- Volume 72, Issue 10, 1991

Comparisons have been made between the p10 and polyhedrin mRNA levels recovered from Spodoptera frugiperda cells infected with Autographa californica nuclear polyhedrosis virus (AcNPV). In molar terms and from 18 h post-infection (p.i.), the polyhedrin mRNA species increased to levels one and a half times to twice as high as the p10 levels. The influence of the polyhedrin leader sequence on the expression of a foreign gene under the control of the polyhedrin promoter was investigated using a series of four recombinant baculoviruses expressing the lymphocytic choriomeningitis virus nucleocapsid (N) protein gene. The different recombinants varied in the length and composition of the upstream polyhedrin mRNA leader sequence. The recombinant containing the full-length polyhedrin leader sequence gave levels of N mRNA comparable to those of AcNPV polyhedrin mRNA. These levels were either equal to (12 h p.i.) or higher (18 to 42 h p.i.) than the p10 levels at corresponding times. Three other recombinants, with different lengths of leader sequence, accumulated significantly lower quantities of N mRNA in comparison to the p10 mRNA levels. However the mRNA levels for the three recombinants were similar (20 to 50% of the p10 level) and did not correspond to their N protein expression levels. By comparing the mRNA and protein levels, it is concluded that the sequence between -8 to +1 of the AcNPV polyhedrin translation-initiating ATG has an important function for mRNA transcription (or accumulation), while the sequences between -32 to -8 affect the overall translation efficiencies.

To contribute to the study of the genetic variability of hepatitis C virus (HCV) we have determined the nucleotide sequence of the E2/NS1 and NS3/NS4 regions of a French isolate using the polymerase chain reaction. Comparison of these nucleotide sequences with those available for American and Japanese isolates showed a significant genetic variability: 5 to 33% and 2 to 30% at the nucleic acid and amino acid levels, respectively. The genetic variability is higher in the E2/NS1 (13 to 33% and 12 to 30% at the nucleic acid and amino acid levels, respectively) than in the NS3/NS4 (5 to 21% and 2 to 7%) regions. The sequence of the French isolate is more closely related to that of the American HCV prototype than to the Japanese HCV isolates. This study confirms the extent of HCV genetic variability.

By the use of strong denaturing agents, a genome-linked protein (VPg)-RNA complex was purified from infectious pancreatic necrosis virus. Ribonuclease treatment of 125I-labelled VPg-RNA released a 90K polypeptide identical to the minor structural polypeptide VP1 (the putative RNA polymerase), as determined by peptide mapping. The polypeptide is linked to the RNA by a serine-5′ GMP phosphodiester bond. The results identify birnaviruses as the only dsRNA viruses with a VPg, the size of which is the largest of the VPgs of RNA viruses.

Human papillomavirus type 6 subtype a (HPV-6a0 was detected in a human invasive tonsillar carcinoma. Southern blot hybridization analysis showed the presence of additional bands when using non-cutting and single-cut restriction enzymes. Molecular cloning yielded two recombinant clones of 8.0 and 1.4 kb in size. The first represents the complete HPV-6a genome. Sequence analysis of the second clone showed a 0.6 kb DNA sequence corresponding to the L2 region of HPV-6a, whereas the rest belongs to cellular sequences. These data show the presence of a usually low risk HPV type in an invasive carcinoma, at an unusual infection site, with viral DNA integrated into the host genome. These findings add evidence in support of the hypothesis of a relationship between HPV infection and at least some ororespiratory cancers.

A one base change (adenine at position 7861) in the long control region (LCR) of the prototype sequence of human papillomavirus type 16 was reported. With this correction, a new E2-binding site was revealed, 111 bp and 143 bp upstream from the TATA box and P97, respectively, and 105 bp downstream of the keratinocyte-dependent enhancer. An A to C mutation at position 41 was found in a patient with invasive carcinoma. This mutation falls within an E2-binding site.

