seroepidemiology of group A rotavirus in suburban São Paulo, Brazil.

Age-specific patterns of rotavirus infection were investigated using a randomly selected and representative sample of sera from a suburban community of São Paulo, Brazil screened for class-specific antibodies to group A rotavirus. Age-serology of anti-rotavirus IgG showed primary infection predominant in young infants with a median age of around 18 months consistent with IgM serology suggesting highest rates of recent infection between ages 4 and 48 months. Anti-rotavirus serum IgA prevalence increased gradually with age. Paired samples from infants, collected 1 month apart, indicated high exposure rates with seroconversion occurring in several infants during the reported low transmission season. Between 5 and 10% of adults had elevated IgM levels indicative of recent infection and, potentially, of an important contribution adults may play to rotavirus transmission. Further understanding of the dynamics of rotavirus transmission within populations, at group and serotype level, would benefit the design and monitoring of future immunization programmes.

Mapping of the target antigens of the rotavirus-specific cytotoxic T cell response.

The cytotoxic T cell (CTL) response in C57/B16 (H-2b) mice to rotavirus has been analysed using a cognate set of vaccinia virus recombinants covering the 12 primary gene products of the UKtc strain of bovine rotavirus. The gene products of RNA segments 5 (VP5/NSP-1) and 8 (VP7) both elicited a classic CD8+ Class I MHC restricted CTL response. Using L cells transfected with specific Class I MHC loci as targets the VP5/NSP-1 response was found to be restricted at Db and the VP7 response at Kb. Vaccinia virus recombinants expressing VP7 genes from seven G serotypes were used to show that the CTL response to this antigen is completely cross-reactive. By contrast, using the same strategy the CTL response to VP5/NSP-1 was found to be virus strain specific. A vaccinia virus recombinant carrying RNA segment 5 from the deletion mutant P9D delta 5 was used to localize at least one CTL epitope in VP5/ NSP-1 to the first 150 amino acids of the protein. The expression of a number of fragments of VP7 in vaccinia virus recombinants was used to show that the CTL epitope (amino acids 31-40) previously identified through the use of synthetic peptides is virus serotype specific rather than cross-reactive.

Caprine and bovine B rotaviruses in western France: group identification by Northern hybridization.

In a survey of coronavirus and rotavirus-induced neonatal diarrhoea in 373 calves from 284 farms, nine (2.4%) of the animals were found to be infected with non-group A rotaviruses when their faeces were analysed in a commercial ELISA and by PAGE. Seven out of eight 1-4- day-old kids from a single farm were also infected with similar viruses. In a mini-PAGE, all the viruses displayed group B- and/or E-like 4223 electrophoretypes. In Northern hybridizations with cDNA chemiluminescent probes specific to rotavirus groups A (RF strain), B (adult diarrhoea rotavirus, ADRV) and C (Cowden strain) all the viruses belonged to group B.

Molecular biology of rotaviruses. IX. Conservation and divergence in genome segment 5.

Nucleotide sequencing of RNA segment 5 from seven strains of group A rotavirus has been carried out to investigate the extent of diversity and conservation, as well as possible selective pressures involved in driving the fixation of sequence changes in this gene. Analyses of the derived sequences revealed that sequence conservation could not be correlated either with rotavirus serotype or the species of origin of the virus strain. These sequences together with other published and unpublished sequences of this gene have raised the total number available for comparison to 17. Alignment of all the available sequences revealed that only 88 amino acid positions (17.6%) in the protein encoded by gene 5 (VP5) are absolutely conserved but that the metal-binding motif reported by others is conserved in all sequences. Despite the high degree of sequence divergence, alignment of secondary structure predictions for VP5 showed a high level of conservation, suggesting that constraints on sequence divergence may operate at the level of overall higher-order structure of the encoded protein.

Sequence analysis of two porcine rotaviruses differing in growth in vitro and in pathogenicity: distinct VP4 sequences and conservation of NS53, VP6 and VP7 genes.

The VP4, VP7, NS53 and VP6 genes of two porcine rotavirus variants which differ in their in vitro growth properties and pathogenicity have been cloned and sequenced. The VP4 genes show only 67.2% nucleic acid and 70.6% amino acid identity. The VP4 gene of one variant (4S) is closely related to that of the bovine UK rotavirus strain, whereas the VP4 gene of the other variant (4F) is only distantly related to known VP4 genes and is likely to represent a new P serotype. In contrast the NS53 (VP5), VP6 and VP7 genes of the 4F and 4S variants show greater than 99% nucleotide and amino acid identity, indicating that the two viruses are genetically related by a reassortment event. The implications for the role of VP4 in the determination of in vitro growth characteristics and pathogenicity are discussed.

