Molecular cloning of Lassa virus RNA: nucleotide sequence and expression of the nucleocapsid protein gene

Vaccine platforms for the prevention of Lassa fever

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The epidemiological significance of Lassa fever in West Africa is discussed.

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Viral ecology, pathology, and immunobiology of Lassa virus infection is described.

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Multiple vaccine candidates have been tested in pre-clinical models.

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Lassa fever vaccine candidates have yet to progress to clinical trials.

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Five platform technologies have been selected for expedited development.

Lassa fever is an acute viral haemorrhagic illness caused by Lassa virus (LASV), which is endemic throughout much of West Africa. The virus primarily circulates in the Mastomys natalensis reservoir and is transmitted to humans through contact with infectious rodents or their secretions; human-to-human transmission is documented as well. With the exception of Dengue fever, LASV has the highest human impact of any haemorrhagic fever virus. On-going outbreaks in Nigeria have resulted in unprecedented mortality. Consequently, the World Health Organization (WHO) has listed LASV as a high priority pathogen for the development of treatments and prophylactics. Currently, there are no licensed vaccines to protect against LASV infection. Although numerous candidates have demonstrated efficacy in animal models, to date, only a single candidate has advanced to clinical trials. Lassa fever vaccine development efforts have been hindered by the high cost of biocontainment requirements, the absence of established correlates of protection, and uncertainty regarding the extent to which animal models are predictive of vaccine efficacy in humans. This review briefly discusses the epidemiology and biology of LASV infection and highlights recent progress in vaccine development.

Lassa fever vaccine

Lassa fever remains a serious challenge to public health in West Africa threatening both local residents in rural areas and those who serve them, particularly medical care providers. Given the ecology of the rodent host and conditions in the endemic area, a vaccine is mandatory for control. The challenge is to overcome the scientific, political and economic obstacles to producing a human use vaccine candidate. There are some scientific issues to resolve. It is known that the G-protein confers protection but we do not know its duration. If the N-protein is also included there may be a better duration of protection but it is unclear whether the N-protein as a vaccine may possibly enhance the infection. The original vaccinia vector must be replaced by new vectors, chimeras or by delivering DNA in some format. A live vaccine is attractive because it can confer protection in a single shot. A killed vaccine is more stable, particularly for distribution in the tropics but usually requires repeated shots. For practical reasons a live vaccine format should probably be pursued, which could then be combined with a yellow fever vaccine, using the same cold chains, since this disease occupies the same endemic areas in West Africa. Lassa vaccine initiatives have suffered from a lack of funding in the past but bioterrorism has brought new resources to Lassa virus science. Adequate funding and applications of new vaccine technologies give hope that we may soon see a vaccine in clinical trials. However, the difficulty of conducting trials in endemic areas and lack of political stability remain serious problems.

The role of myristoylation in the membrane association of the Lassa virus matrix protein Z

The Z protein is the matrix protein of arenaviruses and has been identified as the main driving force for budding. Both LCMV and Lassa virus Z proteins bud from cells in the absence of other viral proteins as enveloped virus-like particles. Z accumulates near the inner surface of the plasma membrane where budding takes place. Furthermore, biochemical data have shown that Z is strongly membrane associated. The primary sequence of Z lacks a typical transmembrane domain and until now it is not understood by which mechanism Z is able to interact with cellular membranes. In this report, we analyzed the role of N-terminal myristoylation for the membrane binding of Lassa virus Z. We show that disruption of the N-terminal myristoylation signal by substituting the N-terminal glycine with alanine (Z-G2A mutant) resulted in a significant reduction of Z protein association with cellular membranes. Furthermore, removal of the myristoylation site resulted in a relocalization of Z from a punctuate distribution to a more diffuse cellular distribution pattern. Finally, treatment of Lassa virus-infected cells with various myristoylation inhibitors drastically reduced efficient Lassa virus replication. Our data indicate that myristoylation of Z is critical for its binding ability to lipid membranes and thus, for effective virus budding.

