Sequence analysis of the Ebola virus genome: organization, genetic elements, and comparison with the genome of Marburg virus.

Sequence analysis of the second through the sixth genes of the Ebola virus (EBO) genome indicates that it is organized similarly to rhabdoviruses and paramyxoviruses and is virtually the same as Marburg virus (MBG). In vitro translation experiments and predicted amino acid sequence comparisons showed that the order of the EBO genes is: 3'-NP-VP35-VP40-GP-VP30-VP24-L. The transcriptional start and stop (polyadenylation) signals are conserved and all contain the sequence 3'-UAAUU. Three base intergenic sequences are present between the NP and VP35 genes (3'-GAU) and VP40 and GP genes (3'-AGC), and a large intergenic sequence of 142 bases separates the VP30 and VP24 genes. Novel gene overlaps were found between the VP35 and VP40, the GP and VP30, and the VP24 and L genes. Overlaps are 20 or 18 bases in length and are limited to the conserved sequences determined for the transcriptional signals. Stem-and-loop structures were identified in the putative (+) leader RNA and at the 5' end of each mRNA. Hybridization studies showed that a small second mRNA is transcribed from the glycoprotein gene, and is produced by termination of transcription at an atypical polyadenylation signal located in the middle of the coding region. The predicted amino acid sequence of the glycoprotein contains an N-terminal signal peptide sequence, a hydrophobic anchor sequence, and 17 potential N-linked glycosylation sites. Alignment of predicted amino acid sequences showed that the structural proteins of EBO and MBG contain large regions of homology despite the absence of serologic cross-reactivity.

Ebola protein analyses for the determination of genetic organization.

Amino-acid sequencing of the purified major nucleoprotein (NP), VP35 and VP40 from purified Ebola virus proved that they are the protein products of the first three genes, and that the open reading frame (ORF) of the NP begins at nucleotide 470. Because of the many unusual features of the ORFs of Ebola virus, we thought that our conclusions should be substantiated. Comparisons of in vitro-translation products to purified viral proteins were used to demonstrate conclusively that the NP, VP35 and VP40 were the protein products of genes one, two, and three, respectively. Studies using antibodies to synthetic peptides matching the N- and C-termini of the deduced sequences from these genes confirmed these conclusions and that the ORF for the NP begins at nucleotide 470. Subsequent studies confirmed that VP30 is encoded by the fifth gene.

Marburg virus, a filovirus: messenger RNAs, gene order, and regulatory elements of the replication cycle.

The genome of Marburg virus (MBG), a filovirus, is 19.1 kb in length and thus the largest one found with negative-strand RNA viruses. The gene order - 3' untranslated region-NP-VP35-VP40-GP-VP30-VP24-L-5' untranslated region-resembles that of other non-segmented negative-strand (NNS) RNA viruses. Six species of polyadenylated subgenomic RNAs, isolated from MBG-infected cells, are complementary to the negative-strand RNA genome. They can be translated in vitro into the known structural proteins NP, GP (non-glycosylated form), VP40, VP35, VP30 and VP24. At the gene boundaries conserved transcriptional start (3'-NNCUNCNUNUAAUU-5') and stop signals (3'-UAAUUCUUUUU-5') are located containing the highly conserved pentamer 3'-UAAUU-5'. Comparison with other NNS RNA viruses shows conservation primarily in the termination signals, whereas the start signals are more variable. The intergenic regions vary in length and nucleotide composition. All genes have relatively long 3' and 5' end non-coding regions. The putative 3' and 5' leader RNA sequences of the MBG genome resemble those of other NNS RNA viruses in length, conservation at the 3' and 5' ends, and in being complementary at their extremities. The data support the concept of a common taxonomic order Mononegavirales comprising the Filoviridae, Paramyxoviridae, and Rhabdoviridae families.

Inactivated Lassa virus elicits a non protective immune response in rhesus monkeys.

We attempted to protect three rhesus monkeys from Lassa fever by vaccination with a preparation of purified whole Lassa virus which had been inactivated by gamma irradiation. The vaccinated monkeys developed antibodies against the three major viral proteins of Lassa virus demonstrated by radioimmunoprecipitation. When the three vaccinated monkeys and two unvaccinated control monkeys were challenged all five became severely ill and died. Prior to death a secondary, high-titer antibody response to Lassa virus was observed in the three vaccinated monkeys, whereas the two unvaccinated monkeys developed a primary, low-titer antibody response. Though titers of Lassa virus in serum reached peak levels earlier following challenge in the non vaccinated, at the time of death serum and organ virus titers did not differ significantly. Changes in platelet aggregation, leukocyte counts, and liver enzymes, abnormalities of which have been associated with severity of Lassa fever, were found to be comparable in the two groups. The humoral antibody response measured in these animals following vaccination, although of the same magnitude as found in humans recovered from Lassa fever, was insufficient to protect the animals from this fatal disease. Evidence is now accumulating that the cell-mediated immune response must be activated in order to protect against challenge with arenaviruses.

