Solution hybridization and enzyme immunoassay for biotinylated DNA-RNA hybrids to detect enteroviral RNA in cell culture

A non-isotopic hybridization assay is described for detection of enteroviral RNA in cell culture. Two biotin-labelled cDNA probes, corresponding to 1 kb from the 5' end and 3.5 kb from the 3' end of the coxsackievirus B3 genome, were hybridized in solution with protease and detergent-treated cell culture suspensions. Labelled DNA-RNA hybrids were captured on microtiter plates coated with anti-biotin antibody and bound hybrids were measured with a beta-galactosidase-labelled monoclonal antibody specific for DNA-RNA hybrids. Coxsackie B3 was detected at a concentration of 500 pfu ml-1. The limit of detection for other enteroviruses ranged from 10(3.3) to 10(5.8) pfu ml-1. The enteroviruses that could be detected included coxsackie B1 and 3, coxsackie A1-6 and 15, poliovirus types 1-3, and enteroviruses 7, 11, and 71. ECHO 22 was the only enterovirus, of those that were tested, that could not be detected. The solution hybridization reaction and enzyme immunoassay for DNA-RNA hybrids does not require the use of radiolabelled probes or extraction of RNA with phenol. The assay yields a quantitative endpoint, which avoids the subjectivity inherent in membrane-based methods. These features would make the assay more adaptable to clinical laboratories than other formats which have been devised for measurement of viral RNA.

Polymerase chain reaction for human picornaviruses

We have used enzymic amplification of specific nucleic acid sequences followed by hybridization, for the rapid detection and typing of human picornaviruses after cell culture isolation. The test is based on the synthesis of cDNA, the polymerase chain reaction and the use of oligonucleotide probes. The primers were selected from the 5' non-coding region of the genome representing highly conserved regions. Sequences specific to enteroviruses and rhinoviruses were used as probes. The assay was able to identify all the picornavirus reference strains analysed and it was also possible to discriminate between enteroviruses and rhinoviruses by the hybridization procedure. When 29 picornavirus clinical isolates were analysed, all except one were detected by gel electrophoresis and a specific hybridization signal was obtained with all except three strains using the oligonucleotide probes.

The nucleotide sequence of coxsackievirus A9; implications for receptor binding and enterovirus classification

The complete nucleotide sequence of the genome of coxsackievirus A9 (CAV-9) has been determined from cDNA cloned in Escherichia coli. Excluding the 3' poly(A) stretch, the RNA genome is 7452 nucleotides long and encodes a single polyprotein of 2201 amino acids. Comparison of the nucleotide and predicted amino acid sequences with those of the coxsackieviruses B1, B3 and B4 reveals a surprising degree of homology, with overall amino acid homologies of 86.9%, 86.2% and 87.0%, respectively. In contrast, there is much less homology to another coxsackie A virus, CAV-21, 60.4% overall amino acid homology. This demonstrates the high degree of diversity within the CAV group and indicates that the current classification does not directly correlate with molecular genetic properties. One major feature of CAV-9 is an insertion, relative to all other enteroviruses sequenced to date, which is located at the C terminus of VP1, and includes an arginine-glycine-aspartic acid tripeptide. Such sequences in a number of other proteins are known to have activity in promoting attachment to cell receptors and the implications for CAV-9 receptor binding are discussed.

Polyprotein processing of Theiler's murine encephalomyelitis virus

To investigate polyprotein processing of Theiler's murine encephalomyelitis viruses, we analyzed in vitro translation reactions programmed by in vitro-derived transcripts from an infectious full-length cDNA clone of the DA strain of Theiler's virus. To help identify the proteinases that carried out the processing, we modified the DA cDNA clone transcription template by linearization with different restriction endonucleases that generate templates of different lengths or by constructing linker insertion or deletion mutations or both in putative proteinase-coding regions. Protein 3C carried out most of the cleavages of the polyprotein, as is true for the other picornaviruses that have been studied. A second proteinase also appeared active at the LP12A-2B junction. A protein of slightly faster mobility than the leader protein was seen with translation of transcripts derived from DA cDNA but not GDVII cDNA. This protein may be synthesized from an alternative initiation site in the DA leader-coding region out of phase with the polyprotein reading frame. Our findings are relevant to ongoing investigations of the abnormal virus expression seen in DA virus late demyelinating disease, since polyprotein processing is critical in regulating picornaviral gene expression.