Induction of rotavirus-specific cytotoxic T lymphocytes by vaccinia virus recombinants expressing individual rotavirus genes.

We determined the capacity of vaccinia virus recombinants expressing individual rotavirus genes to induce virus-specific cytotoxic T lymphocytes (CTLs) in mice. Mice were orally inoculated with vaccinia virus recombinants containing genes which encode rotavirus outer capsid proteins vp4 or vp7, single-shelled virus proteins vp1, vp2, or vp6, or rotavirus nonstructural proteins NS53, NS35, NS28, or NS26/NS12. We found that (i) the greatest frequencies of virus-specific CTLs were induced by vaccinia virus recombinants expressing vp7, (ii) transport of vp7 beyond the endoplasmic reticulum was not necessary for induction of CTLs, (iii) recombinants expressing vp7 induced CTLs which reacted with different rotavirus serotypes, and (iv) CTLs were induced among both intestinal and nonintestinal lymphocytes after oral inoculation. These findings may be relevant to vaccine strategies which utilize vectors expressing individual rotavirus genes.

Genomic concatemerization/deletion in rotaviruses: a new mechanism for generating rapid genetic change of potential epidemiological importance.

Three variants of group A rotavirus with large changes in their gene 5 structures have been analyzed at the molecular level. The first of these, P9 delta 5, was obtained during plaque purification undertaken as part of the biological cloning of a field isolate of virus. The gene 5 homolog in this isolate migrated just ahead of the normal segment 6 RNA, giving an estimated size of 1,300 bp. Molecular cloning and sequencing of this homolog revealed it to have a single 308-bp deletion in the center of the normal gene 5 sequence extending between nucleotides 460 and 768 of the normal gene sequence. This deletion caused a frameshift in the gene such that a stop codon was encountered 8 amino acids downstream of the deletion point, giving a predicted size for the protein product of this gene of 150 amino acids compared with the 490 amino acids of its normal-size counterpart. Attempts to detect this shortened protein in virus-infected cells were not successful, indicating that it was much less stable than the full-length protein and/or had suffered a large change in its antigenicity. The second two variants, brvA and brvE, were generated in an earlier study following the high-multiplicity passage of the UKtc strain of bovine rotavirus. Polyacrylamide gel electrophoresis analysis of these nondefective variants showed that brvA had a gene 5 homolog approximately equal in size to the normal RNA segment 2 (approximately 2,700 bp) and that brvE had a size of approximately 2,300 bp. Both variants showed changes in their gene 5 protein products, with brvA mimicking P9 delta 5 in failing to produce a detectable product whereas brvE produced a new virus-specific protein approximately 80 kDa in size. Full-length cDNA clones of the brvE gene 5 homolog were isolated, and analysis of their structure revealed a head-to-tail concatemerization of the normal gene 5 sequence with the first copy of the concatemer covering nucleotides 1 to 808 and the second covering nucleotides 92 to 1579, giving a total length of 2,296 bp. Sequencing across the junction region of the two copies of the gene showed that they were joined in frame to give a predicted combined open reading frame of 728 amino acids with the amino-terminal region consisting of amino acids 1 to 258 fused at the carboxy terminus to amino acids 21 to 490.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of the stimulation of reporter gene expression by the sigma 3 protein of reovirus in co-transfected cells.

The stimulation of reporter gene expression following co-transfection with the S4 gene of mammalian reoviruses was analysed. The sigma 3 protein of type 3 reovirus gave a five- to eightfold increase in expression of chloramphenicol acetyltransferase and beta-galactosidase but this was found to be dependent upon the nature of the promoter being used to drive reporter gene expression. The sigma 3 protein of reovirus type 1 failed to stimulate reporter gene expression under any of the conditions used. Hybrid constructs between the S4 genes of reoviruses type 1 and 3 were used to map the stimulation characteristic to the carboxy-terminal third of the gene. Analysis of the level of sigma 3 protein accumulation in transfected cells showed that the reovirus type 3 protein accumulated to a much higher level than that of reovirus type 1. Using the hybrid gene constructs this higher level of protein accumulation was shown to co-segregate with the ability to stimulate reporter gene expression.

Development of cDNA probes for typing group A bovine rotaviruses on the basis of VP4 specificity.

