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Transformation-defective (td) mutants with different sizes of genomic RNA were isolated from the Prague strain of Rous sarcoma virus, subgroup C(PR-C). All six td viruses (tdTYPR-C) isolated from a single UV-irradiated stock of PR-C (clone 2 of TYPR-C) had slightly longer RNA than did the ordinary class b RNA of tdB77 and Rous-associated virus-7. td viruses spontaneously segregated in uncloned TYPR-C also contained genomic RNA of a size similar to tdTYPR-C RNA. On the other hand, two td mutants isolated from another stock of PR-C (LAPR-C) had the class b RNA. Fingerprint analysis confirmed that tdTYPR-C and tdLAPR-C were derived by deletion from clone 2 of TYPR-C and LAPR-C, respectively, and also showed that clone 2 of TYPR-C had sequences in its genome RNA different from those of LAPR-C, although it gave a fingerprinting pattern similar to the latter. These results strongly suggest that differences between the nucleotide sequences in TYPR-C and LAPR-C RNA may result in different extents of deletion.

The level of nucleotide sequence conservation between the RNAs of type A and type O foot-and-mouth disease virus (FMDV) has been compared by three methods. (I) RNA hybridization of fragments containing either the poly(C) tract at the 5' end of the RNA of the poly(A) tract at the 3' end of the RNA indicates that there is a similar level of sequence conservation (65% homology) across the genome. RNase T1 fingerprinting of these fragments did not show the presence of any long regions of completely conserved nucleotides apart from the poly(C) and the poly(A) tracts. (2) RNase T1 fingerprints of the RNA on the 5' side of the the poly(C) tract (the S fragment) show that there is more conservation in this region of the RNA than indicated by the hybridization results. (3) Direct nucleotide sequencing of the poly(C) tract and of the 54 nucleotides at the 5' end of the two genomes shows that there is considerable sequence conservation at the extreme 5' end of the RNA.

The functionally active fragments MS2 R(-53 leads to 6) and MS2 R(-53 leads to 3) comprising the regulatory region for the replicase cistron have been isolated from MS2 RNA-coat protein complex following T1 RNase digestion. In order to obtain shorter fragments, active in coat protein binding and initiation of translation, MS2 R(-53 leads to 6) was cleaved with S1 nuclease. The results indicate that S1 nuclease attacks the most susceptible loop regions of the two hairpin helices of MSZ R(-53) leads to 6). Among the three fragments which have been isolated, only MS2 R(-35/33 leads to 6) containing the intact hairpin (b) region with initiation codon AUG is active in the coat protein binding. Functional activity exerted by another polynucleotide MS R(-17 leads to 6) supports the assumption that specific binding with the coat protein is determined by the hairpin (b) region prior to the replicase cistron.

Retroviruses have been isolated from the tissues of human leukemia patients. Previous studies have shown that these isolates share some antigenic determinants with the family of viruses isolated from the woolly monkey and gibbon ape and that they exhibit partial nuclei acid homology with this same group of viruses. We have compared the RNAs of the viruses by two-dimensional polyacrylamide gel electrophoresis of the large RNase T1-resistant oligonucleotides. The degree of sequence identity between the RNAs was determined by the similarity of their RNase T1-resistant oligonucleotide pattern on gels, fingerprints, and in some cases by partial sequence analysis of individual oligonucleotides. This technique permits us to determine the degree of sequence identity among related RNA species. From our studies we conclude that viruses isolated from the tissues of two human leukemia patients, A1476 and SKA 21-3, as well as some subcultures of a virus isolated from the leukemic tissues of a third patient, HL23V, are closely related to the wooly monkey virus. However, the fingerprints of other HL23 viral isolates are very similar to that of GaLVSF, a gibbon ape leukemia virus isolated from a lymphosarcoma.

The 3' end of the genomic RNA of Newcastle disease virus (NDV) has been sequenced and the leader RNA defined. Using hybridization to a 3'-end-labeled genome, leader RNA species from in vitro transcription reactions and from infected cell extracts were found to be 47 and 53 nucleotides long. In addition, the start site of the 3'-proximal mRNA was determined by sequence analysis of in vitro [beta-82P]GTP-labeled transcription products. The genomic sequence extending beyond the leader region demonstrated an open reading frame for at least 42 amino acids and probably represents the amino terminus of the nucleocapsid protein (NP). The terminal 8 nucleotides of the NDV genome were identical to those of measles virus and Sendai virus while the sequence of the distal half of the leader region was more similar to that of vesicular stomatitis virus. These data argue for strong evolutionary relatedness between the paramyxovirus and rhabdovirus groups.