A total of 140 sera originating from healthy women and women with either cervical intraepithelial neoplasia or cervical cancer were tested for the presence of IgG antibody against E7 of human papillomavirus type 16 (HPV-16) by ELISA using a synthetic icosapeptide, denoted 16/E7-2, representing amino acids 11 to 30, and by Western blotting (WB) using a genetically engineered HPV-16 E7 fusion protein. Eighteen sera were found positive in either one or the other test. Positive reactions were more frequently detected in cervical carcinoma patients (12 of 34, 35.2%) than in the other individuals (six of 106, 5.7%). Ten children’s (1 to 3 years of age) sera reacted in neither ELISA nor WB with HPV-16 E7. A high degree of concordance between the two tests was found suggesting that both tests detect the same or similar activity. To locate the reacting epitopes in the E7 protein, absorption tests were performed with peptides corresponding to various sections of the protein. Based on the results obtained, sera possessing antibody to HPV-16 E7 could be differentiated into those reactive with only the 16/E7-2 peptide and those reactive with other HPV-16 E7 epitopes.

The thymidine kinases encoded by herpesviruses of higher vertebrates form a distinct group and are unrelated to the thymidine kinases (TKs) of other organisms. Their evolutionary source has not been identified, but our analysis has revealed a clear relationship with a sequence of human deoxycytidine kinase (dCK) published recently. We report the sequence of the putative TK of channel catfish virus, a herpesvirus of a lower vertebrate, and show that it is also related to dCK. We propose, therefore, that the TKs of herpesviruses of higher and lower vertebrates have evolved, either independently or successively, from a cellular dCK.

DNA clones complementary to the 3′-terminal 3426 nucleotides of the genomic RNA of the carlavirus chrysanthemum virus B (CVB) have been sequenced. The sequence contains six open reading frames (ORFs) which encode putative proteins (in the 5′ → 3′ direction) of M r 25749 (ORF2), M r 11435 (ORF3), M r 6984 (ORF4), the triple gene block proteins, a protein M r 34638 (ORF5); the coat protein, and a protein of M r 12609 (ORF6). The latter protein is basic and contains a putative zinc finger motif. The 5′-proximal ORF1 encodes a product with substantial homology to the C-terminal portions of the putative RNA replicases of two other carlaviruses, potato viruses M and S. The analysis of the minus-sense sequence shows one ORF which encodes a polypeptide of M r 16817. The sequenced portion of the CVB genomic RNA contains three short internal non-coding regions, two of which are typical for carlaviruses (those between ORFs 1 and 2, and between ORFs 4 and 5), and one (between ORFs 5 and 6) is unusual. There is significant similarity in the amino acid sequences of the CVB RNA-encoded proteins and the corresponding proteins of other carlaviruses.

Cowpea mosaic virus M RNA is translated in vitro as well as in vivo into two C-coterminal polyproteins of M r 105K and 95K. Initiation of translation of the 95K protein gene occurs at an AUG codon at position 512 of M RNA, 351 nucleotides downstream of the initiation codon of the 105K protein gene at position 161. By employing an in vitro transcription and translation system it was determined that this 351 nucleotide sequence has the capacity to direct ribosomes to initiate translation at a downstream start codon. This effect is independent of the position of this sequence in an mRNA. Furthermore, evidence has been obtained that scanning ribosomes can bypass the AUG at position 161. Thus, both leaky scanning and internal entry are mechanisms for the initiation of translation of the 95K protein gene.

cDNA clones representing the ssRNA genome of the NY-RPV isolate of barley yellow dwarf luteovirus (BYDV) were sequenced and 5600 nucleotides of the genome were determined. The deduced genome organization has limited similarity to that of another BYDV isolate, Vic-PAV, but is identical to that of beet western yellows (BWYV) and potato leafroll (PLRV) luteoviruses. NY-RPV has six major positive-sense open reading frames (ORFs) and, by comparison with RNA-dependent RNA polymerase and nucleic acid helicase consensus sequence motifs, it is postulated that NY-RPV ORF2 and ORF3 encode the viral replicase, which is expressed by a translational frame-shift mechanism. The region of the NY-RPV genome containing the 22K coat protein ORF, the apparently associated internal apparent VPg ORF and the ORF immediately 3′-proximal (ORF6) to the coat protein ORF are organized as reported for other luteoviruses. Evidence is presented showing that ORF6 is expressed by readthrough of the coat protein gene termination codon, and that this protein is associated with the intact virus as a 65K protein. Although NY-RPV infects graminaceous rather than dicotyledonous plants, the taxonomic relationships between BYDV isolates and other luteoviruses deduced from the genome organization and sequence data strongly suggest that NY-RPV is distinct from the PAV-like isolates of BYDV and is more closely related to BWYV and PLRV.