Dot and Northern (RNA) blot hybridization assays were developed for the P typing of group A bovine rotaviruses (BRV) by using cDNA probes prepared from gene segment 4. The probes were prepared by polymerase chain reaction amplification of hyperdivergent regions (nucleotides 211 to 686) of BRV strain UK, IND, NCDV, and Cr VP4 cDNA by using specific oligonucleotide primers. The probes were P type specific (VP4) and exhibited little or no cross-reactivity with double-stranded RNA from heterologous rotavirus P types. Our studies indicate that at least three P types, as defined by polymerase chain reaction-derived VP4 gene probes from the UK, NCDV, and Cr strains, exist among the seven BRV isolates tested.

Experimental reovirus type 3-induced murine biliary tract disease.

The aims of this experiment were: (1) to establish a reovirus type 3-induced murine model of biliary atresia/neonatal hepatitis that as far as possible corresponds to the human disease; (2) to demonstrate that the disease is histologically similar to the human disease, and to investigate the natural history of reovirus type 3 infection in this model; (3) to study the host-virus interrelationships at a molecular level; and (4) to develop sensitive assays that could be translated to the human disease. In this study we were unable to produce an exact model for extrahepatic biliary atresia (EHBA) in the laboratory mouse following a perinatal reovirus type 3 infection. However, the ability of reovirus type 3 to persist in the murine liver and the effects produced in the offspring of infected pregnant mice indicate that this preparation may provide the basis for the eventual development of the experimental model of EHBA.

A serotype 10 human rotavirus.

Rotaviruses with genome rearrangements isolated from a chronically infected immunodeficient child (F. Hundley, M. McIntyre, B. Clark, G. Beards, D. Wood, I. Chrystie, and U. Desselberger, J. Virol 61:3365-3372, 1987) are the first recognized human isolates of serotype 10. This was shown by both a direct enzyme-linked immunosorbent assay and virus neutralization assays using serotype specific monoclonal antibodies. The serotype was confirmed by sequence analysis of the gene encoding VP7, which revealed a 96% amino acid homology to the bovine serotype 10 isolate B223.

Detection and differentiation of bovine group A rotavirus serotypes using polymerase chain reaction-generated probes to the VP7 gene.

Dot and Northern blot hybridization assays were developed to detect and differentiate group A bovine rotavirus serotypes using radiolabeled serotype 6 (Nebraska calf diarrhea virus [NCDV] and United Kingdom [UK] strains) or serotype 10 (Crocker [Cr] strain) VP7 gene probes. Partial length VP7-specific cDNA encompassing areas of major sequence diversity were generated by the polymerase chain reaction (PCR) using either cloned VP7 genes (NCDV and UK strains) or reverse transcribed mRNA (Cr strain) as templates. Radiolabeled probes prepared from the PCR-generated cDNA were tested at various stringency conditions to optimize the hybridization assays. At high stringency conditions (52 C, 50% formamide, 5 x standard saline citrate), the NCDV, UK, and Cr probes serotypically differentiated bovine rotavirus isolates in RNA samples prepared from cell culture propagated viruses or in fecal specimens from infected gnotobiotic calves. The sensitivity and specificity of NCDV and Cr VP7 probes were characterized in dot blot hybridization assays, and the probes were estimated to detect at least 1 ng of viral RNA. The serotyping results obtained using VP7 probes were similar to those obtained using serologic assays. Further development of these assays may provide a useful means for the rapid detection and differentiation of bovine rotavirus serotypes in fecal samples from calves in the field.

Nucleotide sequences of normal and rearranged RNA segments 10 of human rotaviruses.

Normal and rearranged RNA segments 10 of group A rotaviruses isolated from a chronically infected immunodeficient child were amplified by the polymerase chain reaction as full-length cDNA copies, and were subsequently cloned and sequenced. Compared with the nucleotide sequence of the normal RNA segment 10, the rearranged form contains a partial non-coding duplication at its 3' end and several point mutations. The normal RNA segment 10 was similar to that of bovine rotavirus.

Outer capsid glycoprotein vp7 is recognized by cross-reactive, rotavirus-specific, cytotoxic T lymphocytes.

Cytotoxic T lymphocytes (CTLs) generated in mice orally inoculated with rotaviruses lyse target cells infected with different rotavirus serotypes (cross-reactive CTLs). Using vaccinia virus recombinants expressing individual rotavirus proteins from two different rotavirus serotypes, we found that cross-reactive CTLs recognize target cells expressing outer capsid protein vp7 better than those expressing outer capsid protein vp4 or inner capsid protein vp6. These findings may be relevant to vaccine strategies which include immunization with reassortant rotaviruses or viral or bacterial vectors expressing individual rotavirus proteins. The region or regions of vp7 which are antigenically conserved among different rotavirus serotypes and recognized by cross-reactive CTLs remain to be determined.