The nucleocapsid gene of infectious hematopoietic necrosis virus, a fish rhabdovirus

The complete nucleotide sequence of the infectious hematopoietic necrosis virus (IHNV) nucleocapsid gene has been determined using cDNA clones of genomic and messenger RNAs. Genomic clones were generated by using random DNA oligomers to prime cDNA synthesis and were mapped to their respective locations on the genome by the use of cDNA probes derived from viral mRNAs. Interesting features of the IHNV nucleocapsid gene sequence elucidated by the sequencing of these clones include short homologies with N genes of other rhabdoviruses at the 5' and 3' nontranslated termini of the mRNA, as well as an exceptionally long 5' noncoding region of the mRNA, suggesting a leader RNA may be coupled to the N mRNA. A comparison of the IHNV N protein coding sequence with other rhabdoviral N genes shows some homologies at the amino acid level which indicates the possible evolutionary relationship of these N proteins. The determination of the nucleotide sequences of IHNV genes and intergenic regions will be useful for studying the mechanisms of rhabdoviral transcription and replication.

Sequence of the 3386 3' nucleotides of the genome of the AVO1 strain rabies virus: structural similarities in the protein regions involved in transcription

DNA fragments complementary to the genome of an avirulent strain (AVO1) of the rabies virus were cloned and sequenced. The sequence of the 3386 nucleotides from the 3' end covers the genes encoding the leader RNA, the nucleoprotein N, the phosphoprotein M1 and the matrix protein M2, as well as the intergenic regions. Comparison of the AVO1 sequence with those of other rabies strains reveals a very high conservation at both the nucleotide and the amino acid levels. The non-protein coding regions of the genome (leader gene, untranslated regions flanking mRNAs, untranscribed intergenic regions) are discussed in terms of their possible involvement in the rabies virus biology. Comparison of the rabies genome with those of other unsegmented negative strand RNA viruses (rhabdoviruses and paramyxoviruses) indicates that the start and stop transcription signals, located at the border of each gene encoding a protein, and the regions of the phosphoprotein and matrix proteins that could be implicated in the transcription process, retain a similar overall structure. Thus, it appears that during evolution, these virus genomes have diverged while keeping the protein structures and regulatory sequence important in transcription. These results prompt us to propose that the major distinctive feature of the rabies transcription may arise from the highly variable intergenic regions where the attenuation of transcription is assumed to take place.

[The rhabdovirus program at the Istituto Pasteur--Fondazione Cenci Bolognetti]

Studies carried out under the research program on Rhabdovirus sponsored by the Istituto Pasteur--Fondazione Cenci Bolognetti are reviewed. The program was mainly focused to investigate biologically relevant characteristics of this virus and to evaluate epidemiological and prophylactic aspects involved in sylvatic rabies control measures.

Structure of the M2 protein gene of sonchus yellow net virus

The nucleotide sequence of the gene immediately following the nucleocapsid protein gene of sonchus yellow net virus (SYNV), a plant rhabdovirus, is presented. Serological reactions of SYNV proteins with antibodies elicited by a fusion protein constructed from the sequenced gene indicate that this gene encodes an SYNV structural protein designated M2. The 5' end of the M2 protein mRNA appears to correspond to position 1700 relative to the 3' end of SYNV RNA, because an extension product that maps to this position was synthesized by reverse transcription of polyadenylated [poly(A)+] RNA from infected tobacco that had been primed with an SYNV-specific oligodeoxyribonucleotide. The 3' end of the gene encoding the M2 protein is defined by a recombinant DNA plasmid derived from poly(A)+ RNA from SYNV-infected plants. This plasmid contains an insert with a 3'-terminal region corresponding to a uridylate-rich sequence present at positions 2832 to 2836 on SYNV genomic (g) RNA. These data thus suggest that the M2 protein mRNA is 1132 nucleotides (NT) long, excluding the poly(A) tail, and consists of a 50-NT untranslated 5' region, a 1035-NT open reading frame (ORF), and a 47-NT untranslated 3'region. The ORF is capable of encoding a 345-amino acid protein with a calculated molecular weight of 38,332. A small region of the M2 protein appears to have some similarity to the phosphoproteins of other rhabdoviruses. An identical 14-NT region occurs at the two sequenced gene junctions on SYNV gRNA and shares homology with regions separating the genes of some animal rhabdoviruses.