The complete nucleotide sequence of coxsackievirus A21

We have determined the complete nucleotide sequence of coxsackievirus A21 (CAV-21), the first member of this enterovirus subgroup to be analysed in molecular detail. The sequence, which is 7401 nucleotides long, encodes an open reading frame of 2206 codons, preceded by a 5' non-coding region of 711 nucleotides and followed by a 3' non-coding region of 72 nucleotides plus a poly(A) tract. The most striking feature is the remarkable homology to the poliovirus (greater than 90% at the amino acid level) in the 3' part of the genome. The rest of the genome is much less homologous, suggesting that CAV-21 is a recombinant virus. Rhinovirus-like characteristics, including the length of the 5' non-coding region and a slight --U/--A imbalance in codon usage, may be related to the fact that CAV-21, like rhinoviruses, infects the upper respiratory tract. However, the sequence sheds little light on the molecular basis of the shared receptor specificity.

Molecular cloning of the complete genome of Theiler's virus, strain DA, and production of infectious transcripts

We constructed a complete cDNA clone of the genome of Theiler's virus strain DA in a Bluescript plasmid. This recombinant plasmid, called pTMDA, was used to synthesize full length RNA transcripts of the viral insert. The RNA was infectious for BHK cells. Virus R1-DA, obtained from transfected BHK cells, caused the biphasic disease classically observed with this strain of Theiler's virus. SJL/J mice did not show clinical symptoms during the first week following intracranial inoculation, although viral antigens were found in a few neurons of brain and spinal cord. By 45 days post-inoculation, the mice had developed a chronic demyelinating disease and viral RNA and antigens could be found only in spinal cord white matter in areas surrounded by inflammatory infiltrates. At this stage no RNA or antigens were found in neurons. Therefore the phenotype of R1-DA was indistinguishable from that of genuine DA Theiler's virus.

Use of in situ hybridization for the detection of foot-and-mouth disease virus in cell culture

Biotinylated complementary DNA (cDNA) and RNA probes were prepared from a specific and highly conserved section of the foot-and-mouth disease virus (FMDV) genome coding for the RNA-dependent RNA polymerase. Hybridization was conducted on FMDV-infected, bovine enterovirus (BEV)-infected, and noninfected swine kidney cell cultures. The detection system utilized the enzyme system streptavidin-alkaline phosphatase, the substrate phosphate, and the chromogen nitroblue tetrazolium. Intense cytoplasmic granular staining was present at 2 and 4 hr postinfection (hpi), with less staining observed at 24 hpi. The staining was specific for FMDV, as indicated by a lack of staining of noninfected cells and BEV-infected cells. With the RNA probe, positive cells were detected up to the highest viral dilution assayed, which was approximately 96 TCID50. The cDNA probe was slightly less sensitive, detecting positive cells at 10-fold lower dilutions. This technique could prove useful in the diagnosis of foot-and-mouth disease in animals or in the detection of FMDV in biologics submitted for importation.

Genetic diversity of enterovirus subgroups

Enterovirus serotypes were studied using nucleic acid hybridization and nucleotide sequence analysis. A great majority of enteroviruses could be roughly divided into two larger subgroups the first consisting of poliovirus and certain coxsackievirus A serotypes. The second subgroup included coxsackie B viruses, most ECHO viruses, enterovirus 71 and representatives of coxsackie A viruses. Enterovirus 70 showed low homology to the viruses in both groups. Interestingly, ECHO virus 22 failed to react with any of the hybridization probes indicating a relatively distant relationship. The close relationship between coxsackie B and ECHO viruses as well as between polio and certain coxsackie A viruses was also evident when nucleotide sequences of the 3' end noncoding parts were compared.

A temperature-sensitive defect of enterovirus 70 is located at the uridylylation of the genome-linked protein VPg in vitro

The temperature-sensitive phenotype of enterovirus 70 (EV70) was examined by use of an in-vitro RNA replication system derived from a membrane fraction (crude replication complex, CRC) of EV70-infected HeLa cells. This system was capable of synthesizing the nucleotidyl proteins VPg-pU and VPg-pUpU. Formation of these nucleotidyl proteins was completely abolished when the in-vitro reaction was performed at the nonpermissive temperature for virus replication. Considering our previous observation that the defective stage of the temperature-sensitive growth of EV70 resides in the initiation step of RNA transcription in vivo, it is most likely that the lack of uridylylation of VPg at the restricted temperature in vitro is directly involved in the temperature-sensitive defect of virus growth in vivo.

