Protein sequence database for pathogenic arenaviruses

Genome-Wide Prediction of Potential Vaccine Candidates for Campylobacter jejuni Using Reverse Vaccinology

Campylobacteriosis is a deadly disease which has developed resistance to most of the available chemotherapeutic agents. Although various studies provide evidence of acquired immunity following exposure to Campylobacter jejuni, no effective vaccine has been developed, still. Hence, there is an urgent need to identify potential vaccine candidates for Campylobacter species. In the proposed study, Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) was taken and computational approach was employed to screen C. jejuni genome for promising vaccine candidates. From 1623 protein-coding sequences, 37 potential antigens were screened for epitope prediction based on surface association, consensus antigenicity predictions, solubility, transmembrane domain, and ortholog analysis. Comprehensive immunogenic analysis of these 37 antigens revealed that antigen Q0PA22 shows the greatest potential for experimental immunogenicity analysis. It has several potential CD4+ and CD8+ T-cell epitopes, as well as high probability of B-cell epitope regions as compared to well-characterized antigen Omp18 (Uniprot ID:Q0PC24). Among the highest scoring predicted epitopes, an optimal set of epitopes with respect to overall immunogenicity in target populations for campylobacteriosis viz. Europe, North America and Southwest Asia was determined. An epitope AMLTYMQWL from antigen no. 6(Q0PA22) binds to the most prevalent allele HLA-A*0201, and this epitope has most immunogenicity for all the target populations. In addition, this epitope exhibited highly significant TCR-pMHC interactions having a joint Z value of 4.87. Homology mapping studies of the predicted epitope show best homology to a well-studied antigenic peptide from influenza virus H5N1. Therefore, the predicted epitope might be a suitable vaccine candidate.

[A prototype of oligonucleotide microarray for detection of pathogens relating to arena- and Filoviridae families]

A prototype of oligonucleotide microarray for detection of Lassa, Junin, Machupo, Guanarito viruses (Arenaviridae family), Ebola and Marburg viruses (Filoviridae family) was presented. An original approach founded on virus proteins (nucleocapsid protein for Junin, Guanarito, Machupo viruses and RNA-dependent RNA-polymerase for Lassa, Ebola and Marburg viruses) amino acid sequences analysis with subsequent transform of revealed unique peptides into due sets of oligonucleotides was used to design probes for hybridization and primers.

Arenavirus variations due to host-specific adaptation

Arenavirus particles are enveloped and contain two single-strand RNA genomic segments with ambisense coding. Genetic plasticity of the arenaviruses comes from transcription errors, segment reassortment, and permissive genomic packaging, and results in their remarkable ability, as a group, to infect a wide variety of hosts. In this review, we discuss some in vitro studies of virus genetic and phenotypic variation after exposure to selective pressures such as high viral dose, mutagens and antivirals. Additionally, we discuss the variation in vivo of selected isolates of Old World arenaviruses, particularly after infection of different animal species. We also discuss the recent emergence of new arenaviruses in the context of our observations of sequence variations that appear to be host-specific.

Genomic analysis and pathogenic characteristics of lymphocytic choriomeningitis virus strains isolated in Japan

Lymphocytic choriomeningitis virus (LCMV) is a zoonotic pathogen of which mice are the natural reservoir. Different strains and clones of LCMV show different pathogenicity in mice. Here we determined the complete genomic sequences of 3 LCMV strains (OQ28 and BRC which were isolated from mice in Japan and WE(ngs) which was derived from strain WE). Strains OQ28 and BRC showed high sequence homology with other LCMV strains. Although phylogenetic analyses placed these 2 Japanese strains in different subclusters, they belonged to same cluster of LCMV isolates. WE(ngs) and WE had many sequence substitutions between them but fell into same subcluster. The pathogenicity of the 3 new LCMV isolates was examined by inoculating ICR mice with 10² and 10⁴ TCID₅₀ of virus. ICR mice infected with OQ28 or WE(ngs) exhibited severe clinical signs, and some of the infected mice died. In contrast, all ICR mice infected with BRC showed no clinical signs and survived infection. Virus was detected in the blood, organs, or both of most of the surviving ICR mice inoculated with either OQ28 or WE(ngs). However, virus was below the level of detection in all ICR mice surviving infection with strain BRC. Therefore, LCMV strains OQ28 and BRC were genetically classified in the same cluster of LCMV strains but exhibited very different pathogenicity.

Junín virus. A XXI century update

Junín virus of the Arenaviridae family is the etiological agent of Argentine hemorrhagic fever, a febrile syndrome causing hematological and neurological symptoms. We review historical perspectives of current knowledge on the disease, and update information related to the virion and its potential pathogenic mechanisms.