Lassa virus

Lassa virus is a RNA virus belonging to the family of Arenaviridae. It was discovered as the causative agent of a hemorrhagic fever--Lassa fever--about 30 years ago. Lassa fever is endemic in West Africa and is estimated to affect some 100,000 people annually. Great progress in the understanding of the life cycle of arenaviruses, including Lassa virus, has been made in recent years. New insights have been gained in the pathogenesis and molecular epidemiology of Lassa fever, and state-of the-art technologies for diagnosing this life-threatening disease have been developed. The intention of this review is to summarize in particular the recent literature on Lassa virus and Lassa fever. Several aspects ranging from basic research up to clinical practice and laboratory diagnosis are discussed and linked together.

Towards a human Lassa fever vaccine

Arenaviruses, such as Lassa fever, establish chronic infections in rodents, leading to incidental transmission to humans. Lassa fever is a clinically severe disease, yet the absence of second attacks implies life-long immunity. The aim of this review is to consider whether such immunity could be provided by vaccines. The South American arenaviruses are controlled by neutralising antibody and a clinical trial of live, attenuated vaccine for Argentinian haemorrhagic fever provided 84% protection. In contrast, there is no evidence for protective humoral immunity against Old World arenaviruses which are controlled by cell-mediated immune responses. Nevertheless, vaccination with Lassa glycoproteins can protect monkeys from disease, implying that protection may be achievable, even though the immunological mechanisms are distinct. Recombinant vaccinia viruses expressing various forms of Lassa glycoproteins can protect both guinea-pigs and primates, while additional protective responses can be mounted against nucleocapsid genes. However, vaccines based upon vaccinia constructs are no longer tenable for African populations with a high seroprevalence of HIV infection. The scientific challenge now remains to find alternative methods of delivering T-cell immunity against glycoproteins from Lassa virus in ways which can overcome the local economic and political hurdles to vaccine development.

Allpahuayo virus: a newly recognized arenavirus (arenaviridae) from arboreal rice rats (oecomys bicolor and oecomys paricola) in northeastern peru

Allpahuayo virus was initially isolated from arboreal rice rats (Oecomys bicolor and Oecomys paricola) collected during 1997 at the Allpahuayo Biological Station in northeastern Peru. Serological and genetic studies identified the virus as a new member of the Tacaribe complex of the genus Arenavirus. The small (S) segment of the Allpahuayo virus prototype strain CLHP-2098 (Accession No. AY012686) was sequenced, as well as that of sympatric isolate CLHP-2472 (Accession No. AY012687), from the same rodent species. The S segment was 3382 bases in length and phylogenetic analysis indicated that Allpahuayo is a sister virus to Pichinde in clade A. Two ambisense, nonoverlapping reading frames were identified, which result in two predicted gene products, a glycoprotein precursor (GPC) and a nucleocapsid protein (NP). A predicted stable single hairpin secondary structure was identified in the intergenic region between GPC and NP. Details of the genetic organization of Allpahuayo virus are discussed.

Completion of the Lassa fever virus sequence and identification of a RING finger open reading frame at the L RNA 5' End

Lassa (LAS) fever virus is a highly pathogenic arenavirus with large (L) and small (S) RNA genomic segments. The 5' end of the LAS L segment is described here, thereby completing the sequence of the most virulent arenavirus analyzed to date. In keeping with the ambisense gene structure of the arenaviruses, the LAS L RNA encodes a 250-kDa protein and an 11-kDa protein in opposite senses with respect to each other. The 11-kDa protein, defined previously in arenaviruses lymphocytic choriomeningitis (LCM), Tacaribe (TAC), and Pichinde (PIC), contains a RING type of zinc-binding structure. Expression of the 11-kDa protein in LAS virus-infected cells has been confirmed by binding to peptide-specific antibody.

The Lassa fever virus L gene: nucleotide sequence, comparison, and precipitation of a predicted 250 kDa protein with monospecific antiserum

The large (L) RNA segment of Lassa fever virus (LAS) encodes a putative RNA-dependent RNA polymerase (RdRp or L protein). Similar to other arenaviruses, the LAS L protein is encoded on the genome-complementary strand and is predicted to be 2218 amino acids in length (253 kDa). It has an unusually large non-coding region adjacent to its translation start site. The LAS L protein contains six motifs of conserved amino acids that have been found among arenavirus L proteins and core RdRp of other segmented negative-stranded (SNS) viruses (Arena-, Bunya- and Orthomyxoviridae). Phylogenetic analyses of the RdRp of 20 SNS viruses reveals that arenavirus L proteins represent a distinct cluster divided into LAS-lymphocytic choriomeningitis and Tacaribe-Pichinde virus lineages. Monospecific serum against a synthetic peptide corresponding to the most conserved central domain precipitates a 250 kDa product from LAS and lymphocytic choriomeningitis virus-infected cells.