The nucleotide sequence of the L gene of Marburg virus, a filovirus: homologies with paramyxoviruses and rhabdoviruses.

The nucleotide sequence of the L gene of Marburg virus, strain Musoke, has been determined. The L gene has a single long open reading frame encoding a polypeptide of 2330 amino acids (MW 267,175) that represents the viral RNA-dependent RNA polymerase. The putative transcription start signal (3'CUACCUAUAAUU 5') and the termination signal (3' UAAUUCUUUUU 5') of the gene could be identified. Computer-assisted comparison of the L protein with L proteins of other nonsegmented negative-stranded RNA viruses (Paramyxoviridae: Sendai virus, Newcastle disease virus, human parainfluenza 3 virus, measles virus, human respiratory syncytial virus; Rhabdoviridae: vesicular stomatitis virus, rabies virus) revealed significant homologies primarily in the N-terminal half of the proteins. We have identified three common conserved boxes (A, B, and C) among filo-, paramyxo-, and rhabdovirus L proteins, which are probably involved in the polymerase function. The L proteins can be divided into an N-terminal half, which seems to accommodate the common enzymatic sites, and a C-terminal half carrying virus specific peculiarities. The data presented here suggest a common evolutionary history for all nonsegmented negative-stranded RNA viruses and show that filoviruses are more closely related to paramyxo- than to rhabdoviruses.

Sequence analysis of the Marburg virus nucleoprotein gene: comparison to Ebola virus and other non-segmented negative-strand RNA viruses.

The first 3000 nucleotides from the 3' end of the Marburg virus (MBG) genome were determined from cDNA clones produced from genomic RNA and mRNA. Identified in the sequence was a short putative leader sequence at the extreme 3' end, followed by the complete nucleoprotein (NP) gene. The 5' end of the NP mRNA was determined as was the polyadenylation site for the NP gene. The transcriptional start (3' UUCUUCUUAUAAUU..) and termination (3' ..UAAUUCUUUUU) signals of the MBG NP gene are very similar to those seen with Ebola virus (EBO). In comparison to other non-segmented negative-strand RNA viruses, filovirus transcriptional signals are most similar to members of the Paramyxovirus and Morbillivirus genera. In vitro translation of a run-off transcript containing the entire MBG NP coding region produced an authentic NP. Sequence comparisons of the 3' end of the MBG and EBO genomes revealed weak nucleotide sequence similarity, but the predicted sequence of the first 400 amino acids of these viruses showed a high degree. This homology is encoded in divergent nucleotide sequences through different codon usages and substitutions of similar amino acids. A small region in the middle of the MBG and EBO NP sequences was found to contain a significant amino acid homology with NPs of paramyxoviruses and to a lesser extent with rhabdoviruses. Specific sites of conserved sequence are contained in hydrophobic domains and may have a common function. Alignments of the entire NP amino acid sequences of these viruses also suggest that filoviruses are more closely related to paramyxoviruses than to rhabdoviruses.

Antigenic relatedness between arenaviruses defined at the epitope level by monoclonal antibodies.

Monoclonal antibodies (MAbs) were produced against two African arenaviruses, Lassa virus and Mopeia virus. Competitive binding analysis of MAbs identified four antigenic sites on the nucleoprotein (NP), two on glycoprotein 1 (GP1) and six on glycoprotein 2 (GP2) of the Josiah strain of Lassa virus. 64 virus isolates from western, central and southern Africa were all consistently distinguishable by MAbs to certain epitopic sites on GP1, GP2 and NP viral proteins. Furthermore, MAbs to Lassa virus GP1 and NP uniformly distinguished viruses from the West African countries of Sierra Leone, Liberia and Guinea from those of Nigeria. GP2-directed MAbs to two African arenaviruses reacted broadly with South American arenaviruses demonstrating that an epitopic site on GP2 may be the most highly conserved antigen in the arenavirus group.

Junin virus monoclonal antibodies: characterization and cross-reactivity with other arenaviruses.

Twenty-one monoclonal antibodies reactive with Junin virus structural proteins were produced and characterized. Using radioimmunoprecipitation and Western blot assays, 13 were found to react with the nucleoprotein, seven with the surface glycoprotein and one failed to react, but showed a fluorescent antibody staining pattern consistent with other glycoprotein-specific antibodies. In radioimmunoprecipitation assays, glycoprotein-specific monoclonal antibodies reacted not only with the 35K structural glycoprotein, but also with what is presumed to be the glycoprotein precursor. Four of seven glycoprotein-specific antibodies neutralized Junin virus to high titres. Cross-reactivity with other arenaviruses was found to be restricted to nucleoprotein-specific monoclonal antibodies and occurred only with New World arenaviruses. Cross-reactivity also shows the Junin virus to be most closely related to Machupo and Tacaribe viruses.