Detection of enteroviruses using cDNA and synthetic oligonucleotide probes

This study compares the detection of enterovirus RNA by cDNA probes prepared from both the 5' and 3' end of the genome of coxsackie A21 and B4 with the use of synthetic oligonucleotides prepared from short but highly conserved sequences in the 5' end non-coding region of the picornavirus genome. The cDNA probes detected enteroviruses with a variable level of sensitivity which presumably depended on the degree of genomic homology with the detecting probes. Generally probes from coxsackievirus A21 detected more enteroviruses than did similar probes from coxsackievirus B4. Probes from the 5' end of the genome of both viruses were more sensitive than 3' end probes. In contrast, synthetic oligonucleotides detected all enteroviruses efficiently suggesting that these probes could be useful as 'universal' probes to detect any enterovirus. This paper discusses the application of these probes in the diagnosis and differentiation of enteroviruses.

The complete nucleotide sequence of swine vesicular disease virus

The complete nucleotide sequence of the genome of the enterovirus swine vesicular disease virus (SVDV; H/3 '76) isolated from a healthy pig has been determined using molecular cloning and DNA sequencing techniques. The RNA genome was 7400 nucleotides long, excluding the poly(A) tract, and appeared to encode a single polyprotein of 2185 amino acids. The predicted amino acid sequence of the polyprotein showed close homology (around 90%) to that of the previously sequenced coxsackieviruses B1, B3 and B4, and also showed homology (around 60%) to that of poliovirus. This homology allows us to predict the possible cleavage sites of the polyprotein and to identify other features of structural and functional significance, which seem to be important to the biological integrity of the virus. A detailed analysis of homology between SVDV and coxsackieviruses shows that non-structural proteins are highly conserved whereas the structural proteins are less well conserved. The 5' and 3' non-coding regions are also conserved, although there are several divergent nucleotide stretches. These stretches may differentiate SVDV from coxsackieviruses.

Molecular cloning of the complete genome of strain GDVII of Theiler's virus and production of infectious transcripts

We constructed a complete cDNA clone of strain GDVII of Theiler's virus in Bluescript plasmid. This recombinant plasmid, called pTMGDVII, was used to synthesize full-length RNA transcripts of the viral insert. This RNA was infectious for BHK cells. Virus R1-GDVII, obtained from transfected BHK cells, caused rapidly fatal encephalomyelitis in BALB/c mice. High amounts of viral antigens were present in neurons. No antigens were found in white matter. Therefore, the phenotype of R1-GDVII was indistinguishable from that of genuine GDVII Theiler's virus.

The amino-terminal domain of the hepadnaviral P-gene encodes the terminal protein (genome-linked protein) believed to prime reverse transcription

A series of antisera directed against amino acid sequences from different segments of the duck hepatitis B virus (DHBV) P-gene were shown to immunoprecipitate DHBV DNA molecules that were covalently linked to the DHBV DNA terminal protein. Restriction analysis and sizing after protease treatment demonstrated that the P-gene proteins were bound to the 5'-end of the DHBV DNA minus-strand which was mapped to a G-residue in the centre of the repeat sequence DR1. Resistance to alkali treatment indicated a phosphodiester linkage to tyrosine between protein and DNA. Limited protease treatment prior to immunoprecipitation cleaved C-terminal P-proteins from the viral DNA, indicating that the terminal protein forms a separate domain encoded in the N-terminal part of the P-gene. Functional analysis of a deletion mutant confirmed the notion that a non-essential spacer separates the terminal protein from the polymerase domain residing in the C-terminal half of the P-gene. Thus, the major proteins required for hepadnaviral reverse transcription, namely the primer, DNA polymerase, and possibly also RNase H, appear to be synthesized as a polyprotein precursor which is at least initially linked as such to its first DNA product.

Nonisotopic oligomeric probes for the human enteroviruses

Oligonucleotide probes were prepared from highly conserved regions of human enteroviral genomes. These reagents were labeled with either 32P or alkaline phosphatase and were successfully used in blot assays to detect a wide variety of human enteroviruses, proving the potential utility of oligomeric sequences as pan-enteroviral probes. The availability of nonisotopic probes will ultimately make a hybridization assay for enteroviruses easier, shorter, and more adaptable for routine diagnostic laboratories.

