- Volume 74, Issue 4, 1993

The E1b gene of human adenovirus 5 (Ad5) encodes a 55K product previously shown to be required for the efficient accumulation of mRNAs derived from the major late primary transcript in the cytoplasm of infected cells. This finding is extended here to include the transcripts from other viral promoters activated during the late phase of infection. Conversely, accumulation of mRNA derived from the major late promoter at early times is not dependent on this E1b function. Cytoplasmic levels of the various differentially spliced products of the major late unit are not equally dependent on the E1b 55K protein. Rather, the longest mRNA species within each 3′-coterminal family shows the greatest dependence. These findings support a model in which the Ad5 E1b 55K protein acts to facilitate the movement of mature viral mRNA away from the nuclear matrix of the infected cell.

Human adenovirus early region 1A (E1A) proteins act as transcriptional regulators and function in the control of DNA synthesis and cell transformation. Little is known about how these viral products are functionally regulated. E1A proteins of adenovirus serotype 5 (Ad5) are phosphorylated at several serine residues and previous studies had indicated that both Ser-89 and Ser-219 are substrates for one or more of the cdc2 family of cell cycle kinases. A second residue near the amino terminus, Ser-96, may also be a site. Although phosphorylation of Ser-89 causes a major shift in gel mobility, the effect on E1A biological activity is unclear. In the present studies we have shown by mutational analysis that phosphorylation at Ser-89 also regulates phosphorylation at Ser-96, suggesting that the gel mobility shift is the result of multiple phosphorylation events. Phosphorylation at Ser-89 did not seem to affect E1A-mediated repression of the simian virus 40 enhancer or trans-activation of the E3 promoter significantly, but it did appear to have a modest but significant effect on transformation of primary baby rat kidney cells.

A point mutation at nucleotide 5233 of the polyomavirus (A2 strain) enables it to overcome growth restriction in undifferentiated embryonal carcinoma cells. We analysed the binding of nuclear proteins from F9 cells to a 38 bp region that spans this site of mutation and encompasses two copies of the bovine papillomavirus core sequence, CCACCC, and characterized this domain by mutational analysis. Our results showed that the F441 mutation creates a sequence motif which binds TEF-1 or a TEF-1-like protein from F9 cells more strongly than its wild-type counterpart and increases its activity by about 10-fold. Another protein identified as CP1 binds with increased affinity in the presence of the F441 mutation to the CAT box-like sequences which is contiguous with the downstream CCACCC box. Point mutations within these two motifs that abolished binding in vitro also impaired the activity of the F441 locus in vivo. As neither the wild-type sequence without the F441 mutation, nor the F441 template without the CAT box has appreciable activity in vivo, interaction between these two elements is required for function. At a higher level of organization, this interaction is probably extended to factors bound to other domains in the A and B enhancer.

A rapid and simple two-step scheme for the purification of herpes simplex virus type 1 UL8 protein from insect cells infected with a recombinant baculovirus has been developed. The scheme involves DEAE–Sepharose and phenyl–Sepharose chromatography and yields approximately 1∙5 mg of protein from 2∙4 × 108 infected cells. The protein remains intact during purification as judged by its reactivity with amino and carboxy termini-specific antisera. Gel filtration chromatography showed that the protein exists as a monomer in solution. No binding of the protein to ssDNA or dsDNA or to a DNA/RNA hybrid could be demonstrated using a gel mobility shift assay.

