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Bhattacharya T, Alleman EM, Noyola AC, Emerman M, Malik HS. A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609082. [PMID: 39229031 PMCID: PMC11370586 DOI: 10.1101/2024.08.21.609082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Alphaviruses are enveloped, single-stranded, positive-sense RNA viruses that often require transmission between arthropod and vertebrate hosts for their sustained propagation. Most alphaviruses encode an opal (UGA) termination codon in nonstructural protein 3 (nsP3) upstream of the viral polymerase, nsP4. The selective constraints underlying the conservation of the opal codon are poorly understood. Using primate and mosquito cells, we explored the role and selective pressure on the nsP3 opal codon through extensive mutational analysis in the prototype alphavirus, Sindbis virus (SINV). We found that the opal codon is highly favored over all other codons in primate cells under native 37ºC growth conditions. However, this preference is diminished in mosquito and primate cells grown at a lower temperature. Thus, the primary determinant driving the selection of the opal stop codon is not host genetics but the passaging temperature. We show that the opal codon is preferred over amber and ochre termination codons because it results in the highest translational readthrough and polymerase production. However, substituting the opal codon with sense codons leads to excessive full-length polyprotein (P1234) production, which disrupts optimal nsP polyprotein processing, delays the switch from minus-strand to positive-strand RNA production, and significantly reduces SINV fitness at 37°C; this fitness defect is relieved at lower temperatures. A naturally occurring suppressor mutation unexpectedly compensates for a delayed transition from minus to genomic RNA production by also delaying the subsequent transition between genomic and sub-genomic RNA production. Our study reveals that the opal stop codon is the best solution for alphavirus replication at 37ºC, producing enough nsP4 protein to maximize replication without disrupting nsP processing and RNA replication transitions needed for optimal fitness. Our study uncovers the intricate strategy dual-host alphaviruses use at a single codon to optimize fitness.
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2
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Bardossy ES, Volpe S, Suzuki Y, Merwaiss F, Faraj S, Montes M, Saleh MC, Alvarez DE, Filomatori CV. Molecular basis of RNA recombination in the 3'UTR of chikungunya virus genome. Nucleic Acids Res 2024:gkae650. [PMID: 39051569 DOI: 10.1093/nar/gkae650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
Chikungunya virus (CHIKV) is a rapidly spreading re-emergent virus transmitted from mosquitoes to humans. The emergence of epidemic variants has been associated with changes in the viral genome, such as the duplication of repeated sequences in the 3' untranslated region (UTR). Indeed, blocks of repeated sequences seemingly favor RNA recombination, providing the virus with a unique ability to continuously change the 3'UTR architecture during host switching. In this work, we provide experimental data on the molecular mechanism of RNA recombination and describe specific sequence and structural elements in the viral 3'UTR that favor template switching of the viral RNA-dependent RNA polymerase on the 3'UTR. Furthermore, we found that a 3'UTR deletion mutant that exhibits markedly delayed replication in mosquito cells and impaired transmission in vivo, recombines in reference laboratory strains of mosquitoes. Altogether, our data provide novel experimental evidence indicating that RNA recombination can act as a nucleic acid repair mechanism to add repeated sequences that are associated to high viral fitness in mosquito during chikungunya virus replication.
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Affiliation(s)
- Eugenia S Bardossy
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Sebastiano Volpe
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Yasutsugu Suzuki
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Fernando Merwaiss
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), 46022 Valencia, Spain
| | - Santiago Faraj
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Mónica Montes
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Diego E Alvarez
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
| | - Claudia V Filomatori
- Escuela de Bio y Nanotecnología, Universidad de San Martín - CONICET, Buenos Aires, Argentina
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
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3
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Morgenlander WR, Chia WN, Parra B, Monaco DR, Ragan I, Pardo CA, Bowen R, Zhong D, Norris DE, Ruczinski I, Durbin A, Wang LF, Larman HB, Robinson ML. Precision arbovirus serology with a pan-arbovirus peptidome. Nat Commun 2024; 15:5833. [PMID: 38992033 PMCID: PMC11239951 DOI: 10.1038/s41467-024-49461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
Arthropod-borne viruses represent a crucial public health threat. Current arboviral serology assays are either labor intensive or incapable of distinguishing closely related viruses, and many zoonotic arboviruses that may transition to humans lack any serologic assays. In this study, we present a programmable phage display platform, ArboScan, that evaluates antibody binding to overlapping peptides that represent the proteomes of 691 human and zoonotic arboviruses. We confirm that ArboScan provides detailed antibody binding information from animal sera, human sera, and an arthropod blood meal. ArboScan identifies distinguishing features of antibody responses based on exposure history in a Colombian cohort of Zika patients. Finally, ArboScan details epitope level information that rapidly identifies candidate epitopes with potential protective significance. ArboScan thus represents a resource for characterizing human and animal arbovirus antibody responses at cohort scale.
