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Ritsch M, Cassman NA, Saghaei S, Marz M. Navigating the Landscape: A Comprehensive Review of Current Virus Databases. Viruses 2023; 15:1834. [PMID: 37766241 PMCID: PMC10537806 DOI: 10.3390/v15091834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.
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Affiliation(s)
- Muriel Ritsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Noriko A. Cassman
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Shahram Saghaei
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
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Schein CH, Rafael G, Baker WS, Anaya ES, Schmidt JG, Weaver SC, Negi S, Braun W. PCP consensus protein/peptide alphavirus antigens stimulate broad spectrum neutralizing antibodies. Peptides 2022; 157:170844. [PMID: 35878658 DOI: 10.1016/j.peptides.2022.170844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022]
Abstract
Vaccines based on proteins and peptides may be safer and if calculated based on many sequences, more broad-spectrum than those designed based on single strains. Physicochemical Property Consensus (PCPcon) alphavirus (AV) antigens from the B-domain of the E2 envelope protein were designed, synthesized recombinantly and shown to be immunogenic (i.e. sera after inoculation detected the antigen in dotspots and ELISA). Antibodies in sera after inoculation with B-region antigens based on individual AV species (eastern or Venezuelan equine encephalitis (EEEVcon, VEEVcon), or chikungunya (CHIKVcon) bound only their cognate protein, while those designed against multiple species (Mosaikcon and EVCcon) recognized all three serotype specific antigens. The VEEVcon and EEEVcon sera only showed antiviral activity against their related strains (in plaque reduction neutralization assays (PRNT50/80). Peptides designed to surface exposed areas of the E2-A-domain of CHIKVcon were added to CHIKVcon inocula to provide anti-CHIKV antibodies. EVCcon, based on three different alphavirus species, combined with E2-A-domain peptides from AllAVcon, a PCPcon of 24 diverse AV, generated broad spectrum, antiviral antibodies against VEEV, EEEV and CHIKV, AV with less than 35% amino acid identity to each other (>65% diversity). This is a promising start to a molecularly defined vaccine against all AV. Further study with these antigens can illuminate what areas are most important for a robust immune response, resistant to mutations in rapidly evolving viruses. The validated computational methods can also be used to design broad spectrum antigens against many other pathogen families.
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Affiliation(s)
- Catherine H Schein
- Departments of Biochemistry and Molecular Biology, UTMB; Institute for Human Infections and Immunity (IHII), UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Grace Rafael
- Microbiology and Immunology, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Wendy S Baker
- Departments of Biochemistry and Molecular Biology, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | | | | | - Scott C Weaver
- Microbiology and Immunology, UTMB; Institute for Human Infections and Immunity (IHII), UTMB; World Reference Center for Emerging Viruses and Arboviruses, UTMB; Sealy Center for Structural Biology and Molecular Biophysics, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Surendra Negi
- Departments of Biochemistry and Molecular Biology, UTMB; Sealy Center for Structural Biology and Molecular Biophysics, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Werner Braun
- Departments of Biochemistry and Molecular Biology, UTMB; Sealy Center for Structural Biology and Molecular Biophysics, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
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Braun BA, Schein CH, Braun W. DGraph Clusters Flaviviruses and β-Coronaviruses According to Their Hosts, Disease Type, and Human Cell Receptors. Bioinform Biol Insights 2021; 15:11779322211020316. [PMID: 34163149 PMCID: PMC8188974 DOI: 10.1177/11779322211020316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/05/2021] [Indexed: 01/11/2023] Open
Abstract
Motivation There is a need for rapid and easy-to-use, alignment-free methods to cluster large groups of protein sequence data. Commonly used phylogenetic trees based on alignments can be used to visualize only a limited number of protein sequences. DGraph, introduced here, is an application developed to generate 2-dimensional (2D) maps based on similarity scores for sequences. The program automatically calculates and graphically displays property distance (PD) scores based on physico-chemical property (PCP) similarities from an unaligned list of FASTA files. Such "PD-graphs" show the interrelatedness of the sequences, whereby clusters can reveal deeper connectivities. Results Property distance graphs generated for flavivirus (FV), enterovirus (EV), and coronavirus (CoV) sequences from complete polyproteins or individual proteins are consistent with biological data on vector types, hosts, cellular receptors, and disease phenotypes. Property distance graphs separate the tick- from the mosquito-borne FV, cluster viruses that infect bats, camels, seabirds, and humans separately. The clusters correlate with disease phenotype. The PD method segregates the β-CoV spike proteins of severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Middle East respiratory syndrome (MERS) sequences from other human pathogenic CoV, with clustering consistent with cellular receptor usage. The graphs also suggest evolutionary relationships that may be difficult to determine with conventional bootstrapping methods that require postulating an ancestral sequence.