The influenza virus H1N1 (the A/USSR/90/77 strain) that reappeared in 1977 after the H1N1 influenza viruses had disappeared from the human population, is compared with the A/FM/1/47 and the A/FW/1/50 influenza viruses by the method of oligonucleotide mapping of individual segments of the viral RNAs. Seven genes of the A/USSR/90/77 virus appear to be very similar to the corresponding genes of the A/FW/1/50 virus, whereas the gene coding for the M protein displays considerable homology to the corresponding gene of the A/FM/1/47 virus. The data demonstrate that the A/USSR/90/77 strain is a recombinant virus.

Two plaque-size variants of the neurotropic JHM strain of mouse hepatitis virus have been isolated from the virus stock after eight serial passages in suckling mouse brain. One variant, JHM-DL, produces large plaques, while the other, JHM-DS, produces small plaques in tissue culture. DS replicates more slowly, has a lower virus yield in vitro, and is less virulent for mice than DL. They also differ in their pathogenicity for mice: JHM-DL infection results in acute encephalomyelitis while JHM-DS infection results in demyelination. Oligonucleotide fingerprint analysis of the RNA genomes of these two variants revealed that they had almost identical genetic sequences. Each variant, however, had a unique oligonucleotide spot not found in the other. The unique spot of the large plaque variant, JHM-DL, was localized at approximately 3 to 5 kb from the 3' end, while the JHM-DS unique spot was mapped at 14 to 15 kb from the 3' end of the genome. We have further shown that these oligonucleotide changes are not correlated with the plaque morphology. These two viruses may be useful for studying the molecular basis of virus-induced demyelination.

The src genes of different Rous sarcoma virus (RSV) strains have been reported to be highly conserved by some investigators using RNA-cDNA hybridization, whereas others using oligonucleotide, peptide, and serological analyses have judged src genes to be variable in 30 to 50% of the respective markers. Moreover, distinctive src oligonucleotides and peptides of so-called recovered RSVs (rRSV's) whose src genes were reported to be experimentally transduced from the cell are thought to represent specific markers of host-derived src sequences. By contrast, we have pointed out previously that these markers may represent point mutations of parental equivalents. Here we have compared the src-specific sequences of eight RSV strains and of two rRSV's to each other and to a molecular clone of the src-related chicken locus. Our comparisons are based on RNase T(1)-resistant oligonucleotides of RNA hybridized to src-specific cDNA, which was prepared by hybridizing RSV cDNA with RNA of isogenic src deletion mutants, or to a cloned cellular src-related DNA. All of the approximately 20 src-oligonucleotides of a given RSV strain were recovered by src-specific cDNA's of all other RSV strains or by cellular src-related DNA. The number of oligonucleotides varied slightly with the length of the src deletion used to prepare src-specific cDNA, thus providing a measure for src deletion mutants. Our data indicate that the src genes of all RSV strains tested, including the two reportedly transduced from the cell, are about 98% conserved and completely allelic with only scattered single nucleotide differences in certain variable regions which are subject to point mutations. Hence, based on the src oligonucleotide markers analyzed by us and others, we cannot distinguish between a cellular and viral origin of rRSV's. However, the following are not compatible with a cellular origin of rRSV's. (i) The only putative oligonucleotide marker which is exclusively shared by the two rRSV's studied and which differs from a parental counterpart in a single base was not detectable in cellular src-related DNA. (ii) The number of different allelic src markers observed by us and others in rRSV's was too large to derive from one or two known cellular src-related loci. (iii) The known absence of linkage of the cellular src-related locus with other virion sequences was extended to all non-src oligonucleotides, including some mapping directly adjacent to src. This is difficult to reconcile with the claim that transformation-defective, partial src deletion mutants of RSV which contain both, one, or, as we show here, possibly no src termini nevertheless transduce at the same frequencies, even though homologous, single or double illegitimate recombinations would be involved. Given (i) our evidence that src genes are subject to point mutation under selective conditions similar to those prevailing when rRSV's were generated and (ii) the lack of absolute evidence for the clonal purity of the transformation-defective, partial src deletion mutants of RSV used to generate rRSV's, we submit that the src genes of rRSV's could have been generated by cross-reactivation of nonoverlapping src deletions or mutation of src variants possibly present in transformation-defective, partial src deletion mutants of RSV. To prove experimental transduction, unambiguous markers need to be identified, or it would be necessary to generate rRSV's with molecularly cloned transformation-defective, partial src deletion mutants of RSV. Although our evidence casts doubt on the idea that specific src sequences of rRSV's originated by transduction, the close relationship between viral src and cellular src-related sequences argues that src genes originated at one time in evolution from the cell by events that involved illegitimate recombination and deletion of non-src sequences that interrupt the cellular src locus.