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Affiliation(s)
- William R Morgenlander
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wan Ni Chia
- Program in Emerging Infectious Diseases Duke-NUS Medical School, Singapore, Singapore
| | - Beatriz Parra
- Department of Microbiology, Universidad del Valle, Cali, Colombia
| | - Daniel R Monaco
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Izabela Ragan
- Department of Biomedical Sciences, Colorado State University College of Veterinary and Biomedical Sciences, Fort Collins, CO, USA
| | - Carlos A Pardo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard Bowen
- Department of Biomedical Sciences, Colorado State University College of Veterinary and Biomedical Sciences, Fort Collins, CO, USA
| | - Diana Zhong
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Douglas E Norris
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Durbin
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases Duke-NUS Medical School, Singapore, Singapore
| | - H Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Matthew L Robinson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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4
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Ware BC, Parks MG, da Silva MOL, Morrison TE. Chikungunya virus infection disrupts MHC-I antigen presentation via nonstructural protein 2. PLoS Pathog 2024; 20:e1011794. [PMID: 38483968 DOI: 10.1371/journal.ppat.1011794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/26/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Infection by chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes severe polyarthralgia and polymyalgia, which can last in some people for months to years. Chronic CHIKV disease signs and symptoms are associated with the persistence of viral nucleic acid and antigen in tissues. Like humans and nonhuman primates, CHIKV infection in mice results in the development of robust adaptive antiviral immune responses. Despite this, joint tissue fibroblasts survive CHIKV infection and can support persistent viral replication, suggesting that they escape immune surveillance. Here, using a recombinant CHIKV strain encoding the fluorescent protein VENUS with an embedded CD8+ T cell epitope, SIINFEKL, we observed a marked loss of both MHC class I (MHC-I) surface expression and antigen presentation by CHIKV-infected joint tissue fibroblasts. Both in vivo and ex vivo infected joint tissue fibroblasts displayed reduced cell surface levels of H2-Kb and H2-Db MHC-I proteins while maintaining similar levels of other cell surface proteins. Mutations within the methyl transferase-like domain of the CHIKV nonstructural protein 2 (nsP2) increased MHC-I cell surface expression and antigen presentation efficiency by CHIKV-infected cells. Moreover, expression of WT nsP2 alone, but not nsP2 with mutations in the methyltransferase-like domain, resulted in decreased MHC-I antigen presentation efficiency. MHC-I surface expression and antigen presentation was rescued by replacing VENUS-SIINFEKL with SIINFEKL tethered to β2-microglobulin in the CHIKV genome, which bypasses the requirement for peptide processing and TAP-mediated peptide transport into the endoplasmic reticulum. Collectively, this work suggests that CHIKV escapes the surveillance of antiviral CD8+ T cells, in part, by nsP2-mediated disruption of MHC-I antigen presentation.
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Affiliation(s)
- Brian C Ware
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - M Guston Parks
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Mariana O L da Silva
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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Chykunova Y, Plewka J, Wilk P, Torzyk K, Sienczyk M, Dubin G, Pyrc K. Autoinhibition of suicidal capsid protease from O'nyong'nyong virus. Int J Biol Macromol 2024; 262:130136. [PMID: 38354926 DOI: 10.1016/j.ijbiomac.2024.130136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Alphaviruses pose a significant threat to public health. Capsid protein encoded in the alphaviral genomes constitutes an interesting therapy target, as it also serves as a protease (CP). Remarkably, it undergoes autoproteolysis, leading to the generation of the C-terminal tryptophan that localizes to the active pocket, deactivating the enzyme. Lack of activity hampers the viral replication cycle, as the virus is not capable of producing the infectious progeny. We investigated the structure and function of the CP encoded in the genome of O'nyong'nyong virus (ONNV), which has instigated outbreaks in Africa. Our research provides a high-resolution crystal structure of the ONNV CP in its active state and evaluates the enzyme's activity. Furthermore, we demonstrated a dose-dependent reduction in ONNV CP proteolytic activity when exposed to indole, suggesting that tryptophan analogs may be a promising basis for developing small molecule inhibitors. It's noteworthy that the capsid protease plays an essential role in virus assembly, binding viral glycoproteins through its glycoprotein-binding hydrophobic pocket. We showed that non-aromatic cyclic compounds like dioxane disrupt this vital interaction. Our findings provide deeper insights into ONNV's biology, and we believe they will prove instrumental in guiding the development of antiviral strategies against arthritogenic alphaviruses.