Rhabdovirus sigma, the hereditary CO2 sensitivity agent of Drosophila: nucleotide sequence of a cDNA clone encoding the glycoprotein

Sigma virus, the hereditary agent of a CO2-induced paralysis of Drosophila, is classified as a rhabdovirus on a molecular basis. We have purified its genome which after 32P-labelling was used as a probe to detect mRNAs in infected cells. A cDNA copy of the entire coding region of the glycoprotein mRNA was cloned. Nucleotide and deduced amino acid sequences were determined and compared to previously known sequences of other rhabdovirus glycoproteins to determine the relatedness of Sigma virus to other viruses of this group.

Transcription in vitro of infectious haematopoietic necrosis virus, a fish rhabdovirus

Transcription in vitro by the RNA polymerase of infectious haematopoietic necrosis virus (IHNV), a salmonid rhabdovirus, was investigated using different reaction conditions to maximize RNA synthesis. The use of HEPES buffer rather than Tris buffer, and the addition of S-adenosyl-L-methionine to the reactions resulted in a sixfold increase in RNA synthetic activity to 6400 pmol UMP incorporated/mg viral protein/hour. The RNA transcripts produced in this system contained polyadenylated species which co-migrated with IHNV mRNA species 2, 3, 4 and 5 from IHNV-infected cells. The transcripts were shown to be functional mRNA species by their ability to direct the synthesis of viral proteins in vitro.

Nucleotide sequence of a cDNA clone carrying the glycoprotein gene of infectious hematopoietic necrosis virus, a fish rhabdovirus

The nucleotide sequence of the mRNA encoding the glycoprotein of infectious hematopoietic necrosis virus was determined from a cDNA clone containing the entire coding region. The G-protein cDNA is 1,609 nucleotides long (excluding the polyadenylic acid) and encodes a protein of 508 amino acids. The predicted amino acid sequence was compared with that of the glycoprotein of the Indiana and New Jersey serotypes of vesicular stomatitis virus and with the glycoprotein of rabies virus, using a computer program which determined optimal alignment. An amino acid identity of approximately 20% was found between infectious hematopoietic necrosis virus and the two vesicular stomatitis virus serotypes and between infectious hematopoietic necrosis virus and rabies virus. The positions and sizes of the signal sequence and transmembrane domain and the possible glycosylation sites were determined.

Sequences of Chandipura virus N and NS genes: evidence for high mutability of the NS gene within vesiculoviruses

The nucleotide sequence of the 3' end of the genome of Chandipura (CHP) virus, including the complete sequences of the nucleocapsid (N) and phosphoprotein (NS) genes was determined, principally from cloned cDNAs of the N and NS mRNAs. The NS mRNA of CHP virus is 908 bases in length and encodes a protein of 293 amino acids. Comparison of the CHP virus NS protein sequence with those of vesicular stomatitis virus of the New Jersey serotype (VSV (NJ)) and of the Indiana serotype (VSV (IND] revealed homologies of only 23 and 21%, respectively, with no consecutive stretches of more than four amino acids identical among the three sequences. As with the two VSV serotypes, the highest homology between the NS proteins of CHP and VSV was in a 20-amino acid region near the carboxy termini of the proteins. Of the potential phosphorylation sites, there are eight conserved serine or threonine residues among the three sequences. Despite the dissimilarity among primary sequences of the NS proteins, their overall structure, as assessed by amino acid composition and by the relative hydropathicities of the sequences, has been conserved throughout evolution. The N mRNA of CHP virus is 1291 bases long and encodes a protein of 422 amino acids. In contrast to the NS protein, the CHP N protein is at least 50% homologous to the N proteins of each of the VSV serotypes. We have identified a region near the center of these N protein sequences which is conserved among members of both the rhabdovirus and paramyxovirus families. This extent of conservation of the N protein sequences underscores the high rate of mutability of the NS protein sequences among the vesiculoviruses.