The genomes of influenza C viruses isolated from pigs in Beijing, China during 1981/82 and of human influenza C virus strains isolated between 1947 and 1981 were analysed by comparison of RNA migration patterns on gels and by two-dimensional oligonucleotide (ON) mapping. The genomes of the pig isolates were closely related to one another, though in part distinguishable by point mutations. They were similar to but more distantly related to the genomes of human influenza C viruses. The genome of the C/pig/Beijing/10/81 isolate differed from that of the C/pig/Beijing/32/81 isolate obtained on the same day at the same place by a number of mutations which were all located in RNA segments 1 and 2 as shown by ON mapping. This result suggests that the two isolates are genetically related by a reassortment event which is likely to have occurred in nature. The question whether or not pigs are a natural reservoir for human influenza C viruses cannot be answered at present.

We have recently shown that a newly isolated avian sarcoma virus, UR2, is defective in replication and contains no sequences homologous to the src gene of Rous sarcoma virus. In this study, we analyzed the genetic structure and transforming sequence of UR2 by oligonucleotide fingerprinting. The sizes of the genomic RNAs of UR2 and its associated helper virus, UR2AV, were determined to be 24S and 35S, respectively, by sucrose gradient sedimentation. The molecular weight of the 24S UR2 genomic RNA was estimated to be 1.1 x 10(6), corresponding to 3,300 nucleotides, by gel electrophoresis under the native and denatured conditions. RNase T1 oligonucleotide mapping indicated that UR2 RNA contains seven unique oligonucleotides in the middle of the genome and shares eight 5'- and six 3'-terminal oligonucleotides with UR2AV RNA. From these data, we estimated that UR2 RNA contains a unique sequence of about 12 kilobases in the middle of the genome, and contains 1.4 and 0.7 kilobases of sequences shared with UR2AV RNA at the 5' and 3' ends, respectively. Partial sequence analysis of the UR2-specific oligonucleotides by RNase A digestion revealed that there are no homologous counterparts to these oligonucleotides in the RNAs of other avian sarcoma and acute leukemia viruses studied to date. UR2-transformed non-virus-producing cells contain a single 24S viral RNA which is most likely the message coding for the transforming protein of UR2. On the basis of the uniqueness of the transforming sequence, we concluded that UR2 is a new member of the defective avian sarcoma viruses.

Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. Two strains, MHV-K and MHV-D, which were isolated in Japan and, which cause anaplasia and necrosis of bone marrow and diarrhea, respectively, were found to be closely related to MHV-A59, the prototype MHV. Two other MHV strains, isolated from nude mice, were found to have diverged extensively from the known MHV strains. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. Genetic divergence during persistent infection may be one of the mechanisms by which the MHV diverges.

We used T1 oligonucleotide maps, in conjunction with available nucleotide sequences of appropriate C-type viruses, to identify regions of the viral genome that distinguish two biological classes of mink cell focus-forming (MCF) viruses described previously by Cloyd et al. (J. Exp. Med. 151:542-522, 1980). We found that leukemogenic MCF viruses from thymus differed from non-leukemogenic MCFs isolated from nonthymic neoplasms in nucleotide sequences encoding Prp15E and the U3 portion of the long terminal repeat (LTR). The thymic isolates possessed recombinant Prp15E genes, with the 5' to mid portion derived from their ecotropic parents and the extreme 3' portion invariably derived from their nonecotropic parents. These viruses probably derived the entire U3 portion of their LTRs from their nonecotropic parents. The nonthymic MCFs appeared to inherit their entire Prp15E coding region from their nonecotropic parents. We failed to detect consistent differences in gp70-coding sequences between the two groups of MCFs, but this may simply reflect limitations of the data. The studies presented here, in conjunction with studies from a number of labs indicating a role for MCF gp70 in leukemogenesis, indicate that three genetic elements, gp70, p15E, and the U3 portion of the LTR, may all play a role in determining the leukemogenic phenotype of type C viruses of high-leukemic inbred mice.

Recombinants with a centrally located crossover point were selected from crosses between poliovirus type 1 strains and intertypic (type 3/type 1) recombinants. Two such recombinants were characterized in some detail. In one of them (v1/a1-6), the 5' half of the genome was derived from a virulent type 1 strain, while the 3' half came from an attenuated type 1 strain. The genome of the other recombinant (a1/v1-7) had the reverse organization, with the 5' and 3' halves being derived from the type 1 attenuated and virulent strains, respectively. As deduced from the RNase T1 oligonucleotide maps, the a1/v1-7 genome also had a relatively short centrally located insert of the poliovirus type 3 origin. Both recombinants exhibited ts phenotypes. The RNA phenotypes of the recombinants corresponded to that of the parent donating the 3' half of the genome, v1/a1-6 and a1/v1-7 expressing RNA- and RNA +/- characters, respectively. Despite being a ts RNA- virus, v1/a1-6 proved to be neurovirulent when injected intracerebrally into Cercopithecus aethiops monkeys, although it exhibited a somewhat diminished level of pathogenicity as compared to its virulent type 1 parent. Recombinant a1/v1-7 behaved as an attenuated strain. These data supported our previous conclusion drawn from the experiments with intertypic poliovirus recombinants that the attenuated phenotype of poliovirus depends largely on the structure of the 5' half of its genome, although mutations of the 3' half may alleviate the virulence of the virus to a degree.