Detection of enterovirus RNA in experimentally infected mice by molecular hybridisation: specificity of subgenomic probes in quantitative slot blot and in situ hybridisation

Subgenomic cDNA clones representing defined regions of the genome of Coxsackie B3 virus were used as hybridisation probes to detect RNA of various enteroviruses in cell culture and mouse model systems. Radiolabelled probes were used in slot blots to quantitate the RNA in samples; biotinylated probes were used to localise virus RNA at the cellular level by in situ hybridisation with monolayers of infected cells or thin sections of tissue samples. Probes derived from the 5' or 3' terminal regions of Coxsackie virus RNA, which are highly conserved in the genus Enterovirus, detected RNA of various serotypes in infected cell cultures, but failed to hybridise with hepatitis A virus (HAV) RNA. Although HAV is clearly a Picornavirus, our data support the view that its taxonomic position within the enteroviruses should be reconsidered. The biotinylated probes were also used to detect in situ virus RNA in paraffin-embedded tissue samples from experimental mouse models of Coxsackie B3 virus-induced myocarditis or Coxsackie B1 virus-induced myositis. Since the integrity of the tissues was preserved during the process, and viral RNA was localised in the affected muscle fibres, this has enabled us unequivocally to relate the infecting virus to the underlying tissue injury.

Detection of enteroviruses using subgenomic probes of Coxsackie virus B4 by hybridization

The objective of this research was to develop group- and type-specific probes for the detection of enteroviruses. Coxsackie virus B4 RNA was cloned, and a series of subgenomic clones were generated. Six of these clones, containing sequences from the 3' end or the 5' end of the genome, were tested for their ability to detect these viruses in a small number of infected cells employing nucleic acid hybridization technique and total cytoplasmic RNA from a panel of 11 serotypes of enteroviruses. The RNA from cells infected with Coxsackie B viruses gave characteristic and positive hybridization signals. Coxsackie B-specific probes and a control Echo 9 probe detected Coxsackie A9 and Echo 3 weakly. As little as 0.5 microgram of the RNA--which contained 10-20 ng of poly(A)-containing, virus-specific, hybridizable RNA--was sufficient to successfully conduct the assay, suggesting high sensitivity of these probes. Probes that are 3' end-specific appear to be group specific, while those that are 5' end-specific appear to be type specific among the serotypes tested.

Theiler's virus infection in nude mice: viral RNA in vascular endothelial cells

Infection of athymic (nu/nu) mice with Theiler's murine encephalomyelitis virus results in an acute encephalitis which resembles poliomyelitis. Immunohistochemistry and in situ hybridization were used to delineate the presence of viral proteins and RNA in the nervous systems of nude mice infected with the Daniels strain of Theiler's virus. This system permits the analysis of a viral infection in the absence of an effective immune response. By immunohistochemistry, viral antigen was found in the processes and cell bodies of neurons and glial cells. Besides the presence of viral antigen in these cell types, by in situ hybridization, Theiler's virus RNA was also found in cells associated with vascular endothelium in the brains and spinal cords of these infected mice. Theiler's virus RNA-positive endothelial cells were observed not only near the primary lesions but also away from demonstrable lesions in normal-appearing regions in the central nervous system. Earlier work had suggested an intra-axonal dissemination for this virus (M. C. Dal Canto and H. L. Lipton, Am. J. Pathol. 106:20-29, 1982). Our findings are consistent with this model but also suggest an additional mechanism for virus spread within the central nervous system, i.e., by infecting vascular cells and crossing the blood-brain barrier. Lastly, after Theiler's murine encephalomyelitis virus infection, not only glial cells but also endothelial cells express major histocompatibility complex class II (la) antigen on their surface (M. Rodriguez, M. L. Pierce, and E. A. Howie, J. Immunol. 138:3438-3442, 1987). Our demonstration of Theiler's virus-infected endotheliumlike cells may explain interactions of virus products in stimulating antigen presentation.

Expression of Theiler's murine encephalomyelitis virus protease 3C and polymerase 3D in Escherichia coli and characterization of monospecific sera

Defined DNA fragments of cloned Theiler's murine encephalomyelitis virus genome were used to construct procaryotic recombinant plasmids expressing viral genes 3C and 3D. In these plasmids (pEX-EMBL vectors), viral sequences are fused in-phase behind the Escherichia coli lac Z' gene which is under the control of the inducible lambda Pr promoter. Partially purified fusion proteins were used to immunize Balb/c mice. Sera monospecific for the viral protease 3C and polymerase 3D were obtained. These sera detected their corresponding antigens in situ in infected BHK cells using immunocytochemical reactions.