Fifteen human herpesvirus 6 (HHV-6) strain variants were analysed by PCR amplifications, restriction enzyme site polymorphism and sequence analyses. Three DNA regions were chosen for study: a fragment of a variable glycoprotein gene (210 bp), the conserved glycoprotein H (gH) gene complete with intergenic sequences (2381 bp) and the 5′ intergenic region with the N-terminal coding sequence of gH up to a polymorphic BamHI site (427 bp). Infected cell DNA from five laboratory reference strains including GS, U1102, AJ, Z29 and KF were examined together with DNA from peripheral blood blymphocytes infected with HHV-6 reactivated from blood and/or marrow from five bone marrow transplant (BMT) patients. Separate blood and marrow isolates were obtained from four BMT patients. In addition, HHV-6 sequences were examined directly from one of six Hodgkin′s lymphomas and six B cell proliferations which contained HHV-6 DNA as detected by PCR amplification. The results show two groups of very closely related but heterogeneous strains which correlate with previous groupings by antigenic and restriction site differences. These are variant A strains (including laboratory strains GS, U1102 and AJ) and variant B strains (including laboratory strains Z29 and KF, the Hodgkin′s lymphoma strain, and the nine BMT patient isolates). Variations between the groups were 4 to 6% in nucleotide sequence and 5 to 8∙5% in amino acid sequence. Within each group maximum heterogeneity was observed in different genes. Variant A strains differed by 2∙0% in the variable glycoprotein gene sequence whereas variant B strains were identical in this region; conversely, variant B strains differed by 2 to 3% in the gH N-terminal and intergenic sequences whereas variant A strains differed there by less than 0∙2%. There was evidence for sequence drift independent of selection: relationships between the groups were shown by analyses of amino acid sequence, coding nucleotide sequence as well as intergenic sequence, and the B variant-specific BamHI site in the gH gene was due to a non-coding nucleotide substitution. There was little evidence for in vivo or in vitro variation: the gH nucleotide sequence from the uncultured lymphoma strain (first variant B gH gene identified) was almost identical to the gH sequence from four BMT isolates, and matched BMT isolates from blood and marrow were identical or with a single nucleotide substitution. The overall variation observed between the HHV-6 strain groups was similar or less than that seen between human cytomegalovirus strains such as AD169 or Towne, but clearly distinct from the much greater divergence between currently designated herpesvirus species.

The gene encoding the envelope glycoprotein of a recent Danish isolate of a salmonid rhabdovirus, viral haemorrhagic septicaemia virus (VHSV) has been cloned and sequenced at the cDNA level. When compared with the deduced sequence of a French isolate of VHSV, it was noted that there were 13 amino acid substitutions in the Danish virus. Amino acid homologies with the glycoprotein of a North American salmonid rhabdovirus (infectious haematopoietic necrosis virus) indicate a high degree of structural similarity between the two fish rhabdovirus glycoproteins. Results from partial enzymatic deglycosylation of the viral protein indicate that all four NXT/S sites found in the sequence are N-glycosylated in the virus. The glycoprotein, without the N-terminal leader sequence and C-terminal hydrophobic anchor segment, was expressed in Escherichia coli as a factor Xa protease-cleavable fusion protein. The purified and renatured viral part of the recombinant protein was able to elicit VHSV-specific antibodies and neutralizing antibody activity in serum when injected into rainbow trout.

A previously unidentified morbillivirus was isolated from two harbour porpoises (Phocoena phocoena) that had died in the Dutch Waddensea (North Sea) in 1990. This porpoise morbillivirus (PMV) and a dolphin morbillivirus (DMV), which had recently caused a heavy mortality in Mediterranean striped dolphins (Stenella coeruleoalba), were compared antigenically with other members of the genus Morbillivirus, including the newly recognized phocine distemper virus type 1. DMV and PMV proved to be similar but distinct morbilliviruses, closely related to rinderpest virus and peste-des-petits-ruminants virus. Cell cultures of cetacean, pinniped, ruminant and canine origin showed a different pattern of susceptibility to DMV and PMV infection. Ruminants and dogs proved to be susceptible to experimental infection with DMV and PMV, which both caused a transient leukopenia most pronounced in the ruminants. Pre-exposure of dogs to DMV-and PMV protected them from developing CDV viraemia and clinical signs upon challenge infection with virulent CDV. A serological survey among stranded animals of different cetacean species in Europe indicated that infections with DMV- and PMV-like morbilliviruses are not uncommon among these aquatic mammals.