Biological and biochemical characters of seven enterovirus 71 (E71) isolates were compared. Four isolates (two from patients with hand, foot and mouth disease [HFMD] and two from patients with encephalitis) grew in cynomolgus monkey kidney cells both at 39.5 and 35 degrees C. However, the remaining three strains (from patients with HFMD) grew at 35 degrees C, but not at 39.5 degrees C. Three temperature-resistant and two temperature-sensitive strains were tested for neurovirulence in monkeys. Temperature-resistant strains were shown to be neurovirulent, whereas temperature-sensitive strains were less neurovirulent. The results suggest correlation between temperature-sensitive growth and neurovirulence in monkeys of E71. Variation in the electrophoretic mobility of the viral polypeptides was detected in three out of seven strains. The fingerprinting of oligonucleotides generated from the viral genome showed similar patterns in two isolates from patients with HFMD and one from patient with encephalitis and variable patterns in each genomic map of remaining four strains. These variations of polypeptide patterns and of oligonucleotide maps could not be correlated with pathogenicity (encephalitis or HFMD), temperature-sensitive growth and neurovirulence in monkeys.

The genetic changes occurring in the BeAn strain of Theiler's murine encephalomyelitis virus (TMEV) during persistent infection in the mouse central nervous system (CNS) were studied. RNase T1-oligonucleotide fingerprinting of the RNAs of 28 BeAn viruses isolated at various times postinfection (p.i.) demonstrated that mutation occurred throughout the infection. Although plaque-purified BeAn virus was used to inoculate mice intracerebrally, genetically different viruses were recovered from the CNS. One to three oligonucleotide changes were found up to Day 152 p.i., but all three viruses isolated at Day 180 had four to nine oligonucleotide changes. No pattern of oligonucleotide changes occurring in different virus isolates was found, yet three viruses isolated from different animals at Day 180 had the same four new oligonucleotides. Overall, the number of oligonucleotide changes represented a 0.1 to 1.2% change in the virus genome. In addition, the analytical two-dimensional gel technique of P.Z. O'Farrell, H.M. Goodman, and P.H. O'Farrell (Cell 12, 1133-1142, 1977) suggested that mutation occurred in all virus isolates. In nine isolates, one to three proteins were found to have charge changes, and in general, as many nonstructural proteins had charge changes as structural proteins. P20, a nonstructural protein probably equivalent to the protease described for encephalomyocarditis virus, was found to have shifted cathodally in six different viruses. Several virus isolates had doublet patterns, suggesting the possibility that within the CNS, subpopulations existed which had proteins of slightly different charge or that virus-specified proteins had been modified after translation. Finally, antigenic variation of neutralizing site(s) on BeAn virus isolates as a way for virus to evade immune surveillance and thereby maintain the persistent state was studied. The ability of mouse serum to neutralize persisting virus isolates was not significantly different from the ability to neutralize the infecting virus. Therefore, antigenic variation does not appear to be a factor in TMEV persistence.

Genomic changes occurring in the attenuated W-2 strain of poliovirus 2 during persistent infection of the central nervous system of immunosuppressed mice were analyzed. The RNase T1 oligonucleotide fingerprints of 34 different viruses, isolated from the brains and spinal cords of paralyzed and nonparalyzed mice during a 105-day period, were used to quantitate and compare the mutations occurring in each isolate. Although mice were inoculated with plaque-purified virus, genetically distinct viruses were recovered from the central nervous system. The number of oligonucleotide changes occurring in isolates from paralyzed mice generally was greater than that observed in isolates from nonparalyzed mice. However, differences in the extent of mutation in isolates from the two groups of mice did not appear to be related to the level of virus replication. In paralyzed mice, the number of oligonucleotide changes on average was greater in viruses isolated during the first 60 days of the infection than in the last 45 days. The number of oligonucleotide changes was essentially constant throughout the infection, however, in viruses isolated from the brains of nonparalyzed mice. In addition, several specific oligonucleotide changes were found only in viruses isolated from paralyzed animals.

Six avian paramyxoviruses isolated from wild and domestic ducks in the United States, Hong Kong and Japan were characterized antigenically and genetically. All viruses examined were shown to be antigenically closely related. Oligonucleotide patterns of duck/Miss/334 and duck/Miss/406 were apparently distinguishable from those of duck/Miss/116 and duck/Miss/320 isolated in the same area of the United States. On the other hand, two viruses isolated from a domestic duck in Hong Kong (duck/Hong Kong/D3/75) and from a domestic duck in Japan (duck/Tokyo/41/78) were genetically very similar to that of duck/Miss/116, suggesting that these three viruses represent a genetically homogeneous group and may be of the same origin.