Identification and analysis of Ebola virus messenger RNA

Six messenger RNA species of Ebola virus were identified in infected Vero E6 cells. Virion RNA hybridizes to each of the mRNAs, confirming that Ebola virus possesses a negative-stranded RNA genome. The mRNAs are monocristronic transcripts, are synthesized in the presence of actinomycin D, and are polyadenylated. In vitro translation of mRNA preparations results in the synthesis of five authentic viral proteins and a putative unglycosylated form of the glycoprotein, demonstrated by immunoprecipitation with virus-specific antisera and SDS-PAGE. No mRNA species was detected for the polymerase (L protein) gene.

Effect of melittin on transcription by vesiculovirus mutant and wild-type viruses

The bee venom peptide melittin activated the virion transcriptase activity of three vesiculoviruses with preservation of virion structure. The kinetics of RNA synthesis were similar to those observed with purified transcribing nucleoprotein (TNP) preparations. Six temperature-sensitive host range (tdCE) mutants of Chandipura virus displayed 1.7- to 5.5-fold greater efficiencies of transcription at 39 degrees with melittin-permeabilized virions in comparison with TNP preparations. Comparative study of other host range mutants (tdCE3) and tsB1) of vesicular stomatitis virus (VSV) New Jersey and a thermosensitive polymerase mutant (tsG114) of VSV Indiana suggested that the enhanced transcription at 39 degrees associated with melittin-activated tdCE mutants was due to the retention of host factors in the virions.

Identification and characterization of Bahia Grande, Reed Ranch and Muir Springs viruses, related members of the family Rhabdoviridae with widespread distribution in the United States

Sixteen virus isolates with similar biological characteristics were obtained from salt-marsh mosquitoes collected in south Texas in 1974. When compared antigenically, these and 13 other isolates from mosquitoes collected between 1972 and 1979 in west Texas, New Mexico, Louisiana, Colorado and North Dakota were shown to be related but not identical. Three distinct serotypes were determined: Bahia Grande (prototype strain TB4-1054), Reed Ranch (TB4-222) and Muir Springs (76V-23524). When examined by electron microscopy, these three viruses were shown to be rhabdoviruses. Structural analysis of the prototype strain of Bahia Grande virus from Texas revealed five proteins. Comparative oligonucleotide fingerprint maps showed 51 to 86% sharing of the large oligonucleotides between Bahia Grande virus (strain TB4-1054) and 11 other antigenically related isolates but not with Muir Springs virus (strain 76V-23524), an antigenically distinct isolate from mosquitoes collected in Colorado. A serological survey for antibody to Bahia Grande virus showed that humans, cattle, sheep, reptiles and wild mammals from south Texas had neutralizing antibodies to this virus.

In vitro transcriptase deficiency of temperature-dependent host range mutants of Chandipura virus

Ten of 12 Chandipura virus tdCE mutants, which exhibit temperature-dependent restriction of growth in chick embryo (CE) cells but not in BS-C-1 cells, showed deficient transcriptase activity in vitro at 39 degrees C relative to wild-type virus. A gradation in transcriptional activity at 39 degrees C in vitro was observed. Reversion of the tdCE phenotype to unrestricted growth in CE cells at 39 degrees C was accompanied by partial restoration of normal transcriptase activity at 39 degrees C, suggesting that reversion was mediated by either extragenic or intragenic suppression. Viral protein synthesis was reduced or absent in CE cells at 39 degrees C indicating that transcription was also defective in vivo under these conditions. Induction of heat-shock proteins in CE cells at 39 degrees C occurred normally in tdCE mutant-infected cells and RNA methylation in vitro was unaffected.

Conservation of the 3' terminal nucleotide sequences of Ebola and Marburg virus

The 3' RNA base sequences of several Marburg (MBG) and Ebola (EBO) virus isolates have been determined. A comparison of these 3' terminal noncoding sequences with those of other negative strand RNA viruses suggests a unique phylogenic niche for Marburg and Ebola viruses. The translation initiation site and 35 N-terminal amino acids of the 3' proximal coding gene of a Zaire strain of Ebola virus was predicted. In addition, putative leader RNA sequences preceding the first gene are discussed in terms of possible regulatory functions.