Conserved residues in Lassa fever virus Z protein modulate viral infectivity at the level of the ribonucleoprotein

Arenaviruses are negative-strand RNA viruses that cause human diseases such as lymphocytic choriomeningitis, Bolivian hemorrhagic fever, and Lassa hemorrhagic fever. No licensed vaccines exist, and current treatment is limited to ribavirin. The prototypic arenavirus, lymphocytic choriomeningitis virus (LCMV), is a model for dissecting virus-host interactions in persistent and acute disease. The RING finger protein Z has been identified as the driving force of arenaviral budding and acts as the viral matrix protein. While residues in Z required for viral budding have been described, residues that govern the Z matrix function(s) have yet to be fully elucidated. Because this matrix function is integral to viral assembly, we reasoned that this would be reflected in sequence conservation. Using sequence alignment, we identified several conserved residues in Z outside the RING and late domains. Nine residues were each mutated to alanine in Lassa fever virus Z. All of the mutations affected the expression of an LCMV minigenome and the infectivity of virus-like particles, but to greatly varying degrees. Interestingly, no mutations appeared to affect Z-mediated budding or association with viral GP. Our findings provide direct experimental evidence supporting a role for Z in the modulation of the activity of the viral ribonucleoprotein (RNP) complex and its packaging into mature infectious viral particles.

Coverage of related pathogenic species by multivalent and cross-protective vaccine design: arenaviruses as a model system

The arenaviruses are a family of negative-sense RNA viruses that cause severe human disease ranging from aseptic meningitis to hemorrhagic fever syndromes. There are currently no FDA-approved vaccines for the prevention of arenavirus disease, and therapeutic treatment is limited to the use of ribavirin and/or immune plasma for a subset of the pathogenic arenaviruses. The considerable genetic variability observed among the seven arenaviruses that are pathogenic for humans illustrates one of the major challenges for vaccine development today, namely, to overcome pathogen heterogeneity. Over the past 5 years, our group has tested several strategies to overcome pathogen heterogeneity, utilizing the pathogenic arenaviruses as a model system. Because T cells play a prominent role in protective immunity following arenavirus infection, we specifically focused on the development of human vaccines that would induce multivalent and cross-protective cell-mediated immune responses. To facilitate our vaccine development and testing, we conducted large-scale major histocompatibility complex (MHC) class I and class II epitope discovery on murine, nonhuman primate, and human backgrounds for each of the pathogenic arenaviruses, including the identification of protective HLA-restricted epitopes. Finally, using the murine model of lymphocytic choriomeningitis virus infection, we studied the phenotypic characteristics associated with immunodominant and protective T cell epitopes. This review summarizes the findings from our studies and discusses their application to future vaccine design.

Comparative pathogenesis and systems biology for biodefense virus vaccine development

Developing vaccines to biothreat agents presents a number of challenges for discovery, preclinical development, and licensure. The need for high containment to work with live agents limits the amount and types of research that can be done using complete pathogens, and small markets reduce potential returns for industry. However, a number of tools, from comparative pathogenesis of viral strains at the molecular level to novel computational approaches, are being used to understand the basis of viral attenuation and characterize protective immune responses. As the amount of basic molecular knowledge grows, we will be able to take advantage of these tools not only to rationally attenuate virus strains for candidate vaccines, but also to assess immunogenicity and safety in silico. This review discusses how a basic understanding of pathogenesis, allied with systems biology and machine learning methods, can impact biodefense vaccinology.

A multivalent and cross-protective vaccine strategy against arenaviruses associated with human disease

Arenaviruses are the causative pathogens of severe hemorrhagic fever and aseptic meningitis in humans, for which no licensed vaccines are currently available. Pathogen heterogeneity within the Arenaviridae family poses a significant challenge for vaccine development. The main hypothesis we tested in the present study was whether it is possible to design a universal vaccine strategy capable of inducing simultaneous HLA-restricted CD8⁺ T cell responses against 7 pathogenic arenaviruses (including the lymphocytic choriomeningitis, Lassa, Guanarito, Junin, Machupo, Sabia, and Whitewater Arroyo viruses), either through the identification of widely conserved epitopes, or by the identification of a collection of epitopes derived from multiple arenavirus species. By inoculating HLA transgenic mice with a panel of recombinant vaccinia viruses (rVACVs) expressing the different arenavirus proteins, we identified 10 HLA-A02 and 10 HLA-A03-restricted epitopes that are naturally processed in human antigen-presenting cells. For some of these epitopes we were able to demonstrate cross-reactive CD8⁺ T cell responses, further increasing the coverage afforded by the epitope set against each different arenavirus species. Importantly, we showed that immunization of HLA transgenic mice with an epitope cocktail generated simultaneous CD8⁺ T cell responses against all 7 arenaviruses, and protected mice against challenge with rVACVs expressing either Old or New World arenavirus glycoproteins. In conclusion, the set of identified epitopes allows broad, non-ethnically biased coverage of all 7 viral species targeted by our studies.