Several natural variants of mouse hepatitis viruses have been compared by the T1-oligonucleotide fingerprinting technique. In general, they have diverged quite extensively. However, MHV-3, a hepatotropic strain, and A59, a nonpathogenic strain, were found to be extremely related. Yet, each of them contains 2-4 specific oligonucleotides. One of the MHV-3-specific oligonucleotides was mapped in 30S poly(A)-containing RNA or 6-7 Kb from the 3-end and the other near the 5'-end of the genome. These two genetic regions might be associated with viral pathogenicity. In addition, two JHM plaque variants, DL producing large plaques and DS producing small plaques, were also compared. They share almost all T1-oligonucleotides, but each contains one unique spot. The DL-specific oligonucleotide was mapped in 21S poly(A)-containing RNA or at about 4 kb from the 3'-end. Finally, the MHV genome was found to contain the "cap" structure, confirming that it is a positive-stranded RNA.

We have found that the LA23 t/s mutant of Rous sarcoma virus (phenotype Prague B), even when passaged repeatedly at high multiplicity of infection, does not give rise to transformation defective deletion mutants comparable to those derived from RSV. In view of this fact and of the high rate of production of this mutant at 41 degrees C, we have undertaken a detailed analysis of the genome of this virus by ordering all large T1 oligonucleotides and by determining their nucleotide sequences. The results indicate a high degree of mutation in the onc gene as compared to that of Pr-A or Pr-B.

We have analyzed the viral RNA of a variant of avian acute leukemia virus MC29, termed HBI. This virus was isolated during in vitro passage of a partially transformation-defective (td) mutant of MC29 (td10H-MC29) in chicken macrophages. While td10H-MC29 has a reduced ability to transform macrophages in vitro or to induce tumors in vivo, HBI-MC29 transforms macrophages efficiently and induces in vivo a high incidence of lymphoid tumors. Electrophoretic analysis of HBI-MC29 genomic RNA revealed that it has a complexity of 5.7 kilobases, like the RNA of wild-type (wt) MC29, and that it is 0.6 kilobases longer than the 5.1-kilobase RNA of the deletion mutant td10H-MC29. Analysis of the viral RNAs of two clonal isolates of HBI-MC29 by T1 oligonucleotide fingerprinting showed that sequences from the viral transformation-specific region, v-myc, which are deleted in td10H RNA, are present in HBI RNA. Moreover, hybridization of HBI RNA to molecularly cloned subgenomic fragments of wtMC29 proviral DNA, followed by fingerprint analysis of hybridized RNA, showed that the entire v-myc-specific RNA sequences defined previously are present. Hybridization to cloned DNA of the normal chicken locus c-myc shows a close relationship between HBI v-myc RNA and c-myc DNA, especially in the sequences which were deleted from td10H-MC29. T1 oligonucleotide maps of HBI and td10H RNAs were prepared and compared. Total conservation of the oligonucleotide pattern is observed in the overlapping v-myc regions, while the partial structural genes gag and env show some variations, most of which can be directly proven to be due to point mutations or recombination with helper viral RNAs that were analyzed in parallel. Recombination of td10H-MC29 with c-myc, followed by recombinational and mutational changes in the structural genes during passage with helper virus, could be a possible explanation for the origin of HBI.

The results of ribonuclease T1 oligonucleotide fingerprint analyses indicate that influenza virus messenger RNAs are incomplete transcripts of the corresponding genome RNAs and that in this respect they differ from the unpolyadenylated virus specific complementary RNAs obtained from infected cells. From the position of the untranscribed oligonucleotide in the virus RNA sequence and the ability or inability of the different transcripts to protect the 5' terminal nucleotide of virus RNAs against nuclease S1 digestion, it is concluded that whereas the unpolyadenylated cRNAs are complete transcripts, the polyadenylated messenger RNAs lack sequences complementary to the 5' end of the genome molecules.

We performed antigenic analysis of the haemagglutinin and neuraminidase subunits of a recombinant virus (A/swine/Kanagawa/2/78) isolated from a pig in Japan in 1978, using a series of monoclonal antibodies to H1 (Hsw1) haemagglutinin and N2 neuraminidases of H2N2 and H3N2 viruses. Results obtained in haemagglutination inhibition tests with five monoclonal antibodies to the haemagglutinin of A/NJ/8/76 (H1N1) revealed that the haemagglutinin of three H1N1 and the recombinant viruses were indistinguishable from that of A/NJ/8/76. The neuraminidase of A/swine/Kanagawa/2/78 was found to be antigenically similar to A/Kumamoto/22/76 (H3N2, A/Victoria/3/75-like strain). The oligonucleotide maps of the entire RNAs of H1N1, H1N2 and H3N2 viruses showed that A/swine/Kanagawa/2/78 (H1N2) virus was more similar to swine (H1N1) virus than to A/Kumamoto/22/76 (H3N2) virus. Radioactive cDNA was prepared by reverse transcription of the recombinant virus RNA using a dodecadeoxyribonucleotide primer and used in DNA-RNA hybridization experiments. The results obtained in molecular hybridization based on blotting procedures showed that all cDNA segments except gene 6 hybridized efficiently with RNAs of swine (H1N1) influenza virus. The sixth cDNA segment was homologous to the corresponding RNA segment of H3N2 virus. The genetic relatedness of A/swine/Kanagawa/2/78 (H1N2) with either A/swine/Kanagawa/4/78 (H1N1) or A/Kumamoto/22/76 (H3N2) was clearly established by hybridization between the cDNA segment probes and viral RNA. It was concluded that the neuraminidase gene of A/swine/Kanagawa/2/78 (H1N2) was derived from a human H3N2 virus, while the seven other genes were from a swine H1N1 virus.