The nucleotide sequence of the genomic RNAI, 7342 nucleotides (nt) of grapevine fanleaf virus strain F13 (GFLV-F13) has been determined from cDNA clones. The complete sequence contained only one long open reading frame (ORF) of 6852 nucleotides extending from nucleotide 243 to 7101. The putative polyprotein encoded by this ORF is 2284 amino acids in length with an M r of 253K. The location of genome-linked protein and comparison of the primary structure of the 253K polyprotein to that of other closely related viral proteins of the picornavirus-like family allows the proposal of a scheme for the genetic organization of GFLV-F13 RNA1. The primary structure of the polyprotein includes a putative RNA-dependent RNA polymerase of 92K and a cysteine protease of 25K. This protease shares not only major structural homologies, particularly in the substrate-binding pocket, with the trypsin-like serine proteases of other picorna-like viruses, but also their specificity in terms of cleavage. The large region of M r 133K upstream of the VPg was found to contain at least two domains, one of which could be easily aligned with the NTP-binding sequence pattern and another which may have the characteristics of a protease cofactor. Thus, the 253K protein possesses the same general genetic organization as the corresponding protein of other picorna-like viruses.

Naturally occurring defective interfering RNAs (DI-RNAs) and satellite RNAs greatly reduce the accumulation of their helper virus in vivo, but often modulate symptom expression in an unpredictable manner. Deletion mutants Nc/S, Na/M and Sa/Nc + M/S, derived from brome mosaic virus (BMV) RNA-2, failed to replicate when co-inoculated with BMV RNAs-1 and -2 to barley protoplasts. However, the inoculum RNA corresponding to these deletion mutants was extremely stable and could have been mistaken for plus-strand progeny had minus-strand progeny analysis been omitted. These results accentuate the need for such tests in evaluating the ability of mutant viral sequences to replicate. One of the mutants, Nc/S, effectively interfered with the accumulation of BMV RNAs-1 and -2 in barley protoplasts. This non-replicating interfering RNA was termed NRI RNA-2 Nc/S. When present with RNAs-1 and -2 at low inoculum amounts (1 µg), NRI RNA-2 Nc/S reduced replication of RNA-2, the parental RNA, by 63% and preferentially interfered with minus-strand RNA accumulation. At higher levels (4 µg), it completely displaced replication of both RNAs-1 and -2. Mutations eliminating translation of a truncated p2a protein from NRI RNA-2 Nc/S did not alleviate the interference effect, demonstrating that a defective replicase protein was not responsible for the decreased accumulation of genomic RNA. At an NRI RNA:genomic RNA inoculum molar ratio of 1:1, NRI RNA-2 Nc/S reduced the accumulation of all helper virus RNAs by 55%. Since this reduction was seen for both wild-type RNA-3 and ASGP RNA-3, a deletion mutant of RNA-3 that lacks the subgenomic promoter necessary for coat protein expression, it was evident that the effective interference mediated by NRI RNA-2 Nc/S was not mitigated by encapsidation. The ability of the NRI RNAs to mimic satellite DI RNAs in depressing helper virus replication suggests that their expression in transgenic plants may provide a new and widely applicable approach for inducing resistance to viral infection.

During a series of mechanical transfers of tomato spotted wilt virus, two distinct types of mutants were generated. Firstly, a morphologically defective isolate was obtained which had lost the ability to produce the membrane glycoproteins and, as a consequence, was not able to form enveloped particles. Analysis of the genomic RNAs of this isolate suggested that this defect was caused by either point mutations or very small deletions in the medium genomic RNA segment. Secondly, isolates were obtained which had accumulated truncated forms of the large (L) RNA segment. These shortened L RNA molecules most likely represented defective interfering RNAs, since they replicated more rapidly than full-length L RNA and their appearance was often associated with symptom attenuation. Defective L RNAs of different sizes were generated after repeated transfers, and hybridization analysis using L RNA-specific cDNA probes showed that the internal regions deleted varied in length. The presence of defective L RNAs in nucleocapsid fractions as well as in enveloped virus particles indicates that all defective molecules retained the sequences required for replication, encapsidation by nucleocapsid proteins and packaging of the nucleocapsid into virus particles.