In-vitro infection of chronic lymphocytic leukemia cells by Epstein-Barr virus (EBV)

We sought to determine the potential of infecting lymphoid cells from patients with chronic leukemia (CLL) with Epstein-Barr virus (EBV) by testing for EBV receptors (EBVR) by flow cytometry, assessing for infectability of these cells by culturing with B95-8-derived virus, and staining for EB nuclear-associated antigens (EBNA) at various times post-infection. EBVR were present on 54-91% of lymphoid cells in seven cases of CLL and on 46% of prolymphocytic leukemia cells. Dynamic changes regarding EBNA positivity, morphology, and viability occurred post-infection with the virus. On day 2 only a few EBNA-positive lymphoblasts were observed. On days 11-21 positivity increased from 2 to 34% of cells. Simultaneously, the viable cell number declined to approximately 1/10th of original number. A significant proportion of the EBNA-positive cells corresponded to the original CLL cells. In 3 of 7 cases of CLL a Pan T-cell phenotype was demonstrated by Leu-1 monoclonal antibody testing. The infected cells did not react with two monoclonal antibodies, EBV-CS 1 and 4, which react with B-cell lymphoblastoid cell lines (B-LCL). Moreover, the B-LCL derived at 1-2 months post-infection of CLL cells did not express the Leu-1 antigen, but expressed EBV-CS 1 or 4 defined antigens. In the prolymphocytic leukemia, 64% of the cells showed EBNA positivity on day 7 and giant cells with huge round or multiple nuclei appeared which were EBNA-positive. CLL and prolymphocytic leukemia cells can be infected as demonstrated by EBNA-positivity. This infection does not lead to immediate transformation, but evokes lymphoblast and multinucleated giant cell production prior to the death of cells.

Isolation and characterization of a tupaia rhabdovirus

Liver tumor biopsies of a 9-year-old moribund Tupaia (tree shrew) were explanted and cultured in vitro. The cell cultures degenerated spontaneously. A virus was isolated from the cell-free supernatant of these cultures and subsequent electron microscopy revealed rhabdovirus-like particles. Negative staining showed typical bullet-shaped particles 125-220 nm in length with a diameter of 68 nm studded with a dense layer of surface projections 9-11 nm in length. One end of the virion was flat, the other end was open; a distinct ribonucleoprotein (RNP) core was visible. The pitch of the RNP was 4.5 nm. Virus was assembled and matured by budding primarily into regions of dilated endoplasmic reticulum. The dimensions of the virion also were determined in ultrathin sections: the diameter and length of the virion were 52 and 125-255 nm, respectively, those of the RNP core were 39 and 120-240 nm. Only tupaia embryonic fibroblasts and kidney cells were susceptible to the rhabdovirus. The virus, when plaque-assayed on tupaia embryonic fibroblasts, grew to a titer of 1 X 10(6) PFU.

Molecular cloning of the six mRNA species of infectious hematopoietic necrosis virus, a fish rhabdovirus, and gene order determination by R-loop mapping

Plasmids carrying cDNA sequences to the mRNA species of infectious hematopoietic necrosis virus were constructed and cloned into Escherichia coli. Characterization of 21 cloned plasmids by hybridization to mRNA blots identified sets of plasmids with homology to each of the six viral mRNA species. R-loop mapping with these cDNA plasmids determined that the gene order on the infectious hematopoietic necrosis virus genome is (3')N-M1-M2-G-NV-L(5').

Characterization of infectious hematopoietic necrosis virus mRNA species reveals a nonvirion rhabdovirus protein

The genome RNA and six mRNA species of infectious hematopoietic necrosis virus were analyzed by denaturing gel electrophoresis. The following molecular weights were determined: genome RNA, 3.7 X 10(6); mRNA 1, 2.26 X 10(6); mRNA 2, 5.63 X 10(5); mRNA 3, 4.84 X 10(5); mRNA 4 (containing two different mRNA species), 3.00 X 10(5); and mRNA 5, 1.95 X 10(5). Densitometer analyses of gels were used to calculate the molar ratios of the intracellular mRNA species: mRNA 1, 0.02; mRNA 2, 0.49; mRNA 3, 1.0; mRNA 4, 2.52; and mRNA 5, 0.41. Hybrid selection studies determined the mRNA coding assignments as follows: mRNA 1 encodes the viral polymerase, L; mRNA 2 encodes the glycoprotein, G; mRNA 3 encodes the nucleocapsid protein, N; mRNA 4 is composed of two comigrating mRNA species which encode the matrix proteins, M1 and M2; and mRNA 5 encodes a previously unrecognized viral protein which is induced in infected cells but is not present in mature virions. This nonvirion protein has been designated the NV protein.