Comparative sequence analysis of the 5' noncoding region of the enteroviruses and rhinoviruses

A comparative sequence analysis of the 5' noncoding region of a subgroup of the picornaviruses, including the polioviruses, coxsackie B3, and the human rhinoviruses, reveals the conservation of certain features despite the divergence of sequence. In this subgroup, for which nine complete sequences are available, two long stretches of sequence, two pyrimidine-rich regions, and 22 hairpins are conserved. Based on these results, similar secondary structures encompassing the entire 5' noncoding regions of these viruses are predicted. The fact that sequence divergence occurred only in a manner that allowed conservation of these structures implicates a biologically functional role for this region. The possible roles it may have in the picornavirus life cycle are discussed.

Molecular cloning and sequence determination of DA strain of Theiler's murine encephalomyelitis viruses

Theiler's murine encephalomyelitis viruses (TMEV) belong to the Picornaviridae, and are divided into two subgroups. TO subgroup strains produce a persistent demyelinating central nervous system infection in mice, while GDVII subgroup strains cause acute polioencephalomyelitis. We generated three overlapping clones of the genome of DA strain, a member of TO subgroup. Sequence analysis revealed that the genome is 8093 nucleotides long with a poly(A) tail. The 5' noncoding region stretches from nucleotides 1 to 1065 and lacks a poly(C) tract. The open reading frame stretches from 1066 to 7968 and encodes 2301 amino acids. DA strain sequence is more closely related to members of the Cardiovirus genus than to members of other Picornavirus genera. Comparison with sequence of BeAn strain, another TO subgroup strain, showed that the P1 area has the greatest number of differences, while the noncoding regions are more well-conserved. The three overlapping clones will be important in recombinant infectious cDNA studies between strains of both subgroups.

The complete nucleotide sequence of a bovine enterovirus

The complete nucleotide sequence of the genome of a bovine enterovirus (strain VG-5-27) has been determined using molecular cloning and DNA sequencing techniques. Excluding the poly(A) tract the genome was 7414 nucleotides long and contained a 5' non-coding region which at 818 nucleotides was longer than that of most picornaviruses. The single large open reading frame encoded a potential polyprotein of 2175 amino acids which showed considerable homology with other enteroviruses. This homology has allowed us to predict the possible cleavage sites of the polyprotein and to identify other features of structural and functional significance which might help us to understand the constraints involved in the evolutionary divergence of these viruses.

Defined recombinants of poliovirus and coxsackievirus: sequence-specific deletions and functional substitutions in the 5'-noncoding regions of viral RNAs

We describe the isolation of a variant of a polio--coxsackie recombinant virus (PCV110) containing a genomic RNA with a chimeric 5'-noncoding region. The variant virus [designated PCV110(1)] has growth and biosynthetic properties that are quite different from the original, temperature-sensitive isolate of the recombinant virus [designated PCV110(4)]. Nucleotide sequencing of the 5'-noncoding region of RNA from PCV110(1) revealed a 4-base deletion within the substituted coxsackievirus region of the chimeric genome that may contribute to the loss of temperature sensitivity of this variant recombinant virus. In addition, we have generated new recombinant viruses that contain (1) coxsackievirus sequences within the N66-N627 region of the poliovirus genome and (2) coxsackievirus sequences substituted from N1-N627 in the poliovirus genome. These recombinant viruses are not temperature sensitive for growth at 37 degrees and have biosynthetic properties similar to those of wild-type poliovirus. Our results provide evidence that replicase recognition signals encoded in the 5' noncoding regions of enterovirus genomic RNAs are not strictly sequence specific.

Use of cRNA probes for the detection of enteroviruses by molecular hybridization

Subgenomic fragments of cDNA from poliovirus type 1 were inserted downstream from the SP6 or the T7 promoter in a Gemini riboprobe vector and their in vitro synthesized RNA transcripts were used as radiolabeled probes for the detection of enteroviral RNAs by molecular hybridization. The cRNA transcripts appeared to be more sensitive probes than the corresponding cDNAs. In vitro transcripts of the 5' noncoding region (5' nc riboprobe) were able to detect all of 14 reference enterovirus strains tested, as well as human rhinovirus 2, by dot blot hybridization with infected cell lysates. The same riboprobe also detected the enteroviral RNAs present in 16 of 18 samples of successive passages of stools in tissue culture and in some cases even in crude stool extracts. A riboprobe from the VP 1 region detected specifically poliovirus types 1, 2, and 3 in lysates of infected cells and in 50% of the infected stool specimens tested. These probes could be of particular interest for the epidemic survey of poliovirus infections.