Oligonucleotide mapping of picornavirus RNAs by two-dimensional electrophoresis

Nucleotide sequence at the 5' extremity of turnip yellow mosaic virus genome RNA

The sequence of the first 110 nucleotides at the 5' extremity of turnip yellow mosaic virus genome RNA has been determined. The sequence is blocked at its 5' terminus with the group pppm(7)G and contains two AUG triplets. The determined sequence bears a strong resemblance to the 5' noncoding region of rabbit beta-globin mRNA. Region 95-103 of the sequence can base-pair with part of the 3' extremity of either the genome RNA or the coat protein mRNA.

Biochemical characterization of a foot-and-mouth disease virus strain attenuated for cattle. Brief report

Wild-type, virulent (A-24 Cruzeiro subtype) foot-and-mouth disease virus (FMDV), a related attenuated strain and revertants of the attenuated strain were examined by titration on primary bovine kidney (PBK) and baby hamster kidney (BHK-21) cells, as well as, by infection of unweaned mice. Wild type virus grew equally well in all three systems, whereas the attenuated strain had a titer 2-3 log lower in PBK cells than in the other 2 assays. Within 9 successive passages in BHK-21 cells the attenuated strain gave rise to revertants that had regained the growth properties of wild-type virus in PBK cells. After cloning of the attenuated strain by plaque isolations, the same revertant phenotype was obtained within 9 successive passages. Oligonucleotide mapping indicated that the attenuated strain differed from the wild-type and revertants by at least one additional oligonucleotide. Differences in poly(C) length were not found among any of the three strains of FMDV. These results correlate attenuation and virulence with point mutation(s) and not with deletions. Possible reversions in nature with this attenuated strain may be anticipated.

Variation among hepatitis A virus strains. I. Genomic variation detected by T1 oligonucleotide mapping

The genomes of eight hepatitis A virus (HAV) strains originating from far distant geographic regions such as Europe, North Africa, Middle and North America, Australia and The People's Republic of China were compared by RNase T1 oligonucleotide mapping. For this purpose, the viruses were propagated in cell cultures and viral RNA was isolated from highly purified mature virions. It could be shown that variation in nucleotide sequence is common among HAV isolates, but is in the order of magnitude reported for other picornaviruses. For viruses isolated in cell culture directly from stool samples of diseased individuals, changes usually amounted to 1-4% of RNA genome sites. Genomic differences between two virus strains derived from one fecal sample but replicating at either 32 or 37 degrees C were in the same order of magnitude. Thereby, the number of consecutive in vitro passages proved to have only limited influence on the development of genetic variation. For two HAV strains, however, adaptation to and passage in marmosets evidently had imposed highly selective conditions which had favored the appearance of viral genomes differing in up to 75% of their large oligonucleotides (about 10% in sequence) from the oligonucleotide map of a reference HAV strain.

Variation in foot-and-mouth disease virus isolates in Kenya: an examination of field isolates by T1 oligonucleotide fingerprinting

Ribonuclease T1 oligonucleotide maps of strains of 4 of the endemic serotypes of foot-and-mouth disease virus isolated in Kenya between 1964 and 1982 have been compared with data obtained in complement-fixation and neutralization tests. There was a continual change in the oligonucleotide maps obtained for all the serotypes examined. This genetic heterogeneity was generally associated with antigenic variation. Viruses isolated during the 12-month course of an epidemic of the SAT 1 serotype showed few changes in their oligonucleotide fingerprints, and were serologically related. These maps form a data base that will be useful in future epidemiological studies on the maintenance and spread of foot-and-mouth disease virus in this region.

Analysis of Ross River virus genomic RNA using HaeIII digests of single-stranded cDNA to infected-cell RNA and virion RNA

To study genetic relationships between isolates of Ross River virus (RRV), an alphavirus with a chromosome of approximately 12,000 nucleotides, total high-molecular-weight RNA from RRV-infected baby hamster kidney (BHK) cells was transcribed into 32P-labeled, complementary DNA using reverse transcriptase and random calf-thymus DNA primers. The cDNA was digested with HaeIII or TaqI (restriction nucleases which cleave single-stranded DNA), and the restriction fragments separated on a standard DNA sequencing gel. The resulting HaeIII or TaqI restriction digest profiles mainly comprised virus-specific bands; cell RNAs were transcribed poorly. In reconstruction experiments, purified 49 S RRV genomic RNA and a 10-fold mass excess of mock-infected-cell RNA were reverse transcribed in the same reaction mix. Under these conditions there was no interference with the transcription of viral RNA sequences. When the level of viral RNA was lowered to one-hundredth that of cell RNA in the reaction mix, there was no qualitative change in restriction digest profiles. The procedure is rapid, simple, uses small amounts of 32P, does not require purification of virus or viral RNA, and permits cross-comparison between several virus strains on a single one-dimensional gel. The method should be applicable to other single-stranded RNA viruses of moderate genome complexity.