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Affiliation(s)
- Benjamin A Braun
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
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Baker WS, Negi S, Braun W, Schein CH. Producing physicochemical property consensus alphavirus protein antigens for broad spectrum vaccine design. Antiviral Res 2020; 182:104905. [PMID: 32800880 DOI: 10.1016/j.antiviral.2020.104905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/19/2020] [Accepted: 08/01/2020] [Indexed: 12/16/2022]
Abstract
There is a pressing need for new vaccines against alphaviruses, which can cause fatal encephalitis (Venezuelan equine encephalitis virus (VEEV) and others) and severe arthralgia (e.g. Chikungunya virus, CHIKV). These positive-strand RNA viruses are diverse and evolve rapidly, meaning that the sequence of any vaccine should cover multiple strains that may be quite different from any previous isolate. Here, consensus proteins were produced to represent the common physicochemical properties (PCPs) of the epitope rich, B domain of the E2 envelope protein. PCP-consensus proteins were based on multiple strains of VEEV (VEEVcon) and CHIKV (CHIKVcon) or the conserved PCPs of 24 different alphaviruses (AllAVcon). The AllAVcon was altered to include binding sites for neutralizing antibodies of both VEEV and CHIKV strains (Mosaikcon). All four designed proteins were produced solubly in E. coli and purified. They formed the β-strand core expected from experimental structures of this region of the wild type E2 proteins as indicated by circular dichroism (CD) spectra. Furthermore, the CHIKVcon protein bound to a structure dependent, CHIKV neutralizing monoclonal antibody. The AllAVcon and Mosaikcon proteins bound to polyclonal antibodies generated during natural infection with either VEEV or CHIKV, indicating they contained epitopes of both serotypes. The Mosaikcon antigen induced antibodies in rabbit sera that recognized both the VEEVcon and CHIKVcon spike proteins. These PCP-consensus antigens are promising starting points for novel, broad-spectrum alphavirus vaccines.
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Affiliation(s)
- Wendy S Baker
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Surendra Negi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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An HER2 DNA vaccine with evolution-selected amino acid substitutions reveals a fundamental principle for cancer vaccine formulation in HER2 transgenic mice. Cancer Immunol Immunother 2019; 68:1143-1155. [PMID: 31177328 DOI: 10.1007/s00262-019-02333-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/26/2019] [Indexed: 12/19/2022]
Abstract
Enhancement of endogenous immunity to tumor-associated self-antigens and neoantigens is the goal of preventive vaccination. Toward this goal, we compared the efficacy of the following HER2 DNA vaccine constructs: vaccines encoding wild-type HER2, hybrid HER2 vaccines consisting of human HER2 and rat Neu, HER2 vaccines with single residue substitutions and a novel human HER2 DNA vaccine, ph(es)E2TM. ph(es)E2TM was designed to contain five evolution-selected substitutions: M198V, Q398R, F425L, H473R and A622T that occur frequently in 12 primate HER2 sequences. These ph(es)E2TM substitutions score 0 to 1 in blocks substitutions matrix (BLOSUM), indicating minimal biochemical alterations. h(es)E2TM recombinant protein is recognized by a panel of anti-HER2 mAbs, demonstrating the preservation of HER2 protein structure. Compared to native human HER2, electrovaccination of HER2 transgenic mice with ph(es)E2TM induced a threefold increase in HER2-binding antibody (Ab) and elevated levels of IFNγ-producing T cells. ph(es)E2TM, but not pE2TM immune serum, recognized HER2 peptide p95 355LPESFDGDPASNTAP369, suggesting a broadening of epitope recognition induced by the minimally modified HER2 vaccine. ph(es)E2TM vaccination reduced tumor growth more effectively than wild-type HER2 or HER2 vaccines with more extensive modifications. The elevation of tumor immunity by ph(es)E2TM vaccination would create a favorable tumor microenvironment for neoantigen priming, further enhancing the protective immunity. The fundamental principle of exploiting evolution-selected amino acid substitutions is novel, effective and applicable to vaccine development in general.
