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.

Stability and movement of mRNAs and their encoded proteins in Xenopus oocytes.

The stability and movement of several polyadenylated (poly A+) and nonpolyadenylated (poly A-) mRNAs in Xenopus oocytes have been examined. At least 50% of the poly A+ mRNA molecules (9S rabbit globin mRNA, chicken ovalbumin, and lysozyme) were stable in oocytes over a 48-h period, irrespective of the amount injected. About 50% of injected poly A- reovirus mRNAs was degraded within the first 24 h of injection, irrespective of the amount injected, although no further degradation was observed over an additional 24 h. The movement of all poly A+ mRNAs injected at either the animal or vegetal pole of the oocyte was very slow. Little movement of RNA from the animal half to the vegetal half was observed even 48 h after injection. In contrast, similar amounts of mRNA were present in both halves 48 h after vegetal pole injection. Similar results were obtained after injection of poly A- reovirus mRNAs. The movement of the proteins encoded by the poly A+ mRNAs was studied in the 6-h period after injection when little mRNA movement had occurred. 85% of the globin synthesized accumulated in the animal half irrespective of injection site. The movement of the sequestered secretory proteins ovalbumin and lysozyme in the same oocytes as globin was much slower; very little lysozyme appeared in the half of the oocyte opposite the site of injection.

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.

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.

Expression of a major bovine rotavirus neutralisation antigen (VP7c) in Escherichia coli.

Sequences from genomic RNA segment 8 of the United Kingdom tissue-culture (t.c.)-adapted bovine rotavirus encoding a major viral neutralisation antigen VP7c have been expressed in Escherichia coli. Expression under the regulated control of the bacteriophage lambda pR promoter was as a C-terminal extension to E. coli beta-galactosidase (beta Gal). Following temperature induction, high levels of the fusion protein were synthesised and accumulated in induced cells, making up 5%-15% of total bacterial cell protein after 2 h of induction. Immunisation of sero-negative rabbits and mice with gel-purified fusion-protein raised antibodies, which gave specific immunofluorescence with virus-infected cells and were able to immunoprecipitate proteins of the VP7 complex from such cells. Hyperimmune sera also gave a virus-type-specific reaction in a solid-phase enzyme-linked immunoabsorbant assay and neutralised virus infectivity in standard plaque-reduction assays.

The molecular biology of rotaviruses. VII. Detailed structural analysis of gene 10 of bovine rotavirus.

cDNA cloning and nucleotide sequence analysis have allowed detailed structural studies on RNA segment 10 of the U.K. bovine rotavirus to be undertaken. The complete sequence of 751 nucleotides was determined and found to contain only a single long open reading frame capable of coding for a protein of 175 amino acids. The gene has an unusually long 3' untranslated region of 184 nucleotides or some 24.5% of the total sequence, whose start was confirmed by analysing the carboxyterminal amino acid of the gene 10 product, the glycoprotein VP10c. Analysis of purified virions radio-labelled with [3H]glucosamine and [3H]mannose showed that VP10c is not a detectable component of the virus particle. The two potential glycosylation sites were found to be very close to the amino terminus of the putative translation product, strongly suggesting that the glycoprotein VP10c does not contain a cleavable signal sequence.

Detailed structural analysis of a genome rearrangement in bovine rotavirus.

A genome rearrangement involving RNA segment 11 of a bovine rotavirus has been analysed by molecular cloning and sequencing. This revealed that the rearranged genome segment was generated by a head to tail concatemerisation of two almost full length copies of segment 11. The upstream copy of the gene has lost its 3' end and the downstream copy its 5' end. The truncation of the upstream copy of the gene occurs within the termination codon for VP11 converting it from a UAG to a UGA, the rearranged gene is therefore still able to encode a normal VP11. The possible mechanisms by which this rearrangement may have been generated are discussed.

A sensitive method for the production of diagnostic fingerprints of the genome segments of field isolates of rotavirus.

The 3'-terminal labelling procedure for analyzing the genome segment profile of field isolates of rotavirus (Clarke and McCrae, 1981, J. Virol. Methods 2, 203) has been further developed to produce a rapid and sensitive method for generating diagnostic fingerprints from individual species of double-stranded RNA. The fingerprints were obtained by a one-dimensional resolution of overlapping terminally labelled oligonucleotides produced by partial nuclease digestion with a base-specific nuclease. This fingerprinting method should be of great value in characterizing the molecular details of genome segment variation and will facilitate detailed molecular epidemiological studies of this important virus group.