In the present study, six lactate dehydrogenase-elevating virus (LDV) isolates obtained independently from inbred mice were compared by RNA oligonucleotide fingerprint analysis. The genome RNAs of four of the isolates gave unique fingerprint patterns. The patterns obtained for the other two isolates were similar, but not identical to one of the four unique patterns. These results indicate that more than one genotype of LDV exists and that virus isolates can be grouped by genotype. We have also demonstrated the presence of a 3'-terminal poly(A) tract by direct sequencing of 3'-32P-labelled LDV genome RNA. The presence of a 3'-terminal poly(A) tract distinguishes LDV from the members of the family Flaviviridae, which lack a 3'-poly(A), and justifies the current classification of LDV within the family Togaviridae.

Previous studies from this laboratory have provided a high resolution map for 16 tRNA genes located on the continuous heavy DNA strand of bacteriophage T5 DNA (Chen, M.-J., Locker, J., and Weiss, S.B. (1976) J. Biol. Chem. 251, 536-547). All of the T5 tRNA genes were located in three clusters within the DNA C segment, except for tRNAArg, which mapped on the left end of the DNA D segment (Desai, S.M., Hunt, C., Locker, J., and Weiss, S.B. (1978) J. Biol. Chem. 253, 6544-6550). In this report, we present evidence for the presence of eight additional T5 tRNA species, five of which are located in two new loci within the DNA C segment. We also describe a two-dimensional gel electrophoresis system for the separation and isolation of T5 tRNA species from crude infected RNA preparations. The gel electrophoresis system separates tRNA isoacceptors specific for different amino acids; evidence is presented that the isoacceptors for isoleucine, histidine, and serine are coded by different T5 genes.

The genetic heterogeneity generated upon passage of foot-and-mouth disease virus (FMDV) in cell culture has been evaluated by T1-oligonucleotide fingerprinting of genomic RNA. Plaque-purified FMDV O-S7 and C-S8 were propagated by serial low multiplicity infections of BHK-21 (c-13) or IBRS-2 (c-26) cells. In independent parallel passage of the same virus, different oligonucleotide variations were fixed in the RNAs. T1-oligonucleotide fingerprinting of RNA from 34 individual viral clones derived from two passaged populations shows an extensive heterogeneity, with some mutations present in only one of the cloned genomes analyzed. Some FMDV variants are phenotypically distinct in that they yield increased progeny in infections of cell monolayers. From the number of variant sequences it can be estimated that each infectious RNA in the population differs in two to eight mutations from the average parental sequence. Thus, passaged FMDV populations consist of a pool of variants, an observation previously made with phage Q beta (E. Domingo, D. Sabo, T. Taniguchi, and C. Weissmann, Cell 13, 735-744, 1978). The FMDV genome must be described as a fluctuating distribution of sequences due to its high mutability. This may be the basis of the extensive genetic and antigenic diversity of this virus in nature.

RNA sequence relationships between the genomes of the Kirsten murine sarcoma virus (MSV-K) complex, the Kirsten murine leukemia virus (MuLV-K) complex, the Gross murine leukemia virus (MuLV-G), and the Moloney murine leukemia virus (MuLV-M) were investigated. Sedimentation analyses revealed the expected 30 and 34 S RNA subunits in the MSV-K complex and a previously undetected 30 S RNA subunit accompanying the 34 S RNA subunit in the MuLV-K complex. Nucleic acid hybridization data indicated that each Kirsten virus 30 S RNA subunit had about 40% sequence homology with the RNA genome of MuLV-G, although these sequences were only partially homologous between the two 30 S subunits. In contrast, the MuLV-K 34 S RNA subunit had 96% sequence homology with the MuLV-G genome, whereas the MSV-K 34 S RNA subunit displayed only 71% sequence homology with the MuLV-G genome. Similar relationships were indicated by oligonucleotide fingerprinting. The oligonucleotide data, taken with published sequence data on the MuLV-G and MuLV-M genomes, enabled us to construct partial sequence maps of the MuLV-K 34 S RNA subunit and the MSV-K 34 and 30 S RNA subunits. The sequence arrangements indicated that (1) the MuLV-K 34 S RNA subunit is a variant of the MuLV-G genome; (2) the MSV-K 34 S RNA subunit is a recombinant molecule, which maintains the length of its leukemia virus parent; and (3) the MSV-K 30 S RNA subunit may have been generated from the MuLV-K 34 S genome by a two-stage process, culminating in the retention of parental sequences only within the U5 and U3 noncoding segments and within several amino-terminal coding segments. Further examination of published retrovirus genome sequences revealed several strategically situated sets of potential recognition signals for transcription and translation and suggested a model for genetic recombination based on mRNA splicing signals and areas of limited sequence homology. This model may explain how foreign gene elements can be inserted into retrovirus genomes to generate either functional or defective recombinant retroviruses.