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Unraveling the web of viroinformatics: computational tools and databases in virus research. J Virol 2014; 89:1489-501. [PMID: 25428870 DOI: 10.1128/jvi.02027-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain--viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc.) as well as distinct applications (comparative/diversity analysis, viral recombination, small interfering RNA [siRNA]/short hairpin RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines. However, information about their access and utility is not available at any single source or on any single platform. Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article.
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Langevin SA, Bowen RA, Reisen WK, Andrade CC, Ramey WN, Maharaj PD, Anishchenko M, Kenney JL, Duggal NK, Romo H, Bera AK, Sanders TA, Bosco-Lauth A, Smith JL, Kuhn R, Brault AC. Host competence and helicase activity differences exhibited by West Nile viral variants expressing NS3-249 amino acid polymorphisms. PLoS One 2014; 9:e100802. [PMID: 24971589 PMCID: PMC4074097 DOI: 10.1371/journal.pone.0100802] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/14/2014] [Indexed: 01/27/2023] Open
Abstract
A single helicase amino acid substitution, NS3-T249P, has been shown to increase viremia magnitude/mortality in American crows (AMCRs) following West Nile virus (WNV) infection. Lineage/intra-lineage geographic variants exhibit consistent amino acid polymorphisms at this locus; however, the majority of WNV isolates associated with recent outbreaks reported worldwide have a proline at the NS3-249 residue. In order to evaluate the impact of NS3-249 variants on avian and mammalian virulence, multiple amino acid substitutions were engineered into a WNV infectious cDNA (NY99; NS3-249P) and the resulting viruses inoculated into AMCRs, house sparrows (HOSPs) and mice. Differential viremia profiles were observed between mutant viruses in the two bird species; however, the NS3-249P virus produced the highest mean peak viral loads in both avian models. In contrast, this avian modulating virulence determinant had no effect on LD50 or the neurovirulence phenotype in the murine model. Recombinant helicase proteins demonstrated variable helicase and ATPase activities; however, differences did not correlate with avian or murine viremia phenotypes. These in vitro and in vivo data indicate that avian-specific phenotypes are modulated by critical viral-host protein interactions involving the NS3-249 residue that directly influence transmission efficiency and therefore the magnitude of WNV epizootics in nature.
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Affiliation(s)
- Stanley A. Langevin
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - William K. Reisen
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christy C. Andrade
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Wanichaya N. Ramey
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Payal D. Maharaj
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Michael Anishchenko
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Joan L. Kenney
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Nisha K. Duggal
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Hannah Romo
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Aloke Kumar Bera
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Todd A. Sanders
- United States Fish and Wildlife Service, Portland, Oregon, United States of America
| | - Angela Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Janet L. Smith
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Aaron C. Brault
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
- * E-mail:
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Schein CH, Bowen DM, Lewis JA, Choi K, Paul A, van der Heden van Noort GJ, Lu W, Filippov DV. Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals. BMC Bioinformatics 2012; 13 Suppl 13:S9. [PMID: 23320474 PMCID: PMC3426803 DOI: 10.1186/1471-2105-13-s13-s9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Analysis of large sets of biological sequence data from related strains or organisms is complicated by superficial redundancy in the set, which may contain many members that are identical except at one or two positions. Thus a new method, based on deriving physicochemical property (PCP)-consensus sequences, was tested for its ability to generate reference sequences and distinguish functionally significant changes from background variability. Methods The PCP consensus program was used to automatically derive consensus sequences starting from sequence alignments of proteins from Flaviviruses (from the Flavitrack database) and human enteroviruses, using a five dimensional set of Eigenvectors that summarize over 200 different scalar values for the PCPs of the amino acids. A PCP-consensus protein of a Dengue virus envelope protein was produced recombinantly and tested for its ability to bind antibodies to strains using ELISA. Results PCP-consensus sequences of the flavivirus family could be used to classify them into five discrete groups and distinguish areas of the envelope proteins that correlate with host specificity and disease type. A multivalent Dengue virus antigen was designed and shown to bind antibodies against all four DENV types. A consensus enteroviral VPg protein had the same distinctive high pKa as wild type proteins and was recognized by two different polymerases. Conclusions The process for deriving PCP-consensus sequences for any group of aligned similar sequences, has been validated for sequences with up to 50% diversity. Ongoing projects have shown that the method identifies residues that significantly alter PCPs at a given position, and might thus cause changes in function or immunogenicity. Other potential applications include deriving target proteins for drug design and diagnostic kits.
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Affiliation(s)
- Catherine H Schein
- Institute for Translational Sciences, Computational Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Texas 77555-0857, USA.