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Affiliation(s)
- Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Piotr Wilk
- Structural Biology Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Karolina Torzyk
- Wroclaw University of Science and Technology, Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Sienczyk
- Wroclaw University of Science and Technology, Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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6
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Kuno G. Mechanisms of Yellow Fever Transmission: Gleaning the Overlooked Records of Importance and Identifying Problems, Puzzles, Serious Issues, Surprises and Research Questions. Viruses 2024; 16:84. [PMID: 38257784 PMCID: PMC10820296 DOI: 10.3390/v16010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/12/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
In viral disease research, few diseases can compete with yellow fever for the volume of literature, historical significance, richness of the topics and the amount of strong interest among both scientists and laypersons. While the major foci of viral disease research shifted to other more pressing new diseases in recent decades, many critically important basic tasks still remain unfinished for yellow fever. Some of the examples include the mechanisms of transmission, the process leading to outbreak occurrence, environmental factors, dispersal, and viral persistence in nature. In this review, these subjects are analyzed in depth, based on information not only in old but in modern literatures, to fill in blanks and to update the current understanding on these topics. As a result, many valuable facts, ideas, and other types of information that complement the present knowledge were discovered. Very serious questions about the validity of the arbovirus concept and some research practices were also identified. The characteristics of YFV and its pattern of transmission that make this virus unique among viruses transmitted by Ae. aegypti were also explored. Another emphasis was identification of research questions. The discovery of a few historical surprises was an unexpected benefit.
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Affiliation(s)
- Goro Kuno
- Formerly at the Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
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7
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Ware BC, Parks MG, Morrison TE. Chikungunya virus infection disrupts MHC-I antigen presentation via nonstructural protein 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565436. [PMID: 37961400 PMCID: PMC10635105 DOI: 10.1101/2023.11.03.565436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Infection by chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes severe polyarthralgia and polymyalgia, which can last in some people for months to years. Chronic CHIKV disease signs and symptoms are associated with the persistence of viral nucleic acid and antigen in tissues. Like humans and nonhuman primates, CHIKV infection in mice results in the development of robust adaptive antiviral immune responses. Despite this, joint tissue fibroblasts survive CHIKV infection and can support persistent viral replication, suggesting that they escape immune surveillance. Here, using a recombinant CHIKV strain encoding a chimeric protein of VENUS fused to a CD8+ T cell epitope, SIINFEKL, we observed a marked loss of both MHC class I (MHC-I) surface expression and antigen presentation by CHIKV-infected joint tissue fibroblasts. Both in vivo and ex vivo infected joint tissue fibroblasts displayed reduced cell surface levels of H2-Kb and H2-Db MHC proteins while maintaining similar levels of other cell surface proteins. Mutations within the methyl transferase-like domain of the CHIKV nonstructural protein 2 (nsP2) increased MHC-I cell surface expression and antigen presentation efficiency by CHIKV-infected cells. Moreover, expression of WT nsP2 alone, but not nsP2 with mutations in the methyltransferase-like domain, resulted in decreased MHC-I antigen presentation efficiency. MHC-I surface expression and antigen presentation could be rescued by replacing VENUS-SIINFEKL with SIINFEKL tethered to β2-microglobulin in the CHIKV genome, which bypasses the need for peptide processing and TAP-mediated peptide transport into the endoplasmic reticulum. Collectively, this work suggests that CHIKV escapes the surveillance of antiviral CD8+ T cells, in part, by nsP2-mediated disruption of MHC-I antigen presentation.
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Affiliation(s)
- Brian C. Ware
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - M. Guston Parks
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Thomas E. Morrison
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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8
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Huang Y, Wang S, Liu H, Atoni E, Wang F, Chen W, Li Z, Rodriguez S, Yuan Z, Ming Z, Xia H. A global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus. Sci Data 2023; 10:305. [PMID: 37208388 DOI: 10.1038/s41597-023-02226-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
Arthropod-borne virus (arbovirus) and arthropod-specific virus (ASV) are viruses circulating amongst hematophagous arthropods that are broadly transmitted in ecological systems. Arbovirus may replicate in both vertebrates and invertebrates and some are known to be pathogenic to animals or humans. ASV only replicate in invertebrate arthropods yet they are basal to many types of arboviruses. We built a comprehensive dataset of arbovirus and ASV by curating globally available data from the Arbovirus Catalog, the arbovirus list in Section VIII-F of the Biosafety in Microbiological and Biomedical Laboratories 6th edition, Virus Metadata Resource of International Committee on Taxonomy of Viruses, and GenBank. Revealing the diversity, distribution and biosafety recommendation of arbovirus and ASV at a global scale is essential to the understanding of potential interactions, evolution, and risks associated with these viruses. Moreover, the genomic sequences associated with the dataset will enable the investigation of genetic patterns distinguishing the two groups, as well as aid in predicting the vector/host relationships of the newly discovered viruses.
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Affiliation(s)
- Ying Huang
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunlong Wang
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China
| | - Evans Atoni
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Wang
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wei Chen
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaolin Li
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sergio Rodriguez
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 77551, USA
| | - Zhiming Yuan
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoyan Ming
- School of Computer and Computing Science, Hangzhou City University, Hangzhou, 310015, China.
| | - Han Xia
- Key Laboratory of Highly pathogenic Viruses and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hubei Jiangxia Laboratory, Wuhan, 430207, China.