The sequences of the 3′-terminal 3∙7 kb of the genome and of a 1∙7 kb 5′ end cDNA clone of one isolate of lactate dehydrogenase-elevating virus (LDV) are reported. The 3′ end sequence encodes six major independent open reading frames (ORFs 2 to 7), which are overlapping by between one and 130 nucleotides. Each ORF is expressed at the 5′ end of one of six 3′-coterminal subgenomic mRNAs (mRNAs 2 to 7, respectively; 3∙5 to 0∙8 kb). The smallest mRNA, mRNA 7, encodes the nucleocapsid protein, VP1; mRNA 6 probably encodes the non-glycosylated envelope protein, VP2; and mRNAs 2 to 5 encode proteins of 26∙0K, 21∙5K, 19∙2K and 22∙4K, respectively, each possessing several potential N-glycosylation sites and membrane-spanning segments. About 72% of the LDV genome segment carrying ORFs 2 to 7 exhibits about 50% or higher nucleotide identity with the corresponding genome segment of swine infertility and respiratory syndrome (Lelystad) virus (LV), whereas only limited similarity is observed in discontinuous regions of the same corresponding genome segments of LDV and equine arteritis virus (EAV). EAV and LV belong to the same new group of positive-strand RNA viruses as LDV. One additional subgenomic mRNA of about 4 kb is produced in LDV-but not in EAV- or LV-infected cells. The 5′ end of this mRNA (1-1) carries a continuous coding sequence. The N-terminal 80 amino acids of the predicted product exhibit about 50% identity with segments in the ORF 1b proteins of both EAV and LV. These segments are located 117 to 150 amino acids upstream of the C termini of the ORF 1b proteins of these viruses. The 5′ end cDNA clone contains part of a 5′ leader associated with all seven subgenomic mRNAs and the 5′ end of ORF 1a. The junctions between the 5′ leader and the bodies of all seven subgenomic mRNAs have been determined. Only a single junction sequence was detected for each mRNA. Linkage occurs between a 5′ UAUAACC 3′ sequence at the 3′ end of the leader and only partially identical segments specified down-stream in the genome preceding ORFs 2 to 7. The generated junctions differ for different subgenomic mRNAs but possess the consensus sequence 5′ UAU GAAA -CC 3′. In mRNA 7, the UA in positions 1 and 2 are derived from the leader, but a G in position 2 in mRNAs 1-1, 3 and 4 and an A in position 3 in mRNA 6 seem to be specified by the 3′ genomic sequences. Thus, the formation of these junctions is difficult to explain by a leader-primed mode of synthesis such as postulated for coronaviruses.

We have analysed the pattern of nucleotide sequence variability in the 5′ non-coding region (5′ NCR) of geographically dispersed variants of hepatitis C virus (HCV). Phylogenetic analysis of sequences in this region indicated the existence of a new virus type, provisionally termed type 4, the identity of which was confirmed by further analysis of the more variable part of the HCV core protein coding region. The geographical distribution of HCV type 4 was distinct from that of other HCV types, it being particularly widespread in Africa and absent or rare in Europe and the Far East. Much of the variability in the 5′ NCR appears to be constrained by a requirement for specific secondary structures in the viral RNA. In one of the most variable regions of the 5′ NCR (positions − 169 to − 114), most of the nucleotide changes that are characteristic of different HCV types were covariant, with complementary substitutions at other positions. According to the proposed secondary structure of the 5′ NCR, such changes preserved base pairing within a stem–loop structure, whereas the nucleotide insertions found in a proportion of 5′ NCR sequences, including those of type 4, localized exclusively to the non-base-paired terminal loop. The specific nucleotide substitutions in the 5′ NCR that differentiate each of the four HCV types can be detected by restriction enzyme cleavage, providing a rapid and reliable method for virus typing.

To study possible extrahepatic sites for the replication of hepatitis C virus (HCV), we examined fresh and cultured peripheral blood mononuclear leukocytes (PBML), as well as different subpopulations of PBML of HCV-infected patients, for the presence of viral genomic and antigenomic RNA. Sense and antisense oligonucleotide primers derived from HCV sequences were used for reverse transcription (RT) followed by an amplification with the polymerase chain reaction assay (PCR). Using antisense primers for RT, genomic viral RNA could be detected in serum, liver, total PBML and B lymphocytes of chronically infected patients. However, only liver tissue and PBML specimens were positive when a sense primer was used. To demonstrate further the specificity of these findings, total PBML were stimulated using pokeweed mitogen and synthesis of HCV RNA was determined by incorporation of [3H]uridine into nascent viral RNA molecules using a hybrid release assay. Additionally, total PBML from an uninfected person could be infected in vitro using an HCV RNA-positive serum. The PCR products obtained from serum, liver and PBML specimens of an HCV-positive individual were found to have nearly identical sequences. Our findings suggest that PBML could be a site for viral replication of HCV during the natural course of infection and may represent a reservoir for hepatitis C virions.