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West nile virus infections suppress early viral RNA synthesis and avoid inducing the cell stress granule response. J Virol 2012; 86:3647-57. [PMID: 22258263 DOI: 10.1128/jvi.06549-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
West Nile virus (WNV) recently became endemic in the United States and is a significant cause of human morbidity and mortality. Natural WNV strain infections do not induce stress granules (SGs), while W956IC (a lineage 2/1 chimeric WNV infectious clone) virus infections produce high levels of early viral RNA and efficiently induce SGs through protein kinase R (PKR) activation. Additional WNV chimeric viruses made by replacing one or more W956IC genes with the lineage 1 Eg101 equivalent in the W956IC backbone were analyzed. The Eg-NS4b+5, Eg-NS1+3+4a, and Eg-NS1+4b+5 chimeras produced low levels of viral RNA at early times of infection and inefficiently induced SGs, suggesting the possibility that interactions between viral nonstructural proteins and/or between viral nonstructural proteins and cell proteins are involved in suppressing early viral RNA synthesis and membrane remodeling during natural WNV strain infections. Detection of exposed viral double-stranded RNA (dsRNA) in W956IC-infected cells suggested that the enhanced early viral RNA synthesis surpassed the available virus-induced membrane protection and allowed viral dsRNA to activate PKR.
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Langevin SA, Bowen RA, Ramey WN, Sanders TA, Maharaj PD, Fang Y, Cornelius J, Barker CM, Reisen WK, Beasley DWC, Barrett ADT, Kinney RM, Huang CYH, Brault AC. Envelope and pre-membrane protein structural amino acid mutations mediate diminished avian growth and virulence of a Mexican West Nile virus isolate. J Gen Virol 2011; 92:2810-2820. [PMID: 21865445 DOI: 10.1099/vir.0.035535-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hallmark attribute of North American West Nile virus (WNV) strains has been high pathogenicity in certain bird species. Surprisingly, this avian virulent WNV phenotype has not been observed during its geographical expansion into the Caribbean, Central America and South America. One WNV variant (TM171-03-pp1) isolated in Mexico has demonstrated an attenuated phenotype in two widely distributed North American bird species, American crows (AMCRs) and house sparrows (HOSPs). In order to identify genetic determinants associated with attenuated avian replication of the TM171-03-pp1 variant, chimeric viruses between the NY99 and Mexican strains were generated, and their replicative capacity was assessed in cell culture and in AMCR, HOSP and house finch avian hosts. The results demonstrated that mutations in both the pre-membrane (prM-I141T) and envelope (E-S156P) genes mediated the attenuation phenotype of the WNV TM171-03-pp1 variant in a chicken macrophage cell line and in all three avian species assayed. Inclusion of the prM-I141T and E-S156P TM171-03-pp1 mutations in the NY99 backbone was necessary to achieve the avian attenuation level of the Mexican virus. Furthermore, reciprocal incorporation of both prM-T141I and E-P156S substitutions into the Mexican virus genome was necessary to generate a virus that exhibited avian virulence equivalent to the NY99 virus. These structural changes may indicate the presence of new evolutionary pressures exerted on WNV populations circulating in Latin America or may signify a genetic bottleneck that has constrained their epiornitic potential in alternative geographical locations.
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Affiliation(s)
- Stanley A Langevin
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Wanichaya N Ramey
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Todd A Sanders
- Colorado Division of Wildlife, Fort Collins, CO 80526, USA
| | - Payal D Maharaj
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Ying Fang
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Jennine Cornelius
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Christopher M Barker
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - William K Reisen
- Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - David W C Beasley
- Departments of Pathology and Microbiology and Immunology, Center for Emerging Infectious Diseases and Biodefense, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alan D T Barrett
- Departments of Pathology and Microbiology and Immunology, Center for Emerging Infectious Diseases and Biodefense, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Richard M Kinney
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Claire Y-H Huang
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA.,Center for Vectorborne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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11
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Gijavanekar C, Añez-Lingerfelt M, Feng C, Putonti C, Fox GE, Sabo A, Fofanov Y, Willson RC. PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'. FEBS J 2011; 278:1676-87. [PMID: 21410643 DOI: 10.1111/j.1742-4658.2011.08091.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PCR detection of viral pathogens is extremely useful, but suffers from the challenge of detecting the many variant strains of a given virus that arise over time. Here, we report the computational derivation and initial experimental testing of a combination of 10 PCR primers to be used in a single high-sensitivity mixed PCR reaction for the detection of dengue virus. Primer sequences were computed such that their probability of mispriming with human DNA is extremely low. A 'cocktail' of 10 primers was shown experimentally to be able to detect cDNA clones representing the four serotypes and dengue virus RNA spiked into total human whole blood RNA. Computationally, the primers are predicted to detect 95% of the 1688 dengue strains analyzed (with perfect primer match). Allowing up to one mismatch and one insertion per primer, the primer set detects 99% of strains. Primer sets from three previous studies have been compared with the present set of primers and their relative sensitivity for dengue virus is discussed. These results provide the formulation and demonstration of a mixed primer PCR reagent that may enable the detection of nearly any dengue strain irrespective of serotype, in a single PCR reaction, and illustrate an approach to the broad problem of detecting highly mutable RNA viruses.