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10
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Terradas G, Novelo M, Metz H, Brustolin M, Rasgon JL. Anopheles albimanus is a Potential Alphavirus Vector in the Americas. Am J Trop Med Hyg 2023; 108:412-423. [PMID: 36535260 PMCID: PMC9896319 DOI: 10.4269/ajtmh.22-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/04/2022] [Indexed: 12/23/2022] Open
Abstract
Despite its ecological flexibility and geographical co-occurrence with human pathogens, little is known about the ability of Anopheles albimanus to transmit arboviruses. To address this gap, we challenged An. albimanus females with four alphaviruses and one flavivirus and monitored the progression of infections. We found this species is an efficient vector of the alphaviruses Mayaro virus, O'nyong-nyong virus, and Sindbis virus, although the latter two do not currently exist in its habitat range. An. albimanus was able to become infected with Chikungunya virus, but virus dissemination was rare (indicating the presence of a midgut escape barrier), and no mosquito transmitted. Mayaro virus rapidly established disseminated infections in An. albimanus females and was detected in the saliva of a substantial proportion of infected mosquitoes. Consistent with previous work in other anophelines, we find that An. albimanus is refractory to infection with flaviviruses, a phenotype that did not depend on midgut-specific barriers. Our work demonstrates that An. albimanus may be a vector of neglected emerging human pathogens and adds to recent evidence that anophelines are competent vectors for diverse arboviruses.
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Affiliation(s)
- Gerard Terradas
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania;,Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania;,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Mario Novelo
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania;,Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania;,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Hillery Metz
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania;,Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania;,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Marco Brustolin
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania;,Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania;,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Jason L. Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania;,Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania;,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania,Address correspondence to Jason Rasgon, Department of Entomology, The Pennsylvania State University, Millennium Science Complex, Rm. W127, University Park, PA 16802. E-mail:
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11
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Guarido MM, Fourie I, Meno K, Mendes A, Riddin MA, MacIntyre C, Manyana S, Johnson T, Schrama M, Gorsich EE, Brooke BD, Almeida APG, Venter M. Alphaviruses Detected in Mosquitoes in the North-Eastern Regions of South Africa, 2014 to 2018. Viruses 2023; 15:414. [PMID: 36851627 PMCID: PMC9965626 DOI: 10.3390/v15020414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The prevalence and distribution of African alphaviruses such as chikungunya have increased in recent years. Therefore, a better understanding of the local distribution of alphaviruses in vectors across the African continent is important. Here, entomological surveillance was performed from 2014 to 2018 at selected sites in north-eastern parts of South Africa where alphaviruses have been identified during outbreaks in humans and animals in the past. Mosquitoes were collected using a net, CDC-light, and BG-traps. An alphavirus genus-specific nested RT-PCR was used for screening, and positive pools were confirmed by sequencing and phylogenetic analysis. We collected 64,603 mosquitoes from 11 genera, of which 39,035 females were tested. Overall, 1462 mosquito pools were tested, of which 21 were positive for alphaviruses. Sindbis (61.9%, N = 13) and Middelburg (28.6%, N = 6) viruses were the most prevalent. Ndumu virus was detected in two pools (9.5%, N = 2). No chikungunya positive pools were identified. Arboviral activity was concentrated in peri-urban, rural, and conservation areas. A range of Culicidae species, including Culex univittatus, Cx. pipiens s.l., Aedes durbanensis, and the Ae. dentatus group, were identified as potential vectors. These findings confirm the active circulation and distribution of alphaviruses in regions where human or animal infections were identified in South Africa.