Virus-encoded proteinase activity of hepatitis A virus (HAV) was studied in vitro. Genomic regions coding for segments of the viral polyprotein were expressed by in vitro transcription and translation in rabbit reticulocyte lysates. Polyproteins translated from synthetic transcripts encoding P1–P2 or ΔVP1–P2 were not processed indicating that no proteolytic activity is encoded within P2 of HAV, in contrast to other picornaviruses. Proteinase activity was, however, detected in the genomic region encoding 3C. Mutant transcripts (µ) which encode an alanine in place of the cysteine residue at amino acid position 172 of 3C did not yield proteolytic activity, consistent with the hypothesis that proteinase 3C is a cysteine-containing trypsin-like proteinase. Processing products 3ABC and P3 were identified by immunoprecipitation, providing evidence that proteolytic cleavage occurs at the 2C/3A and less frequently at the 3C/3D junction. For cleavages at either site, the complete 3D moiety was not required. In general, analysis of cleavage products was made difficult by the presence of polypeptides which were translated from internal start sites, predominantly within the P3 region. Since only small amounts of the full-length products P1–P2–P3 or P2–P3 were translated, possible cleavage of P1 and P2 by 3C could not be resolved in this system. Furthermore, no intermolecular cleavage could be detected when in vitro translated polypeptides of the P3 region were incubated with P1, P1–P2 or P2–P3μ as substrates.

The reactivity of D antigen-specific monoclonal antibodies with infectious virus and inactivated virus in commercial poliovaccines from two manufacturers was examined in capture enzyme immunoassays. Epitopes on inactivated poliovirus types 2 and 3 in vaccines were modified by the inactivation process to such an extent that some monoclonal antibodies which bound to the homologous infectious virus strain failed to bind to the inactivated virus in the vaccine. This was especially the case for antibodies specific for site 1, which elicits the major immune response to these serotypes in mice. Other epitopes were partially destroyed resulting in a reduction in reactivity of monoclonal antibodies with inactivated virus in vaccines compared to infectious virus. These studies indicate that inactivated virus in vaccine differs antigenically from native virus so that measuring the potency of vaccine in assays in vitro may require careful selection of an appropriate antibody. In addition it is possible that some of the antibodies produced by recipients of formalin-inactivated polioviruses may not contribute to the protective immune response.

A speculative model for reverse transcription of a viral RNA template into proviral dsDNA is presented. It has two essential features that are not included in current models: (i) the functional complex is dimeric, with two polymerization/RNase H sites and (ii) two templates are initially attached to the complex at their 3′ ends. The model also has the optional features that (iii) the complex is rotationally symmetrical and (iv) attached to the virion core. The model attempts to explain why the viral genome is dimeric, the specificity of the ‘jumps’ between the ends of templates and how recombination occurs so readily. It also suggests novel targets for drug therapy during retroviral infection, for example, in AIDS.

The product of the envelope gene (gp55) of Friend spleen focus-forming virus is responsible for the acute form of erythroleukaemia caused by this virus. In order to investigate the role that the four known N-linked carbohydrate side-chains of gp55 play in pathogenesis, we have inactivated the four N-glycosylation signals by mutating the asparagine residues of these four sites into serine. When glycosylation sites 1 and/or 2 were altered, the viruses remained fully pathogenic. However, mutation at either of glycosylation sites 3 or 4 rendered the virus apathogenic, independent of mutations at other sites. Furthermore, when site 3 was changed, a new product appeared which seemed to have acquired a carbohydrate chain at a position normally not glycosylated, presumably at position Asn378.

Ten mutations were generated in the env gene of Moloney murine leukaemia virus DNA. The mutations were made by site-directed mutagenesis to alter basic amino acids (lysine or arginine) in the surface glycoprotein gp70. Mutants were investigated following transfection into NIH/3T3 cells. All 10 mutants released virion particles into the medium, suggesting that none of the mutations affected overall viral gene expression or virion budding. Two mutants were positive in XC plaque assay, reverse transcriptase assay and re-infection experiments, showing that these mutations occurred in parts of the molecule not essential for infection. Three mutants were negative in both the XC plaque assay and re-infection experiments, suggesting that they make non-infectious virus particles. The results indicate a defect in the early phase of infection, perhaps in receptor binding or in the fusion of virion and host membranes. The other mutations resulted in reduced infectivity of released virion particles.