Characterization and myocarditic capabilities of coxsackievirus B3 variants in selected mouse strains

Two variants of coxsackievirus B3 (CVB3) were compared with the original myocarditic parent variant (CVB3m) for myocarditic properties in several strains of mice. The ts1R variant produced little to no myocarditis in any of the nine mouse strains examined. The ts10R variant and CVB3m could be differentiated on the basis of the extent of myocarditis induced in mice of selected H-2b and H-2k haplotypes and in the female versus the male responses of two other inbred strains. Virus quantities recovered from the hearts of myocarditic mice did not correlate with the extent of disease. The three variants could not be differentiated on the basis of: (i) rate and extent of adsorption to heart tissue homogenates, (ii) kinetic neutralization rates with antiserum directed against CVB3m, (iii) 125I labeling of surface regions of polypeptides on purified particles, or (iv) rates of heat inactivation of infectivity at 50 degrees C. These data suggest that differences in pathogenicity cannot be attributed to major alterations in capsid polypeptides. Oligonucleotide fingerprint maps of T1 RNase digests of the genomes of purified particles of the three CVB3 variants showed distinct differences. Thus, the extent of myocarditis induced by CVB3 variants in a mouse model is affected by some subtle expression of the genome, presumably not involving capsid polypeptides, as well as by the haplotype and sex of a given mouse host species.

Applications of Oligonucleotide Fingerprinting to the Identification of Viruses

This chapter focuses on applications of oligonucleotide fingerprinting to the identification of viruses. Fingerprinting is a technique by which oligonucleotides, produced by cleavage of RNA molecules with specific ribonucleases, are separated in two dimensions. It is a definitive method of identifying RNA viruses according to their genotypes. It is not subject to the problems of antigenic drift or antigenic convergence that complicate serological identification. Furthermore, it provides a semiquantitative means of following the evolution of viral genomes in nature. Because all regions of the genome are represented by the large diagnostic oligonucleotides, a survey of the total genomic changes can be monitored. Fingerprinting has two limitations as a diagnostic tool. First, although highly definitive, fingerprinting is not as rapid or inexpensive as serological techniques and cannot be as easily scaled up for routine identification of a large number of samples. Second, the evolutionary range of fingerprinting is short and relationships may not be evident for isolates of rapidly evolving viruses obtained over long intervals. However, these limitations are not large, compared to the full benefits offered to the virologist by the fingerprinting method.

Application of RNase T1 one- and two-dimensional analyses to the rapid identification of foot-and-mouth disease viruses

The analysis of several isolates of foot-and-mouth disease virus by RNase T1 fingerprinting of the 32P-labeled RNA is described. It has been shown that use of the 35S induced RNA instead of the virus particle RNA has two advantages. (i) About 40 times more radioactivity is incorporated into the induced RNA. (ii) The RNA can be prepared much more rapidly, thus increasing the value of the technique in rapid diagnosis. One-dimensional maps, in which the RNase T1 oligonucleotides are separated according to size, have been shown to provide a valuable screening method for distinguishing between viruses. Those viruses giving similar one-dimensional maps also gave similar two-dimensional maps. The value of using the length of the polycytidylic acid tract of foot-and-mouth disease virus as a diagnostic tool is also discussed.

A molecular approach to the diagnosis of virus infections

Virus diseases are usually diagnosed by serological methods, provided specific antisera are available. With a "new" virus, however, knowledge of its physical and chemical properties is necessary before it can be assigned to one of the existing families. If a specimen contains sufficient virus, electron microscopy is the most valuable first test to apply because this often allows the agent to be placed immediately in a virus family. Further characterization can be achieved by measuring the stability of the virus in lipid solvents. With unenveloped viruses, the density in cesium chloride is a valuable diagnostic property. A more exact characterization can be made by examining the nucleic acid and protein of the virus. RNA viruses, for example, can be identified with great precision using base sequence homology and ribonuclease T1 mapping. Similar precision can be achieved with DNA viruses by the use of restriction endonucleases. Examination of the proteins of both RNA and DNA viruses also allows similar viruses to be distinguished. These methods have proved valuable in the epidemiology of those diseases for which serological methods did not allow the isolates to be identified with certainty.