Nucleotide sequence of the S RNA of Lassa virus (Nigerian strain) and comparative analysis of arenavirus gene products

The nucleotide sequence of the small (S) genomic RNA of Lassa virus (strain GA391, of Nigerian origin) has been determined. The RNA has features which conform to those seen in most other arenavirus S RNAs which have been characterised, including conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. Comparison of the nucleotide sequence with that of the Josiah strain of Lassa virus (from Sierra Leone) reveals considerable nucleotide divergence in the third base of codons in the reading frames of all three proteins, although the resulting protein sequences are highly conserved, with 92, 94 and 91% identical residues for the mature glycoproteins G1 and G2 and the N protein, respectively. Sequence alignments of the available arenavirus structural proteins and dendrograms summarising the relationships between the viral proteins are presented.

Sequence analysis of the S RNA of the African arenavirus Mopeia: an unusual secondary structure feature in the intergenic region

Mopeia virus is an apparently nonpathogenic African arenavirus which can protect animals from subsequent challenge by the closely related Lassa virus. As a step toward understanding these differences in pathogenicity and the means by which Mopeia virus infection can protect against subsequent Lassa virus infection, cDNA clones corresponding to 3419 nucleotides of Mopeia virus S RNA were isolated and sequenced. Two open reading frames, encoding the glycoprotein precursor (GPC) and nucleocapsid (N) proteins, were located in the ambisense arrangement characteristic of the arenaviruses. Comparison of the amino acid sequences of the translation products with those of two Lassa virus strains showed considerable conservation, with 74 and 80% identity for the two glycoproteins G1 and G2, and 74% identity for the N protein. The putative dibasic site of GPC cleavage (R-R) was conserved, as were the potential N-linked glycosylation sites. A striking difference between Mopeia virus and Lassa virus was identified in the noncoding intergenic region. Instead of the single hairpin structure formed by base-pairing of complementary sequences which is usually found, the Mopeia virus S RNA has the potential to form two hairpins. These hairpins were similar in sequence and may have been formed in a duplication event during RNA replication. The possible contribution of this secondary structure feature to differences in pathogenicity between Mopeia and Lassa viruses is discussed.

Detection of Lassa virus RNA in specimens from patients with Lassa fever by using the polymerase chain reaction

Suitable oligonucleotide primers and probes were synthesized to amplify Lassa virus (Josiah strain)-specific nucleoprotein and glycoprotein gene fragments by using reverse transcription combined with the polymerase chain reaction (PCR). Our primers did not amplify the related lymphocytic choriomeningitis virus. By using PCR, about 50 50% tissue culture infective doses could be detected in the supernatant of infected cells. Furthermore, in all five serum specimens and four of five urine specimens of patients with acute Lassa fever, viral RNA could be demonstrated. Negative results were obtained with all serum and urine specimens of healthy subjects. Our data suggest that PCR may be applied as an alternative to virus isolation in the rapid diagnosis of Lassa fever.

Nontemplated bases at the 5' ends of Tacaribe virus mRNAs

Centrifugation of Tacaribe arenavirus-infected cell extracts on CsCl density gradients was used to separate genomes and antigenomes, which band at 1.31 g/ml as nucleocapsids, from mRNAs which pellet. Primer extensions on the banded RNAs showed that the 5' ends of the genomes and antigenomes were unique, whereas primer extensions on the mRNAs showed that their 5' ends were heterogenous in length, extending 0-4 bases beyond the 3' ends of the templates for their synthesis. This suggests that arenavirus mRNAs may initiate by a cap-snatching mechanism, somewhat similar to influenza viruses and bunyaviruses. We also found an extra G residue at the 5' end of the genome RNA, which was not predicted according to current models. This is now the third time that the unexpected G residue has been found at the 5' end of arenavirus genomes.