Molecular interactions between herpes simplex virus type 1 (HSV-1) and human immunodeficiency virus (HIV) were investigated in the promonocytic cell line U937. HSV-1-mediated activation was observed in transient expression assays with hybrid constructions containing the HIV long terminal repeat (LTR)-directed chloramphenicol acetyltransferase gene. Comparison of constructions that differ in the GGTCA palindrome located within the negative regulatory region of the LTR revealed four- to eightfold lower activation levels for the wild-type as compared to the mutant sequence. Three protein species, 37K, 59K/64K and 75K, that bind to the wild-type GGTCA palindrome were resolved in nuclear extracts of uninfected U937 cells by gel retardation and u.v.-crosslinking experiments. The 37K protein did not bind to the mutant palindrome sequence. However, a distinct 120K protein was detected. The 37K and 59K/64K binding proteins were not resolved in similar experiments performed with nuclear extracts from HSV-1-infected U937 cells but there was a novel p50 species that binds only to the wild-type palindrome sequence. These findings raise the possibility that interaction of these proteins at the GGTCA palindrome is involved in HSV-1-mediated regulation of the HIV LTR in U937 cells.

Highly purified natural killer (NK) cell lines and clones, displaying the typical phenotype, morphology and function and obtained from healthy blood donors, were infected in vitro with the BRU isolate of human immunodeficiency virus type 1 (HIV-1). There was no significant increase in reverse transcriptase activity and levels of p24 antigen in the supernatants, but positive staining was observed using an immunogold technique with polyclonal anti-HIV-1 antibodies. When infected NK cells were co-cultivated with autologous non-infected CD4+ mitogen-activated cells, significant levels of reverse transcriptase activity and p24 antigen in supernatants were detected. Giant syncytial cells and a high number of mature virion particles were also evident. When NK cell lines or clones from HIV-1-infected patients were studied, neither the presence of p24 antigen nor reverse transcriptase activity was detected in the supernatants after stimulation with mitogens, cytokines or co-culture with allogeneic CD4+ mitogen-activated cells. PCR studies did not detect HIV-1 genes in freshly purified NK cells, cell lines or clones from infected patients. Taken together these results suggest that (i) normal NK cells can be infected in vitro by the HIV-1 BRU isolate in a non-productive fashion, (ii) PCR with NK cell DNA of HIV-1-infected patients indicates that in vivo few of these cells, if any, are infected by HIV-1 and (iii) the mechanisms responsible for the impairment of NK cell function during HIV-1 infection remain to be determined and are probably not related to a direct cytopathic effect of the virus.

A sequence motif that is conserved in a number of S-adenosylmethionine (SAM)-utilizing methyltransferases and is implicated in SAM binding was identified in the N-terminal portion of NS5 proteins of flaviviruses and in λ2 protein of reovirus. An additional conserved motif was shared by these viral proteins and two distinct groups of methyltransferases including as the prototypes Rhodobacter capsulatus hydroxyneurosporene methylase (crtF gene product) and yeast 3,4-dihydroxy-5-hexaprenylbenzoate methylase (COQ3 gene product), respectively. Statistically significant similarity was revealed between the region of flavivirus NS5 containing the SAM-binding motif and a newly characterized family of putative methyltransferases from bacteria, yeast and plants, which is related to the Coq3 group. Amino acid sequence signatures were derived that are unique for NS5 proteins and different subsets of (putative) cellular methyltransferases. It is hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. Thus NS5 may be a two-domain protein, with its C-terminal domain comprising the RNA-dependent RNA polymerase. The putative methyltransferase domain of flaviviruses is unrelated to the methyltransferase domain previously characterized in positive-strand RNA viruses of the alphavirus-like supergroup. The lack of sequence similarity and different location of the putative methyltransferase domain underscores the drastic difference in the genome layout of flaviviruses and alphaviruses. The identification of the putative methyltransferase domain in reovirus λ2 protein is compatible with the available evidence that this protein is the viral capping enzyme.