We have analyzed the structure of OK10-BM virus, an avian acute leukemia virus produced by a bone marrow-derived cell line of macrophage origin, and compared it with that of OK10 AV, an associated virus originally present in the OK10 virus stock. The RNAs of OK10-BM virus and OK10 AV had the same mobility in agarose gels, corresponding to 8.0 to 8.5 kilobases, a size considerably larger than that of the transforming component (5 to 6 kb) of most other avian acute leukemia viruses. Fingerprint analysis showed a close relationship between OK10-BM virus and OK10 AV RNAs. The polypeptide compositions of OK10-BM and OK10 AV viruses were similar except for the envelope glycoproteins. In analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the large envelope glycoprotein of OK10-BM virus migrated at M(r) = 78,000 (gp78), whereas OK10 AV had the characteristic 85,000-dalton glycoprotein (gp85) of nondefective avian leukemia viruses. gp78 was weakly labeled with methionine, glycine, proline, or mannose, suggesting that purified OK10-BM virus had reduced amounts of the modified envelope glycoprotein. In cell-free rabbit reticulocyte lysates, OK10-BM virion RNA directed the synthesis of a 200,000-dalton polypeptide (p200), a 180,000-dalton polypeptide (pr180), and a 76,000-dalton polypeptide (pr76), whereas OK10 AV RNA gave rise only to pr180 and pr76, suggesting that p200 may represent an OK10-BM-encoded transforming protein. No biochemical evidence for the presence of an associated helper virus was found in the OK10-BM virus population produced by the macrophage cell line. However, when OK10-BM virus was serially passaged in chicken embryo fibroblasts, a virus having structural properties similar to those of OK10 AV (OK10 AV-specific oligonucleotides and gp85) appeared after three passages. Moreover, nonproducer clones of transformed cells could be readily obtained in OK10-BM virus-infected quail cell cultures. It is thus likely that the bone marrow-derived macrophage cell line produces a transforming virus defective in its env gene and low amounts of an associated helper virus, which upon transfer to fibroblasts is preferentially replicated.

The nucleotide sequence of an infectious molecular clone of the Akv murine leukemia virus has been determined by the dideoxy chain termination method after subcloning in bacteriophage M13 vectors. The sequence predicts an RNA genome of 8371 nucleotides containing three large open reading frames corresponding to the gag, pol, and env genes. Signal sequences for transcription, splicing, and translation have been identified. The positions of 95 major RNase T1 resistant oligonucleotides of the Akv RNA genome have been located.

Genetic variation in dengue 2 isolates from various geographic areas was examined by oligonucleotide fingerprinting of the 40 S genome RNA. Oligonucleotide maps of geographically isolated and epidemiologically unrelated viruses were very distinct. Direct comparison of the oligonucleotide map of the dengue 2 prototype New Guinea 2 virus, isolated in 1944, with the fingerprints of more recent isolates from the South Pacific indicated that the genome of dengue 2 virus had undergone extensive change although the viruses are serologically indistinguishable. The oligonucleotide map of an isolate from a recent case in Jamaica and a mosquito isolate from Upper Volta, Africa, were recognized to be almost identical, suggesting that virus may have been introduced into the Caribbean from West Africa. Likewise, the fingerprints of isolates from Puerto Rico and the South Pacific shared 80 to 95% of their large oligonucleotides, suggesting that the virus involved in these epidemics may have spread throughout Tahiti, American Samoa, Fiji, and to Puerto Rico in the Caribbean or vice versa. On the basis of these studies, five genetic variants or topotypes of dengue 2 virus have been established: (1) Puerto Rico-South Pacific, (2) Burma-Thailand, (3) the Seychelles, (4) the Philippines, and (5) Jamaica-West Africa. Oligonucleotide fingerprinting offers a highly sensitive and reproducible technical approach to the investigation of dengue 2 virus intratypic variation and possibly to the understanding of the biological variation associated with dengue fever and hemorrhagic disease.