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Affiliation(s)
- Milehna M. Guarido
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0031, South Africa
| | - Isabel Fourie
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
| | - Kgothatso Meno
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
| | - Adriano Mendes
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
| | - Megan A. Riddin
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
- UP Institute for Sustainable Malaria Control (UP ISMC), Faculty of Health Sciences, University of Pretoria, Pretoria 0007, South Africa
| | - Caitlin MacIntyre
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
| | - Sontaga Manyana
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Todd Johnson
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
- Department of Biological Sciences, Copperbelt University, Kitwe 21692, Zambia
| | - Maarten Schrama
- Institute of Environmental Sciences, Leiden University, 2333 CC Leiden, The Netherlands
| | - Erin E. Gorsich
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry CV4 7AL, UK
| | - Basil D. Brooke
- Centre for Emerging Zoonotic & Parasitic Diseases, National Institute for Communicable Diseases/NHLS, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Antonio Paulo G. Almeida
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
- Institute of Hygiene and Tropical Medicine (IHMTNOVA), Medical Parasitology Unit/GHTM, NOVA University of Lisbon, 1349-008 Lisbon, Portugal
| | - Marietjie Venter
- Zoonotic Arbo- and Respiratory Virus Program, Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria, Pretoria 0031, South Africa
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12
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Targeting the alphavirus virus replication process for antiviral development. Antiviral Res 2023; 210:105494. [PMID: 36574906 DOI: 10.1016/j.antiviral.2022.105494] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022]
Abstract
Many alphaviruses, including chikungunya virus (CHIKV) are known human pathogens that lack specific and effective antivirals or vaccines available. The upstream portion of the positive-sense single-stranded RNA genome of alphaviruses encodes four nonstructural proteins: nsP1 to nsP4. They are expressed and autoprocessed to nonstructural proteins which assemble into a replication complex (RC) playing multiple essential roles on viral RNA replication and communication with the host components. The assembly of alphavirus RC and its RNA genome initiates the membrane-derived ultrastructure known as spherule which facilitates viral RNA synthesis protected from host immune responses. Recent advances in the molecular understanding of the high-resolution CHIKV RC heteromeric ultrastructure have provided new insights into the viral replication process. Hence, alphavirus RC presents as an ideal multi-enzyme target for the development of structure-based antiviral drugs. Moreover, the alphavirus RC has therapeutic potential in the form of self-amplifying RNA technology against both infectious and non-infectious diseases.
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13
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Reyna RA, Weaver SC. Sequelae and Animal Modeling of Encephalitic Alphavirus Infections. Viruses 2023; 15:v15020382. [PMID: 36851596 PMCID: PMC9959775 DOI: 10.3390/v15020382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Eastern (EEEV), Venezuelan (VEEV), and western equine encephalitis viruses (WEEV) are members of the genus Alphavirus, family Togaviridae. Typically spread by mosquitoes, EEEV, VEEV, and WEEV induce febrile illness that may develop into more severe encephalitic disease, resulting in myriad severe neurologic sequelae for which there are no vaccines or therapeutics. Here, we summarize the clinical neurologic findings and sequelae induced by these three encephalitic viruses and describe the various animal models available to study them. We emphasize the crucial need for the development of advanced animal modeling combined with the use of telemetry, behavioral testing, and neuroimaging to facilitate a detailed mechanistic understanding of these encephalitic signs and sequelae. Through the use of these systems, much-needed therapeutics and vaccines can be developed.
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Affiliation(s)
- Rachel A. Reyna
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Scott C. Weaver
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Correspondence:
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14
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Pujhari S, Brustolin M, Heu CC, Smithwick R, Larrosa M, Hafenstein S, Rasgon JL. Characterization of Mayaro virus (strain BeAn343102) biology in vertebrate and invertebrate cellular backgrounds. J Gen Virol 2022; 103:001794. [PMID: 36215156 PMCID: PMC10019088 DOI: 10.1099/jgv.0.001794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Mayaro virus (MAYV) is an emerging New World alphavirus (genus Alphavirus, family Togaviridae) that causes acute multiphasic febrile illness, skin rash, polyarthritis and occasional severe clinical phenotypes. The virus lifecycle alternates between invertebrate and vertebrate hosts. Here we characterize the replication features, cell entry, lifecycle and virus-related cell pathology of MAYV using vertebrate and invertebrate in vitro models. Electron-dense clathrin-coated pits in infected cells and reduced viral production in the presence of dynasore, ammonium chloride and bafilomycin indicate that viral entry occurs through pH-dependent endocytosis. Increase in FITC-dextran uptake (an indicator of macropinocytosis) in MAYV-infected cells, and dose-dependent infection inhibition by 5-(N-ethyl-N-isopropyl) amiloride (a macropinocytosis inhibitor), indicated that macropinocytosis is an additional entry mechanism of MAYV in vertebrate cells. Acutely infected vertebrate and invertebrate cells formed cytoplasmic or membrane-associated extracytoplasmic replication complexes. Mosquito cells showed modified hybrid cytoplasmic vesicles that supported virus replication, nucleocapsid production and maturation. Mature virus particles were released from cells by both exocytosis and budding from the cell membrane. MAYV replication was cytopathic and associated with induction of apoptosis by the intrinsic pathway, and later by the extrinsic pathway in infected vertebrate cells. Given that MAYV is expanding its geographical existence as a potential public health problem, this study lays the foundation for biological understanding that will be valuable for therapeutic and preventive interventions.