The nucleoprotein gene of Ebola virus: cloning, sequencing, and in vitro expression.

Genomic and messenger RNAs of a Zaire strain of Ebola virus were cloned, and inserts specific for the nucleoprotein gene were isolated and sequenced. The nucleoprotein gene is located proximal to the 3' end of the genome and is preceeded by a putative leader sequence. The gene begins with the transcriptional start site sequence 3'-UACUCCUUCUAAUU..., and ends with the polyadenylation site sequence 3'-... UAAUUCUUUUUU. The predicted coding region is 2217 bases in length and encodes a protein that contains 739 amino acids, with a calculated molecular weight of 83.3 kDa. The protein has an approximate net charge of -30 and can be divided into a hydrophobic N-terminal half and a hydrophilic and highly acidic C-terminal half. An in vitro transcript, generated from plasmid DNA containing the entire coding region, directs the synthesis of authentic nucleoprotein in a rabbit reticulocyte lysate system. The genomic organization and transcriptional signals of Ebola are similar to those of other nonsegmented, negative-strand RNA viruses, but nucleic acid or amino acid sequence comparisons indicate a lack of similarity.

Genetic variation among Lassa and Lassa-related arenaviruses analysed by T1-oligonucleotide mapping.

Total RNA and small RNA species of several African arenavirus strains have been studied by T1-oligonucleotide mapping. Genetic heterogeneity is observed and discussed on the basis of evolutionary biology of the Lassa complex.

Physicochemical properties of Marburg virus: evidence for three distinct virus strains and their relationship to Ebola virus.

The physicochemical and antigenic properties of three groups of Marburg (MBG) virus isolates, separated temporally and geographically, were compared to each other and to another member of the same family, Ebola (EBO) virus. Each MBG isolate contained seven virion proteins, one of which was a glycosylated surface protein. Peptide mapping of glycoproteins, nucleoproteins (NP) and viral structural protein (VP40) demonstrated extensive sequence conservation in the proteins of viruses isolated over a 13-year period, but homology was not evident in VP24. Some homology between the NPs of MBG and EBO was observed. A close antigenic relationship between MBG strains was found by radioimmunoassay but no evidence was found of antigenic cross-reactivity with EBO viruses. MBG virion proteins are produced from virus-specific monocistronic mRNA species. Five of the seven viral proteins were produced by in vitro translation of these RNAs. MBG virions contained one RNA species with an Mr of 4.2 x 10(6) and virions had a density of 1.14 g/ml in potassium tartrate. Virus isolates from different outbreaks had distinct T1 oligonucleotide maps, but had approximately 95% homology in base sequence. No two geographically distinct virus pairs were more closely related to each other than to a third virus isolate. MBG viruses are thus similar to EBO viruses in morphology and other physicochemical properties and are very similar to each other in RNA and protein composition. Each of the three geographically and temporally distinct MBG virus outbreaks appears to have been due to a genetically distinguishable, but antigenically closely related virus strain. In addition, these studies confirm the belief that MBG and EBO viruses are members of the new virus family, the Filoviridae.

Standardization of a plaque assay for Lassa virus.

The plaque reduction neutralization test (PRNT) has been used routinely in serological studies with such arenaviruses as Junin, Machupo, and Parana. However, difficulties have been encountered in using the PRNT for LCM virus, while conflicting views have been expressed about the reliability and efficacy of the test with Lassa virus. We have therefore investigated and evaluated the plaque assay for Lassa virus. In addition, the suitability of the PRNT for determining the potency of a serum and its efficacy in passive immunization for the treatment of Lassa fever was also investigated. The Lassa virus plaque assay satisfied the criteria proposed by Cooper [1961] for determining satisfactory plaque technique. Lassa virus plaques appear within 3 days of inoculating Vero cell cultures. By day 5, the plaques are clearly defined, discrete, and measure 1.5 to 2.0 mm. In the plaque reduction neutralization test, the use of native non-inactivated serum was required for a reliable and reproducible determination of serum antibody titer. The potency and suitability of a serum for Lassa fever serotherapy was determined by the use of a constant serum-varying virus (CS-VV) and/or a constant virus-varying serum (CV-VS) PRN technique.

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.

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.

Descriptive analysis of Ebola virus proteins.

The virion proteins of two strains of Ebola virus were compared by SDS-polyacrylamide gel electrophoresis (PAGE) and radioimmunoprecipitation (RIP). Seven virion proteins were described; an L (180K), GP (125K), NP (104K), VP40 (40K), VP35 (35K), VP30 (30K), and VP24 (24K). The RNP complex of the virus contained the L, the NP, and VP30, with VP35 in loose association with them. The GP was the major spike protein, with VP40 and VP24 making up the remaining protein content of the multilayered envelope.