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.

The endogenous viruses of chickens are closely related to the exogenous avian leukosis viruses (ALV) yet as a group differ from these viruses in their host range, growth rate, and oncogenicity. The present study was undertaken to determine the patterns of relationship among the genomes of endogenous and exogenous ALVs. Complete or partial T1 oligonucleotide maps were prepared from the genomes of endogenous viruses that reside at eight distinct loci in chickens. Selected endogenous viruses and recombinants of endogenous or endogenous and exogenous viruses were characterized for host range and growth rate. From these data we could infer the following: (1) Endogenous viruses form a distinct lineage of ALVs with the most distinctive differences occurring in the portion of env that encodes host range and the U3 portion of the long terminal repeat; (2) The U3 sequences of endogenous ALVs determine the low growth rates of these viruses; and (3) Endogenous ALVs have distinctive oligonucleotide markers that allow them to be subclassified into distinct lineages. Our results suggest that endogenous viruses are derived from one another and not from exogenous field strains of ALV. This phenomenon may be related to the unique env encoded host range of endogenous ALVs, their unique U3 encoded growth rates, or perhaps their unique access, as residents of germ line DNA, to germ line cells.

We used two-dimensional gel electrophoresis to obtain fingerprints of RNase T1-resistant oligonucleotides derived from the genomes of Akv-1 and Akv-2 type C viruses of AKR mice. The fingerprints of these two viruses look identical. The products of pancreatic RNase digestion of corresponding oligonucleotides of the two viruses were indistinguishable. These observations are consistent with, but not proof of, the possible identity of the genomes of the Akv-1 and Akv-2 viruses and, thus, of the viral genetic material believed to comprise the Akv-1 and Akv-2 loci of AKR mice.

Avian infectious bronchitis virus, a coronavirus, directed the synthesis of six major single-stranded polyadenylated RNA species in infected chicken embryo kidney cells. These RNAs include the intracellular form of the genome (RNA F) and five smaller RNA species (RNAs A, B, C, D, and E). Species A, B, C, and D are subgenomic RNAs and together with the genome form a nested sequence set, with the sequences of each RNA contained within every larger RNA species (D. F. Stern and S. I. T. Kennedy, J. Virol 34:665-674, 1980). In the present paper we show by RNase T1 oligonucleotide fingerprinting that RNA E is also a member of the nested set. Partial alkaline fragmentation of the genome followed by sucrose fractionation, oligodeoxythymidylate-cellulose chromatography, and RNase T1 fingerprinting gave a partial 3'-to-5' oligonucleotide spot order. A comparison of the oligonucleotides of each of the five subgenomic RNAs with this spot order established that all of the RNAs are comprised of nucleotide sequences inward from the 3' end of the genome. This result is discussed in relation to the multiplication strategy both of coronaviruses and of other RNA-containing viruses.

An intertypic reassortant arenavirus has been obtained from co-infection of BHK-21 cells by two strains of lymphocytic choriomeningitis virus (LCM virus), WE and Armstrong (ARM), having the large/small (L/S) viral RNA genotype of WE/ARM. The two parental viruses have different virulence characteristics in hamsters and guniea-pigs. The reassortant virus induces LCM-WE-type plaques in Vero cell monolayers, but has the avirulent characteristics of LCM-ARM in hamsters and two strains of guniea-pigs. These results suggest that the LCM plaque phenotype is determined by L RNA gene products, while the pathogenic potential in guinea-pigs may be determined by S RNA gene products.

The genome of the defective avian tumor virus MH2 was identified as a RNA of 5.7 kilobases by its presence in different MH2-helper virus complexes and its absence from pure helper virus, by its unique fingerprint pattern of RNase T1-resistant (T1) oligonucleotides that differed from those of two helper virus RNAs, and by its structural analogy to the RNA of MC29, another avian acute leukemia virus. Two sets of sequences were distinguished in MH2 RNA: 66% hybridized with DNA complementary to helper-independent avian tumor viruses, termed group-specific, and 34% were specific. The percentage of specific sequences is considered a minimal estimate because the MH2 RNA used was about 30% contaminated by helper virus RNA. No sequences related to the transforming src gene of avian sarcoma viruses were found in MH2. MH2 shared three large T1 oligonucleotides with MC29, two of which could also be isolated from a RNase A- and T1-resistant hybrid formed between MH2 RNA and MC29 specific cDNA. These oligonucleotides belong to a group of six that define the specific segment of MC29 RNA described previously. The group-specific sequences of MH2 and MC29 RNA shared only the two smallest out of about 20 T1 oligonucleotides associated with MH2 RNA. It is concluded that the specific sequences of MH2 and MC29 are related, and it is proposed that they are necessary for, or identical with, the onc genes of these viruses. These sequences would define a related class of transforming genes in avian tumor viruses that differs from the src genes of avian sarcoma viruses.