Arenaviruses cause significant morbidity and mortality worldwide and are also regarded as a potential bioterrorist threat. CD8⁺ T cells restricted by class I MHC molecules clearly play a protective role in murine models of arenavirus infection, yet little is known about the epitopes recognized in the context of human class I MHC (HLA). Here, we defined 20 CD8⁺ T cell epitopes restricted by HLA class I molecules, derived from 7 different species of arenaviruses associated with human disease. To accomplish this task, we utilized epitope predictions, in vitro HLA binding assays, and HLA transgenic mice inoculated with recombinant vaccinia viruses (rVACV) expressing arenavirus antigens. Because our analysis targeted two of the most common HLA types worldwide, we project that the CD8⁺ T cell epitope set provides broad coverage against diverse ethnic groups within the human population. Furthermore, we show that immunization with a cocktail of these epitopes protects HLA transgenic mice from challenge with rVACV expressing antigens from different arenavirus species. Our findings suggest that a cell-mediated vaccine strategy might be able to protect against infection mediated by multiple arenavirus species.

Characterization of monoclonal antibodies to Junin virus nucleocapsid protein and application to the diagnosis of hemorrhagic fever caused by South American arenaviruses

Junin virus (JUNV), Machupo virus, Guanarito virus, Sabia virus, and Chapare virus are members of New World arenavirus clade B and are the etiological agents of viral hemorrhagic fevers that occur in South America. In this study, we produced three monoclonal antibodies (MAbs) to the recombinant nucleocapsid protein of JUNV, designated C6-9, C11-12, and E4-2. The specificity of these MAbs was examined by enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence assay, and an epitope-mapping method. Using these MAbs, we developed antigen (Ag) capture ELISA systems. We showed that by using MAb C6-9, JUNV Ag was specifically detected. On the other hand, by using MAb C11-12 or E-4-2, the Ags of all human pathogenic South American arenaviruses were detected. The combined use of these Ag capture ELISA systems in the present study may be useful for the diagnosis of acute-phase viral hemorrhagic fever due to infection by a South American arenavirus.

Unusual molecular architecture of the machupo virus attachment glycoprotein

New World arenaviruses, which cause severe hemorrhagic fever, rely upon their envelope glycoproteins for attachment and fusion into their host cell. Here we present the crystal structure of the Machupo virus GP1 attachment glycoprotein, which is responsible for high-affinity binding at the cell surface to the transferrin receptor. This first structure of an arenavirus glycoprotein shows that GP1 consists of a novel alpha/beta fold. This provides a blueprint of the New World arenavirus attachment glycoproteins and reveals a new architecture of viral attachment, using a protein fold of unknown origins.

Simultaneous analysis of in vivo CD8+ T cell cytotoxicity against multiple epitopes using multicolor flow cytometry

CD8+ T cells play a critical role in host defense against infections and tumors. Analysis of cytotoxic function of antigen-specific CD8+ T cells in animal models would be important in optimizing vaccine design against infections and tumors. In vivo cytotoxicity assays using fluorescent cellular dyes have been used as a popular alternative to traditionally used in vitro (51)Cr-release assays. With the identification of multiple epitopes in various pathogen models, methods to simultaneously analyze cytotoxicity of CD8+ T cells to multiple epitopes in vivo would assist studies which aim to generate protective CD8+ T cell immunity to multiple epitopes. In this study, we evaluate the use of multiple fluorescent cellular dyes for the in vivo cytotoxicity assay. The use of 3 dyes allowed us to analyze the cytotoxicity of antigen-specific CD8+ T cell populations to multiple epitopes generated by virus infections, as well as their functional avidity, in vivo. Our studies extend the use of in vivo cytotoxicity assays to allow direct comparisons of cytotoxicity to various epitopes in the same animal and may also be applicable to assessment of in vitro cytotoxicity of human CD8+ T cells specific for multiple viral or tumor antigens in clinical settings.

Adaptive immunity to Lymphocytic choriomeningitis virus: new insights into antigenic determinants

Lymphocytic choriomeningitis virus (LCMV) is one of the most studied infectious disease models in mice. Human infection with LCMV can result in severe disease, ranging from aseptic meningitis in immunocompetent individuals, hydrocephalus, chorioretinitis or microcephaly in fetal infection, or to a highly lethal outcome in immunosuppressed individuals. This review examines recent advances in our understanding of the adaptive immune response to LCMV and how the cell-mediated and humoral immune responses contribute to protective immunity. New insights into the antigenicity of the LCMV proteome and the complexity of the cell-mediated immune response are addressed. We also discuss state-of-the-art approaches for T-cell epitope discovery in murine and human backgrounds and their recent application to LCMV. New findings regarding CD4+ T-cell dysregulation during chronic LCMV infection, and potential avenues for the treatment of chronic viral infection through modulation of the programmed cell death-1 receptor and/or IL-10 signaling pathways, are also evaluated.