A rapid and sensitive solution hybridisation assay for the quantitative determination of specific viral RNA sequences.

A solution hybridisation assay has been developed which allows the quantitation of specific viral (RNA) sequences in infected cells. The assay makes use of single-stranded (ss) RNA probes of known polarity synthesised at high specific activity in vitro from cDNA clones of the relevant viral gene by the SP6 or T7 RNA polymerase. These probes are used together with samples containing the RNA to be detected at a known concentration to construct a calibration curve to relate RNase resistant radioactivity following solution hybridisation to amount of RNA. The amount of RNA in experimental samples is then determined using the calibration curve that is produced each time the assay is performed. The UKtc strain of Rotavirus growing in BSC-1 cells was used to develop this method but with the substitution of suitable cDNA clones it could be applied to any viral system.

A rapid screening assay for detecting individual RNA species in field isolates of rotaviruses.

A method is described that allows the rapid screening of field isolates of rotavirus for the detection of specific viral RNA segments. Cloned cDNA copies of viral genomic RNAs are employed for detection in the assay which makes use of the dot-hybridization technique of Thomas (1980). The assay developed was shown to be sufficiently sensitive and specific to allow the genetic composition of virions to be determined over a wide range of concentrations. The feasibility of using the method developed for both the analysis of genetic reassortants prepared in vitro and for screening field isolates to detect putative genome reassortment events is demonstrated.

The application of polymerase chain reaction to the detection of rotaviruses in faeces.

An assay protocol based on exploiting the polymerase chain reaction (PCR) for the detection of rotavirus in infected faeces is described. The assay is 100,000 times more sensitive than the standard electropherotype method that is widely used. It also gives a 5000-fold increase in sensitivity over the hybridisation based assay previously developed (Pedley and McCrae, 1984) and does not require the use of radioisotopes. The amplified product is a full length c-DNA copy of the gene encoding the major neutralisation antigen of the virus whose molecular cloning and sequence analysis will allow detailed information on the molecular basis of epidemiological variation to be rapidly collected.

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.

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.

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.

Terminal structure of reovirus RNAs.

S1 nuclease analysis and 3' terminal sequencing of the reovirus genome double-stranded RNAs and in vitro produced viral mRNAs has been used to establish the viral mRNA is a full length copy of the genome template. Sequence determination at the 3' end of the genome minus strand has by transposition allowed determination of the 5' terminal sequences of the viral mRNAs. In all but one case an AUG codon which could function in initiation of protein synthesis has been found within the determined sequence. The 3' ends of the plus strands from all genome segments were found to have a common sequence. The implications of these results on the mechanism of virus replication are discussed.

Nucleic acid-based analyses of non-group A rotaviruses.

Simple genome profile studies on polyacrylamide gels allow all non-group A rotaviruses isolated so far to be recognized by the absence of the tight triplet (7-9) of RNA segments seen in all group A viruses. However, reliance solely on genome profile studies for rotavirus grouping can be misleading and, for virus group definition, additional corroborating nucleic acid and serological studies are essential. Terminal fingerprint analysis was the first generation of nucleic acid-based assays that allowed discrimination between the various rotavirus groups. By means of this technique the clear definition of five rotavirus groups (A-E), correlating exactly with those found by a serological assay, has been possible, with preliminary evidence for at least two additional groups. The technical sophistication of fingerprinting techniques prevents their widespread use in epidemiological studies; the development of a second generation of nucleic acid-based assays is therefore under way. These employ molecularly cloned cDNA probes to the genomes of non-group A viruses which can be widely distributed for use in 'dot-blot' screening of faecal samples and, if expressed as protein in Escherichia coli, should provide a ready source of viral antigen for use in surveying viral prevalence through the screening of serum antibody levels.

Specific secretion of polypeptides from cells infected with vaccinia virus.

The pattern of polypeptides specifically secreted by cells after infection with vaccinia virus has been analyzed. A complex pattern of apparently virus-specified polypeptides exhibiting temporal control of the type seen with intracellular polypeptides after virus infection was observed. Some of the specifically secreted polypeptides were shown to be modified by glycosylation and sulfation. The possible significance of these results is discussed.