Cucumber mosaic virus Y satellite RNA (Y-satRNA) induces distinctive yellow mosaic symptoms on tobacco, whereas S19 satellite RNA (S19-satRNA) causes an attenuated green mosaic on tobacco, although they show considerable sequence identity. Biological assays of infectious chimeric satellite RNA molecules synthesized from cDNA clones of Y-satRNA and S19-satRNA using common restriction sites showed that the determinant for the induction of yellow mosaic symptoms lies in the BstXI-NheI fragment, in which 14 nucleotide differences are found between the two satellite RNAs. To define more precisely the yellow mosaic determinant(s) in this fragment, several site-directed mutants of Y-satRNA were created. The replacement of AUU, at nucleotides 191 to 193 in Y-satRNA, with GC, which mimicks the S19-satRNA sequence at the corresponding site, abolished the ability of Y-satRNA to elicit a yellow mosaic. Conversely, a mutant RNA molecule derived from S19-satRNA in which GC at nucleotides 192 and 193 was changed to AUU induced the yellow mosaic symptoms. Thus, the phenotypes of two satellite RNAs on tobacco can be altered reciprocally by changing the sequences in this limited region.

The coat protein genes of two chlorosis-inducing strains of cucumber mosaic virus (CMV) were compared by nucleotide sequence analysis. The predicted amino acid sequences of the encoded coat proteins were compared with those of two other chlorosis-inducing and four mosaic-inducing CMV strains. Overall, the sequences were highly conserved, with more than 95% amino acid sequence identity between any two strains. However, a proline is present at amino acid 129 of all the mosaic-inducing strains, whereas that position is occupied by either a serine or a leucine in the coat proteins of all the chlorosis-inducing strains. The correlation of chlorosis induction and a substitution for proline with leucine or serine at amino acid 129 suggests that this residue is the determinant of chlorosis induction.

The discrepancy between published sequences of the 5′ non-coding regions of RNA of a Scottish (S) and that of Dutch (D), Australian and Canadian isolates of potato leafroll virus (PLRV) was investigated. Reverse transcription followed by amplification by polymerase chain reaction showed that RNA from three distinct Scottish isolates of PLRV contained molecules with 5′ ends like that of the original Scottish isolate. However, determination of the 5′-terminal sequences of RNA in two of these preparations showed that most RNA molecules had 5′ termini like those of the Dutch and other non-Scottish sequences. Northern blot analysis confirmed that only a small fraction of PLRV RNA contained sequences homologous to the 5′-terminal 119 nucleotides of the PLRV-S sequence. Most PLRV-S RNA molecules therefore have termini like that reported for PLRV-D. The 5′-terminal 119 nucleotides of the minor species of PLRV-SRNA were very similar (109/119 nucleotides were identical) in sequence to an exon of tobacco chloroplast DNA open reading frame 196. The results therefore suggest that recombination has occurred between virus RNA and host RNA.

A tomato spotted wilt-like virus (TSWV-I) is a distinct member of the Tospovirus genus of the Bunyaviridae and is distinguished from the typical TSWV by having a serologically distinct nucleoprotein (N). A cDNA clone extending from the 3′ terminus of the viral RNA through the entire N open reading frame (ORF) was sequenced. The TSWV-IN ORF is capable of encoding a polypeptide of 262 amino acids with a predicted M r of 28.8K. In vitro transcription and translation of the clone produced a protein which comigrated with TSWV-I N and was immunoprecipitated by TSWV-I antibodies. Hybridization analysis of lithium chloride-precipitated RNA from healthy and TSWV-I-infected tissue detected a virus-specific 1.2 kb subgenomic RNA. The TSWV-I S RNA terminal consensus sequence (8 nucleotides) was identical to that of TSWV; the remaining TSWV-I untranslated region showed only 51% identity with that of TSWV. Comparison of the TSWV-I and TSWV N proteins showed 67% identity at the amino acid level. The degree of similarity in the terminal sequence, untranslated region and N ORF is similar to that expected between distinct serogroups within certain genera of the Bunyaviridae.

An important phase of the multiplication cycle of the pararetrovirus cauliflower mosaic virus (CaMV) is transcription of the viral minichromosome in the nucleus. Leaves of infected turnip plants at the vein clearing stage were found to contain a relatively low level of minichromosome DNA, and abundant viral transcripts and characteristic reverse transcription products. In contrast, at the much later stage of severe leaf chlorosis, an elevated level of minichromosome DNA but less RNA, especially the 35S RNA reverse transcription template, was observed. Changes in the composition of virus nucleic acid intermediates were also seen in roots and stems early, compared with late, in infection. A possible feedback mechanism controlling the level of viral minichromosome DNA and its importance in regulation of the CaMV multiplication cycle are discussed in the light of these observations.