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Affiliation(s)
- Charul Gijavanekar
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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Danecek P, Schein CH. Flavitrack analysis of the structure and function of West Nile non-structural proteins. ACTA ACUST UNITED AC 2010; 6:134-46. [PMID: 20223736 DOI: 10.1504/ijbra.2010.032117] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Flavitrack database groups Flaviviruses (FV), evolutionarily related organisms with high subtype variability, according to their phenotypes. Here, PCPMer tools were used to calculate consensus sequences based on conservation of Physicochemical Properties (PCP) for 919 sequences of NS2a, a non-structural protein involved in preventing host interferon response to infection. Conserved PCP-motifs were detected, primarily in the N-terminal half of NS2a. One model structure, based on a nuclear receptor, groups residues essential for West Nile (WN) infectivity (I59, V61, and M103) in a pocket on the protein surface. These methods will aid in the design of vaccines and specific therapies against FV.
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Affiliation(s)
- Petr Danecek
- Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX 77555-0857, USA.
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Danecek P, Lu W, Schein CH. PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype. J Mol Biol 2009; 396:550-63. [PMID: 19969003 DOI: 10.1016/j.jmb.2009.11.070] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 11/18/2009] [Accepted: 11/30/2009] [Indexed: 01/11/2023]
Abstract
BACKGROUND Computational methods are needed to design multivalent vaccines against flaviviruses (FVs) such as the West Nile virus or the dengue virus (DENV). OBJECTIVE We aimed to use physicochemical property (PCP) consensus sequences of FV strains to delineate conserved motifs, areas of maximum variability, and specific loci that correlate with arthropod vector, serotype, and disease severity. METHODS PCP consensus sequences for 27 species were prepared from 928 annotated sequences catalogued in Flavitrack. Alignments of these correlated well with the known structures of the NS3 protease domain and envelope (E) proteins. The PCPMer suite was used to identify motifs common to all FVs. Areas of PCP variability that correlated with phenotype were plotted on the structures. RESULTS Despite considerable diversity at the amino acid level, PCPs for both proteins were well conserved throughout the FVs. A series of insertions in E separated tick- from mosquito-borne viruses and all arthropod-borne viruses from isolates with no known vector or directly from insects. Comparison of a PCP consensus sequence of E derived from 600 DENV strains (DENV600) with individual ones for DENV1-DENV4 showed that most major serotype-specific variation occurs near these insertions. The DENV600 differed from one prepared from eight hemorrhagic or fatal strains from four DENV serotypes at only three positions, two of which overlap known escape mutant sites. CONCLUSIONS Comparing consensus sequences showed that substantial changes occur in only a few areas of the E protein. PCP consensus sequences can contribute to the design of multivalent vaccines.
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Affiliation(s)
- Petr Danecek
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0857, USA
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Valdivia-Granda W, Larson F. ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2009; 2009:bap014. [PMID: 20157487 PMCID: PMC2790308 DOI: 10.1093/database/bap014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 09/06/2009] [Accepted: 09/07/2009] [Indexed: 12/12/2022]
Abstract
Viruses, viroids and prions are the smallest infectious biological entities that depend on their host for replication. The number of pathogenic viruses is considerably large and their impact in human global health is well documented. Currently, the International Committee on the Taxonomy of Viruses (ICTV) has classified approximately 4379 virus species while the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) database has mapped 617 705 proteins to eight large taxonomic groups. Despite these efforts, an automated approach for mapping the ICTV master list and its officially accepted virus naming to the NCBI-VGR's taxonomical classification is not available. Due to metagenomic sequencing, it is likely that the discovery and naming of new viral species will increase by at least ten fold. Unfortunately, existing viral databases are not adequately prepared to scale, maintain and annotate automatically ultra-high throughput sequences and place this information into specific taxonomic categories. ORION-VIRCAT is a scalable and interoperable object-relational database designed to serve as a resource for the integration and verification of taxonomical classifications generated by the ICTV and NCBI-VGR. The current release (v1.0) of ORION-VIRCAT is implemented in PostgreSQL and it has been extended to ORACLE, MySQL and SyBase. ORION-VIRCAT automatically mapped and joined 617 705 entries from the NCBI-VGR to the viral naming of the ICTV. This detailed analysis revealed that 399 095 entries from the NCBI-VGR can be mapped to the ICTV classification and that one Order, 10 families, 35 genera and 503 species listed in the ICTV disagree with the the NCBI-VGR classification schema. Nevertheless, we were eable to correct several discrepancies mapping 234 000 additional entries.Database URL:http://www.orionbiosciences.com/research/orion-vircat.html.