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Affiliation(s)
- Sujit Pujhari
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmacology Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Marco Brustolin
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Chan C. Heu
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- USDA-ARS, Maricopa, AZ, USA
| | - Ronald Smithwick
- Department of Pharmacology Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Mireia Larrosa
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susan Hafenstein
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jason L. Rasgon
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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15
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TMEΜ45B Interacts with Sindbis Virus Nsp1 and Nsp4 and Inhibits Viral Replication. J Virol 2022; 96:e0091922. [PMID: 35938871 PMCID: PMC9472651 DOI: 10.1128/jvi.00919-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alphavirus infection induces the expression of type I interferons, which inhibit the viral replication by upregulating the expression of interferon-stimulated genes (ISGs). Identification and mechanistic studies of the antiviral ISGs help to better understand how the host controls viral infection and help to better understand the viral replication process. Here, we report that the ISG product TMEM45B inhibits the replication of Sindbis virus (SINV). TMEM45B is a transmembrane protein that was detected mainly in the trans-Golgi network, endosomes, and lysosomes but not obviously at the plasma membrane or endoplasmic reticulum. TMEM45B interacted with the viral nonstructural proteins Nsp1 and Nsp4 and inhibited the translation and promoted the degradation of SINV RNA. TMEM45B overexpression rendered the intracellular membrane-associated viral RNA sensitive to RNase treatment. In line with these results, the formation of cytopathic vacuoles (CPVs) was dramatically diminished in TMEM45B-expressing cells. TMEM45B also interacted with Nsp1 and Nsp4 of chikungunya virus (CHIKV), suggesting that it may also inhibit the replication of other alphaviruses. These findings identified TMEM45B as an antiviral factor against alphaviruses and help to better understand the process of the viral genome replication. IMPORTANCE Alphaviruses are positive-stranded RNA viruses with more than 30 members. Infection with Old World alphaviruses, which comprise some important human pathogens such as chikungunya virus and Ross River virus, rarely results in fatal diseases but can lead to high morbidity in humans. Infection with New World alphaviruses usually causes serious encephalitis but low morbidity in humans. Alphavirus infection induces the expression of type I interferons, which subsequently upregulate hundreds of interferon-stimulated genes. Identification and characterization of host antiviral factors help to better understand how the viruses can establish effective infection. Here, we identified TMEM45B as a novel interferon-stimulated antiviral factor against Sindbis virus, a prototype alphavirus. TMEM45B interacted with viral proteins Nsp1 and Nsp4, interfered with the interaction between Nsp1 and Nsp4, and inhibited the viral replication. These findings provide insights into the detailed process of the viral replication and help to better understand the virus-host interactions.
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16
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Epidemiological and Genomic Characterisation of Middelburg and Sindbis Alphaviruses Identified in Horses with Febrile and Neurological Infections, South Africa (2014-2018). Viruses 2022; 14:v14092013. [PMID: 36146819 PMCID: PMC9501102 DOI: 10.3390/v14092013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/28/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Although Old World alphaviruses, Middelburg- (MIDV) and Sindbis virus (SINV), have previously been detected in horses and wildlife with neurologic disease in South Africa, the pathogenesis and clinical presentation of MIDV and SINV infections in animals are not well documented. Clinical samples from horses across South Africa with acute or fatal neurologic and febrile infections submitted between 2014-2018 were investigated. In total, 69/1084 (6.36%) and 11/1084 (1.01%) horses tested positive for MIDV and SINV, respectively, by real-time reverse transcription (RT) PCR. Main signs/outcomes for MIDV (n = 69): 73.91% neurological, 75.36% fever, 28.99% icterus and anorexia, respectively, 8.70% fatalities; SINV (n = 11): 54.54% neurological, 72.73% fever, 36.36% anorexia and 18.18% fatalities. MIDV cases peaked in the late summer/autumn across most South African provinces while SINV cases did not show a clear seasonality and were detected in fewer South African provinces. MIDV could still be detected in blood samples via RT-PCR for up to 71,417 and 21 days after onset of signs in 4 horses respectively, suggesting prolonged replication relative to SINV which could only be detected in the initial sample. Phylogenetic analyses based on partial sequences of the nsP4 (MIDV n = 59 and SINV n = 7) and E1 (MIDV n = 45) genes, as well as full genome sequences (MIDV n = 6), clustered the MIDV and SINV strains from the present study with previously detected strains. MIDV infection appears to be more prevalent in horses than SINV infection based on RT-PCR results, however, prevalence estimates might be different when also considering serological surveillance data.