Tacaribe virus L gene encodes a protein of 2210 amino acid residues

The nucleotide sequence of Tacaribe virus (TV) L gene was obtained from two sets of overlapping cDNA clones constructed by walking along the virus L RNA using two successive synthetic DNA primers. Analysis of the sequence indicated the existence of a unique long open reading frame in the viral complementary strand. The first in-phase AUG codon is in positions 31-33 from the 5' end of the viral complementary L RNA surrounded by a sequence favorable for initiation of protein synthesis. The open reading frame ends at positions 6661-6663. The predicted TV L protein is a 2210 amino acid long polypeptide with an estimated molecular weight of 251,942. Comparison of the amino acid sequence of TV L protein with peptide sequences predicted from L-derived cDNA clones of lymphocytic choriomeningitis virus shows an overall 42% of homology.

Nucleotide sequence of the Lassa virus (Josiah strain) S genome RNA and amino acid sequence comparison of the N and GPC proteins to other arenaviruses

The complete nucleotide sequence of the S genome RNA of the Josiah strain of Lassa virus was determined from cloned cDNA. The S RNA is 3402 nucleotides long with a calculated molecular weight of 1.09 x 10(6) Da. The nucleotide base composition is 26.84% adenine, 21.40% guanine, 22.75% cytosine, and 29.01% uridine. The 5' and 3' terminal nucleotide sequences are conserved and complimentary for 19 nucleotides, the nucleoprotein and glycoprotein genes are arranged in ambisense coding strategy, and the intergenic region contains an inverted complimentary sequence, as do all other arenavirus S RNAs characterized to date. Amino acid sequence comparisons between the nucleoproteins and glycoproteins of the Josiah and Nigerian (N sequences only) strains of Lassa virus, the WE and ARM strains of lymphocytic choriomeningitis virus (LCMV), Tacaribe, and Pichinde viruses are presented. These findings reveal that the G2 envelope glycoprotein is more conserved among different arenaviruses than the internal nucleoprotein.

Vaccinia recombinant expressing Lassa-virus internal nucleocapsid protein protects guineapigs against Lassa fever

The Lister strain of vaccinia virus was used to construct a recombinant that expressed the nucleocapsid gene of Lassa virus. Guineapigs immunised with the recombinant virus were protected against challenge with Lassa virus, whereas control animals showed the usual disease course, including pyrexia, anorexia, viraemia, and death. These data indicate not only that protective immunity to Lassa fever can be evoked by an experimental vaccine, but also that this response can be mediated by an internal protein component of the virus.

Molecular structure and early events in the replication of Tacaribe arenavirus S RNA

Tacaribe arenavirus S RNA was cloned and analysis of its nucleotide sequence revealed two open reading frames of significant size, one in the virus-sense strand, the other in the virus-complementary strand. The predicted amino acid sequences of the two reading frames were compared with the predicted primary structures of the nucleoprotein (N) and glycoprotein precursor (GPC) of LCM, Pichinde and Lassa viruses. The results indicated a high degree of homology between the proteins of similar properties. It was also found that in Tacaribe virus-infected cells a subgenomic viral-sense GPC RNA and a subgenomic viral-complementary N RNA are synthesized in addition to the full length viral (v) RNA and viral complementary (vc) RNAs. These results support the conclusion that in Tacaribe virus--as in Pichinde and lymphocytic choriomeningitis arenavirus-S RNA encodes the viral N and GPC proteins and has an 'ambisense' coding strategy. Analysis of the S-derived RNA species at early times post-infection in cells incubated with or without inhibitors of protein synthesis indicated that for primary transcription of the N mRNA, protein synthesis is not required; whereas synthesis of the vc RNA, GPC mRNA and v RNA does require protein synthesis to take place.