Nucleotide sequence heterogeneity of the RNA from a natural population of foot-and-mouth-disease virus

The genomic RNA from isolates of foot-and-mouth-disease virus (FMDV) of serological types O or C obtained during epizootic outbreaks have been analysed by two-dimensional gel electrophoresis of the T1 RNase-generated oligonucleotides (T1 fingerprinting). Among virus isolates that are closely related serologically, 4-12 oligonucleotide changes were detected constitute the genome, the variations affect 0.7%-2.2% positions in FMDV RNA. Higher nucleotide-sequence divergence exists between the genomic RNAs from serologically unrelated viruses, while a 100-fold lower RNA sequence heterogeneity has been detected by analysis of individual clones derived from one viral isolate. Oligonucleotide mapping indicates that the variant oligonucleotides are scattered throughout the FMDV genome. We suggest that extensive genetic variability at many RNA sites is the basis for the antigenic diversity of FMDV.

Analysis of the genome of an endogenous, ecotropic retrovirus of the AKR strain of mice: micromethod for detailed characterization of high-molecular-weight RNA

A detailed characterization of the genome of an endogenous, ecotropic type C virus, the Akv virus, is presented. Approximately 100 RNase T1-resistant oligonucleotides characteristic of the Akv genome were identified by two-dimensional gel electrophoresis, and the complete nucleotide sequence is presented for 75 of these oligonucleotides. A correspondence between the sequence of some of these oligonucleotides and the amino acid sequence of some virus-coded gag gene proteins is reported. For this study we developed methods suitable for the analysis of high-molecular-weight RNA species in nanogram quantities. The in vitro labeling procedures used here led to uniform labeling of the unique oligonucleotides.

Nucleotide sequences adjacent to the proteins covalently linked to the cowpea mosaic virus genome. Sequence determination after labelling in vitro using RNA ligase

The sequences of the first 17 nucleotides of cowpea mosaic virus middle and bottom RNAs adjacent to the covalently-linked proteins have been determined. Sequences of the oligonucleotides, produced by complete T1 RNase digestion, were established after labelling of the 3' termini in vitro using RNA ligase. Both sequences are A/U-rich, the first nine nucleotides being identical.

Nucleotide sequence of turnip yellow mosaic virus coat protein mRNA

The primary structure of the coat protein messenger RNA of turnip yellow mosaic virus is presented. This sequence is the first complete nucleotide sequence of the coat protein messenger of a plant virus to be reported. The coding region, consisting of 567 nucleotides, is flanked by a 5' noncoding region of 19 nucleotides (not including the initiation codon and the cap structure) and by a 3' noncoding region of 109 nucleotides (including the termination signal). The coat protein mRNA has a base composition identical to that of the genome RNA with, in particular, the same high content in cytosine (38%). The codons that govern the incorporation of amino acids into the coat protein are nonrandomly utilized: is greater than 50% of the time the third base of the codons used is a cytosine. This pattern of codon preference is particularly marked for Leu, lle Val, Thr and Cys.

Nucleotide sequence at the 5' extremity of tobacco-mosaic-virus RNA. 1. The noncoding region (nucleotides 1-68)

The sequence of the 5' noncoding region of tobacco mosaic virus RNA has been determined. The noncoding region is 68 nucleotides long and is unusual in that it contains no internal guanosine residues. The long T1 oligonucleotide containing the guanosine-free tract was isolated from a T1 ribonuclease digest of tobacco mosaic virus RNA and sequenced by labelling techniques in vitro using polynucleotide kinase. The guanosine-free tract is terminated by the first potential initiation codon in the RNA molecule and several lines of evidence suggest that this AUG triplet is operational in initiating viral protein synthesis (see following paper). The 5'-noncoding region cannot base-pair extensively with the 3'-terminal sequence of 18-S ribosomal RNA from rabbit reticulocytes.