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17
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Lasswitz L, Zapatero-Belinchón FJ, Moeller R, Hülskötter K, Laurent T, Carlson LA, Goffinet C, Simmons G, Baumgärtner W, Gerold G. The Tetraspanin CD81 Is a Host Factor for Chikungunya Virus Replication. mBio 2022; 13:e0073122. [PMID: 35612284 PMCID: PMC9239085 DOI: 10.1128/mbio.00731-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV) is an arthritogenic reemerging virus replicating in plasma membrane-derived compartments termed "spherules." Here, we identify the human transmembrane protein CD81 as host factor required for CHIKV replication. Ablation of CD81 results in decreased CHIKV permissiveness, while overexpression enhances infection. CD81 is dispensable for virus uptake but critically required for viral genome replication. Likewise, murine CD81 is crucial for CHIKV permissiveness and is expressed in target cells such as dermal fibroblasts, muscle and liver cells. Whereas related alphaviruses, including Ross River virus (RRV), Semliki Forest virus (SFV), Sindbis virus (SINV) and Venezuelan equine encephalitis virus (VEEV), also depend on CD81 for infection, RNA viruses from other families, such as coronaviruses, replicate independently of CD81. Strikingly, the replication-enhancing function of CD81 is linked to cholesterol binding. These results define a mechanism exploited by alphaviruses to hijack the membrane microdomain-modeling protein CD81 for virus replication through interaction with cholesterol. IMPORTANCE In this study, we discover the tetraspanin CD81 as a host factor for the globally emerging chikungunya virus and related alphaviruses. We show that CD81 promotes replication of viral genomes in human and mouse cells, while virus entry into cells is independent of CD81. This provides novel insights into how alphaviruses hijack host proteins to complete their life cycle. Alphaviruses replicate at distinct sites of the plasma membrane, which are enriched in cholesterol. We found that the cholesterol-binding ability of CD81 is important for its function as an alphavirus host factor. This discovery thus broadens our understanding of the alphavirus replication process and the use of host factors to reprogram cells into virus replication factories.
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Affiliation(s)
- Lisa Lasswitz
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hanover, Germany
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Francisco J. Zapatero-Belinchón
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hanover, Germany
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
| | - Rebecca Moeller
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hanover, Germany
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Kirsten Hülskötter
- Department of Pathology, University of Veterinary Medicine Hanover, Hanover, Germany
| | - Timothée Laurent
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Lars-Anders Carlson
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Christine Goffinet
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Graham Simmons
- Vitalant Research Institute, University of California, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hanover, Hanover, Germany
| | - Gisa Gerold
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hanover, Germany
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
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18
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Masika MM, Korhonen EM, Smura T, Uusitalo R, Ogola J, Mwaengo D, Jääskeläinen AJ, Alburkat H, Gwon YD, Evander M, Anzala O, Vapalahti O, Huhtamo E. Serological Evidence of Exposure to Onyong-Nyong and Chikungunya Viruses in Febrile Patients of Rural Taita-Taveta County and Urban Kibera Informal Settlement in Nairobi, Kenya. Viruses 2022; 14:v14061286. [PMID: 35746757 PMCID: PMC9230508 DOI: 10.3390/v14061286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Several alphaviruses, such as chikungunya (CHIKV) and Onyong-nyong (ONNV), are endemic in Kenya and often cause outbreaks in different parts of the country. We assessed the seroprevalence of alphaviruses in patients with acute febrile illness in two geographically distant areas in Kenya with no previous record of alphavirus outbreaks. Blood samples were collected from febrile patients in health facilities located in the rural Taita-Taveta County in 2016 and urban Kibera informal settlement in Nairobi in 2017 and tested for CHIKV IgG and IgM antibodies using an in-house immunofluorescence assay (IFA) and a commercial ELISA test, respectively. A subset of CHIKV IgG or IgM antibody-positive samples were further analyzed using plaque reduction neutralization tests (PRNT) for CHIKV, ONNV, and Sindbis virus. Out of 537 patients, 4 (0.7%) and 28 (5.2%) had alphavirus IgM and IgG antibodies, respectively, confirmed on PRNT. We show evidence of previous and current exposure to alphaviruses based on serological testing in areas with no recorded history of outbreaks.
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Affiliation(s)
- Moses Muia Masika
- KAVI Institute of Clinical Research, University of Nairobi, POB 19676, Nairobi 00202, Kenya; (J.O.); (O.A.)
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
- Correspondence: ; Tel.: +254-721770306
| | - Essi M. Korhonen
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- HUS Diagnostic Center, HUSLAB, Virology and Immunology, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland
| | - Joseph Ogola
- KAVI Institute of Clinical Research, University of Nairobi, POB 19676, Nairobi 00202, Kenya; (J.O.); (O.A.)
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
| | - Dufton Mwaengo
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
| | - Anne J. Jääskeläinen
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- HUS Diagnostic Center, HUSLAB, Virology and Immunology, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Hussein Alburkat
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
| | - Yong-Dae Gwon
- Department of Clinical Microbiology, Umeå University, 90185 SE Umeå, Sweden; (Y.-D.G.); (M.E.)
| | - Magnus Evander
- Department of Clinical Microbiology, Umeå University, 90185 SE Umeå, Sweden; (Y.-D.G.); (M.E.)
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, POB 19676, Nairobi 00202, Kenya; (J.O.); (O.A.)