Molecular characterization of the genomic S RNA segment from lymphocytic choriomeningitis virus

We have used cDNA clones derived from the genomic S RNA segment of lymphocytic choriomeningitis virus (LCMV), Armstrong strain, as hybridization probes to monitor virus gene expression during acute infections. Our results with strand-specific probes confirm the ambisense character of the LCMV S RNA segment and document the presence of both genomic sense and genomic complementary sense RNA species over the time course of infection. We have used nucleotide sequence information to predict primary amino acid sequences for the major viral structural proteins, nucleoprotein (NP) and glycoprotein (GP-C). Antibodies raised against synthetic peptides derived from these predicted protein sequences have indicated that the gene order for the S segment is 3' NP----5' GP-C and provided direct demonstration that the GP-1 portion of the GP-C precursor is encoded nearest the 5' end of the S segment. Comparison of the predicted amino acid sequences for NP and GP-C between the Armstrong CA-1371 strain and the WE strain shows over 90% amino acid identity. This suggests that significant differences described for the pathogenic potential of the Arm and WE strains in C3H mice reside in one or a very few critical amino acid changes.

Expression of Lassa virus nucleocapsid protein segments in bacteria: purification of high-level expression products and their application in antibody detection

The Lassa virus nucleocapsid protein gene and segments from it were expressed in Escherichia coli under the control of the lac promoter in pUC-based plasmids. Expression of the near full-length protein [amino acid (aa) residues 12-570] fused to an N-terminal sequence of vector-derived 6 aa was not particularly efficient, and neither was that of a smaller N-terminal segment (aa 6-201) which was also fused at its C terminus to the remainder of the lacZ gene product. By contrast, the C-terminal 370 aa could be expressed at levels approaching 10% of total cellular protein. All the recombinant proteins were associated with the insoluble fraction after sonication of the bacteria. The inefficiently expressed products did not appear to be any more susceptible to proteolytic degradation. The distribution of codons rarely used in E. coli genes was relatively uniform along the nucleocapsid gene sequence. These results are consistent with the regulation of transcriptional or translational efficiency by features of the sequence downstream from the promoter and ribosome-binding site. The C-terminal segment (aa 201-570 representing 65% of the authentic protein) was purified by ion exchange chromatography and shown to be active when used as antigen in enzyme-linked immunoassays for virus-specific antibodies.

Nucleotide sequence of the glycoprotein gene and intergenic region of the Lassa virus S genome RNA

Two overlapping cDNA clones corresponding to the 5' region of the Lassa virus S genome RNA were isolated and their nucleotide sequences determined. Similar to Pichinde and lymphocytic choriomeningitis viruses (LCMV), Lassa virus has an ambisense S RNA. The precursor to the viral glycoproteins (GPC) is encoded in viral RNA sequence originating at position 56 and terminating at position 1529 from the 5' terminus of the S RNA. A short, noncoding, intergenic region capable of forming a hairpin structure separates the termination codons of the nucleoprotein (N) and GPC genes. Hydropathic analysis of the GPC gene product of Lassa virus indicates the presence of hydrophobic domains near the amino and carboxy termini as previously noted in the corresponding proteins of Pichinde and LCM viruses. A comparison of the nucleotide sequences on the 3' termini of the viral and viral-complimentary S RNA species of Lassa, LCM, and Pichinde viruses reveals slight sequence differences that may possibly be involved in the regulation of RNA synthesis and gene expression.

Ambisense RNA genomes of arenaviruses and phleboviruses

This chapter reviews the evidence that shows that arenaviruses and members of one genus of the Bunyaviridae (phleboviruses) have some proteins coded in subgenomic, viral-sense mRNA species and other proteins coded in subgenomic, viral-complementary mRNA sequences. This unique feature is discussed in relation to the implications it has on the intracellular infection process and how such a coding arrangement may have evolved. The chapter presents a list of the known members of the arenaviridae, their origins, and the vertebrate hosts from which isolates have been reported. It discusses the structural components, the infection cycle, and genetic attributes of arenaviruses. In order to determine how arenaviruses code for gene products, the S RNA species of Pichinde virus and that of a viscerotropic strain of LCM virus (LCM-WE) have been cloned into DNA and sequenced. The arenavirus S RNA is described as having an ambisense strategy, to denote the fact that both viral and viral-complementary sequences are used to make gene products. The chapter discusses the infection cycle, the structural and genetic properties of bunyaviridae member.