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de Mora D, Andrea LD, Alvarez M, Regato M, Fajardo A, Recarey R, Colina R, Khan B, Cristina J. Evidence of diversification of dengue virus type 3 genotype III in the South American region. Arch Virol 2009; 154:699-707. [PMID: 19322636 DOI: 10.1007/s00705-009-0343-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 02/23/2009] [Indexed: 11/24/2022]
Abstract
In order to gain insight into the genetic variability of dengue virus type 3 (DENV-3) genotype III isolated in the Latin American region, phylogenetic analysis were carried out using envelope (E) gene sequences from 57 DENV-3 genotype III strains isolated in 11 Latin American countries. At least six different genotype III clades were observed. Amino acids substitutions were found in domain III E protein neutralization epitopes and in surface-exposed domain II and III E protein amino acid sequences.
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Affiliation(s)
- Domenica de Mora
- Instituto Nacional de Higiene y Medicina Tropical "Leopoldo Inquieta Perez", Julian Coronel y Esmeraldas, Guayaquil, Ecuador
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Fajardo A, Recarey R, de Mora D, D' Andrea L, Alvarez M, Regato M, Colina R, Khan B, Cristina J. Modeling gene sequence changes over time in type 3 dengue viruses from Ecuador. Virus Res 2009; 141:105-9. [PMID: 19185597 DOI: 10.1016/j.virusres.2009.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 12/29/2008] [Accepted: 01/08/2009] [Indexed: 02/05/2023]
Abstract
Dengue virus (DENV) is a member of the genus Flavivirus of the family Flaviviridae. DENV-3 re-emerged in Central America in 1994, and continues to expand into the South American region. Little is known about the evolutionary rates, viral spread and population dynamics of this genotype in the Latin American region. In order to gain insight into these matters, we used a Bayesian Markov chain Monte Carlo (MCMC) approach, to analyze envelope (E) gene sequences of the DENV-3 genotype III of strains included in a monophyletic cluster composed by Ecuadorian as well as strains from Cuba, Puerto Rico and Peru. The results of these studies revealed that the expansion population growth model was the best fit to the data. The most common recent ancestor (MRCA) was placed around 1989, in agreement with the first reports of the emergence of this new DENV-3 type. A mean rate 1.033 x 10(-3) nucleotide substitution per site per year was obtained. This rate is comparatively higher than the ones obtained for DENV-2 and DENV-4 in the same region. Faster population growth and greater population dispersal may have contributed to the vigorous initial transmission dynamics of this genotype in the Latin American region.
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Affiliation(s)
- Alvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo, Uruguay
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Wilder-Smith A, Gubler DJ. Geographic expansion of dengue: the impact of international travel. Med Clin North Am 2008; 92:1377-90, x. [PMID: 19061757 DOI: 10.1016/j.mcna.2008.07.002] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Dengue has emerged as an international public health problem. Reasons for the resurgence of dengue in the tropics and subtropics are complex and include unprecedented urbanization with substandard living conditions, lack of vector control, virus evolution, and international travel. Of all these factors, urbanization has probably had the most impact on the amplification of dengue within a given country, and travel has had the most impact for the spread of dengue from country to country and continent to continent. Epidemics of dengue, their seasonality, and oscillations over time are reflected by the epidemiology of dengue in travelers. Sentinel surveillance of travelers could augment existing national public health surveillance systems.
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Affiliation(s)
- Annelies Wilder-Smith
- Department of Medicine, Travelers' Screening and Vaccination Clinic, National University Hospital of Singapore, National University of Singapore, 5, Lower Kent Ridge, Singapore 119074.
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