Comparison of the primary sequence of spring viremia of carp virus M protein with that of vesicular stomatitis virus

The nucleotide sequence of Spring viremia of carp virus mRNA coding for the matrix protein (M) has been determined from a complete DNA copy cloned in the Escherichia coli plasmid pBR322. The clone is 710 nucleotides long and, excluding the 3' homopolymeric end (representing the mRNA polyadenylic acid sequence), encodes a protein of some 223 amino acids (25,600 Da). The protein has more basic than acidic amino acids and no significant amino- or carboxy-terminal hydrophobic domains. The predicted amino acid sequence of the M protein of Spring viremia of carp virus can be aligned with that of vesicular stomatitis virus, revealing a significant amount of homology (28%). The carboxy-terminal regions of the two proteins exhibit much less homology than their amino termini.

The late functions of Drosophila sigma virus

Several criteria can be used to characterize the temperature-sensitive mutants of sigma virus: the lability of infectious centers initiated by the efficient viral particles following the inoculation; the localization of the temperature-sensitive period; the hereditary transmission of infection in a maternal Drosophila line at high temperature; the evolution of the CO2 sensitivity symptom and of the viral titer per fly for hereditarily infected flies kept at a permissive temperature and shifted to a restrictive one. Experimental data concerning the last two criteria are shown and discussed here. From all the criteria, three classes of ts mutants can be defined: the first class (prototype ts4) are the mutants blocked in hereditary transmission at high temperature. These mutants are affected during the whole viral cycle but the viral maturation is not directly affected. The second class (ts9, haP27) are the mutants directly affected in viral maturation. For these latter, the hereditary transmission in a maternal line is efficient at high temperature, and only a late temperature sensitive period is observed. The third class (prototype haP7) are the mutants for which only an early temperature-sensitive period is observed. In fact, for these mutants, the viral information is strongly heat-sensitive at the beginning of viral cycle. This defect is rapidly corrected, and the hereditary transmission, late viral functions and viral maturation are as efficient as those of wild type virus, at high temperature. Using temperature-sensitive mutants similar to the wild type virus at permissive temperature, a formal description of the viral cycle at 20 degrees C in the standard flies can be obtained. The long period necessary to perform an entire viral cycle (about 60 hours) is a result of the restrictive action on late viral functions at 20 degrees C of the Oe allele of the ref(3)O host gene present in the standard flies.

Effect of overwintering on the frequency of flies infected by the rhabdovirus sigma in experimental populations of Drosophila melanogaster

Artificial overwintering, assuming that adulthood is the overwintering stage, has been performed on six experimental populations of Drosophila melanogaster. In five of them, the frequency of flies infected by the hereditary Rhabdovirus sigma is always in the first spring generation than it was in the last generation of the preceding fall. This result might indicate a higher sensitivity of infected flies to winter conditions, but other interpretations, connected with the genes for resistance to the virus might be considered. In one of the six populations, no effect was detected after any of the three successive winters. It appears therefore that the genetic background of the flies or/and of the propagated virus intervenes in the response to overwintering.

Synthesis of capped and uncapped methylated oligonucleotides by the virion transcriptase of spring viremia of carp virus, a rhabdovirus

Capped and uncapped methylated oligonucleotides, five and six nucleotides in length, were synthesized in vitro in spring viremia of carp virus transcription reaction mixtures containing ATP + CTP, ATP + CTP + GTP, or ATP + CTP + UTP, but not in any other combinations of two or three ribonucleoside triphosphates. The oligonucleotides that have been characterized are consistent with the structures: m7GpppAmpNpCpNpN, GpppAmpNpCpNpN, pppAmpNpCpNpN, and ppAmpNpCpNpN--i.e., similar to those of the termini of transcripts made in complete reaction mixtures. Because both capped and uncapped methylated oligonucleotides were synthesized, it can be concluded that methylation of the penultimate nucleotide can precede capping and methylation of the capping nucleotide. Our results also indicate that capping and methylation are processes that can take place prior to mRNA chain completion.