The 3'-Terminal nucleotide sequence of encephalomyocarditis virus RNA

Poly(A)-containing encephalomyocarditis virus RNA functions as an excellent template for cDNA synthesis in vitro with an RNA-dependent DNA polymerase in the presence of an oligothymidylate primer. Under appropriate conditions, discrete transcripts of increasing chain length were obtained, suitable for sequence analysis. A limited cDNA fragment of 36 nucleotides, primer (dT)10 included, was synthesized when dGTP was omitted from the reaction mixture and its primary structure was elucidated using direct DNA-sequencing methods. The complement corresponds to the 3' end of encephalomyocarditis RNA. The hexanucleotide (5'-3')(A-A-U-A-A-A) found in this sequence is also present in all 3' non-coding regions of poly(A)-containing eukaryotic mRNAs studied until now, in nearly identical positions relative to the poly(A) tail. The possible biological significance of this structural homology is discussed.

The direct anti-viral activity of single stranded polyribonucleotides. I. Potentiation of activity by mixtures of polymers which do not anneal

Mixtures containing equal masses of polyinosinic acid (poly (I)) and copoly­mers containing poly(5-hydroxycytidylic acid), (poly(ho 5 C) copolymers), protect mice against encephalomyocarditis (e. m. c.) virus infection and the protective effect is greatest 6 h before infection. The batches of poly(ho 5 C) copolymer used in these studies were obtained by bromine water treat­ ment of polycytidylic acid (poly(C)) and contained cytidine, bromocytidine and hydroxycytidine residues with the latter component comprising between 50% and 81% of the total residues in different preparations. These copolymers were used in solution or in a gelled form obtained by freezing in the absence of salt. Evidence is presented which shows that double stranded complexes do not form when the poly(ho 5 C) copolymers are mixed with poly(I). Protection of mice with mixtures of poly(I) and poly(ho 5 C) copolymer was slightly greater than had previously been observed with sequential administration of poly(I) followed by poly(C) or the homopolymer form of poly(ho 5 C). The gelled form of poly(ho 5 C) copolymer conferred slightly greater protection than poly(ho 5 C) copolymer used in the soluble state. The percentage of hydroxycytidine residues in the copolymers did not affect the degree of protection conferred by mixtures of the copolymers with poly (I). Administration of mixtures of poly(I) and soluble poly (ho 5 C) copoly­mer by the intraperitoneal route was more effective than the intravenous route when high doses were used at 6 h before infection. At this time, 200 μg/mouse of a mixture of poly (I) and poly(ho 5 C) copolymer was as protec­tive as 60μg/mouse poly(I:C) but the toxicity of mixtures of poly(I) and poly(ho 5 C) was less than one tenth that of poly(I:C). The mechanism of the protective effect with single stranded polynucleo­ tides cannot yet be stated with confidence. However, the protection by mixtures of poly(I) and poly(ho6C) copolymer does not seem to be through interferon production. Serum from mice treated with the nurture of polynucleotides cannot confer protection on other mice subsequently exposed to infection. Further, the mixtures do not hypo-reactivate the protective effect of poly (I : C) treatment which would have been expected had both effects had a common basis in the interferon phenomenon. Moreover, treatment with the mixture does not result in a stimulation of immune response produced by e. m. c. virus infection.

Structural features of encephalomyocarditis virus RNA from analysis of reverse transcription products

The presence in encephalomyocarditis (EMC) virus RNA of homonucleotide tracts 10 nucleotides or more in length has been investigated by testing the ability of homo-oligodeoxynucleotides to prime DNA synthesis in the reverse transcriptase from avian myeloblastosis virus. Neither (dC)10 nor (dA)10 promoted incorporation of [3H]deoxynucleotides into acid-insoluble material but (dG)10 and (dT)12-18 were effective primers and produced DNA products approximately 2000 nucleotides in length. We conclude that there are single-stranded oligo(rC) and oligo(rA) tracts in native EMC virus RNA at 37 degrees C. Kinetic analysis indicated that oligo(dT) priming is similar to priming on ovalbumin mRNA and that it gives rise to only one DNA product per template molecule. Oligo(dG) priming appears to be complicated by self-aggregation of the primer. Oligo(dT)-primed and oligo(dG)-primed DNA have both been separated on alkaline-sucrose gradients into two peaks of which only the 'heavier' will hybridise to EMC virus RNA. Competitive hybridisation experiments indicate that the 'heavy' oligo(dT)-primed and oligo(dG)-primed DNA fractions hybridise to overlapping sequences of EMC virus RNA and place the priming regions of EMC virus RNA approximately 500 nucleotides apart during reverse transcription.