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Virology and Immunology, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Eili Huhtamo
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
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19
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Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
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Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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20
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Williams JA, Long SY, Zeng X, Kuehl K, Babka AM, Davis NM, Liu J, Trefry JC, Daye S, Facemire PR, Iversen PL, Bavari S, Pitt ML, Nasar F. Eastern equine encephalitis virus rapidly infects and disseminates in the brain and spinal cord of cynomolgus macaques following aerosol challenge. PLoS Negl Trop Dis 2022; 16:e0010081. [PMID: 35533188 PMCID: PMC9084534 DOI: 10.1371/journal.pntd.0010081] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Eastern equine encephalitis virus (EEEV) is mosquito-borne virus that produces fatal encephalitis in humans. We recently conducted a first of its kind study to investigate EEEV clinical disease course following aerosol challenge in a cynomolgus macaque model utilizing the state-of-the-art telemetry to measure critical physiological parameters. Here, we report the results of a comprehensive pathology study of NHP tissues collected at euthanasia to gain insights into EEEV pathogenesis. Viral RNA and proteins as well as microscopic lesions were absent in the visceral organs. In contrast, viral RNA and proteins were readily detected throughout the brain including autonomic nervous system (ANS) control centers and spinal cord. However, despite presence of viral RNA and proteins, majority of the brain and spinal cord tissues exhibited minimal or no microscopic lesions. The virus tropism was restricted primarily to neurons, and virus particles (~61–68 nm) were present within axons of neurons and throughout the extracellular spaces. However, active virus replication was absent or minimal in majority of the brain and was limited to regions proximal to the olfactory tract. These data suggest that EEEV initially replicates in/near the olfactory bulb following aerosol challenge and is rapidly transported to distal regions of the brain by exploiting the neuronal axonal transport system to facilitate neuron-to-neuron spread. Once within the brain, the virus gains access to the ANS control centers likely leading to disruption and/or dysregulation of critical physiological parameters to produce severe disease. Moreover, the absence of microscopic lesions strongly suggests that the underlying mechanism of EEEV pathogenesis is due to neuronal dysfunction rather than neuronal death. This study is the first comprehensive investigation into EEEV pathology in a NHP model and will provide significant insights into the evaluation of countermeasure. EEEV is an arbovirus endemic in parts of North America and is able to produce fatal encephalitis in humans and domesticated animals. Despite multiple human outbreaks during the last 80 years, there are still no therapeutic or vaccines to treat or prevent human disease. One critical obstacle in the development of effective countermeasure is the lack of insights into EEEV pathogenesis in a susceptible animal host. We recently conducted a study in cynomolgus macaques to investigate the disease course by measuring clinical parameters relevant to humans. Following infection, these parameters were rapidly and profoundly altered leading to severe disease. In this study, we examined the potential mechanisms that underlie pathogenesis to cause severe disease. The virus was present in many parts of the brain and spinal cord, however, minimal or no pathological lesions as well as active virus replication were observed. Additionally, neurons were the predominant target of EEEV infection and virus transport was facilitated via axonal transport system to spread neuron-to-neuron throughout the brain and spinal cord. These data show that EEEV likely hijacks essential transport system to rapidly spread in the brain and local/global neuronal dysfunction rather than neuronal death is the principal cause of severe disease.
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Affiliation(s)
- Janice A. Williams
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Simon Y. Long
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Xiankun Zeng
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Kathleen Kuehl
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - April M. Babka
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Neil M. Davis
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jun Liu
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - John C. Trefry
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Sharon Daye
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Paul R. Facemire
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Patrick L. Iversen
- Therapeutics Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Sina Bavari
- Office of the Commander, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Margaret L. Pitt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
- Office of the Commander, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
- * E-mail: (MLP); , (FN)
| | - Farooq Nasar
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
- * E-mail: (MLP); , (FN)
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21
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Abstract
Alphaviruses are enveloped viruses transmitted by arthropod vectors to vertebrate hosts. The surface of the virion contains 80 glycoprotein spikes embedded in the membrane, and these spikes mediate attachment to the host cell and initiate viral fusion. Each spike consists of a trimer of E2-E1 heterodimers. These heterodimers interact at the following two interfaces: (i) the intradimer interactions between E2 and E1 of the same heterodimer and (ii) the interdimer interactions between E2 of one heterodimer and E1 of the adjacent heterodimer (E1'). We hypothesized that the interdimer interactions are essential for trimerization of the E2-E1 heterodimers into a functional spike. In this work, we made a mutant virus (chikungunya piggyback [CPB]) where we replaced six interdimeric residues in the E2 protein of Sindbis virus (wild-type [WT] SINV) with those from the E2 protein from chikungunya virus and studied its effect in both mammalian and mosquito cell lines. CPB produced fewer infectious particles in mammalian cells than in mosquito cells, relative to WT SINV. When CPB virus was purified from mammalian cells, particles showed reduced amounts of glycoproteins relative to the capsid protein and contained defects in particle morphology compared with virus derived from mosquito cells. Using cryo-electron microscopy (cryo-EM), we determined that the spikes of CPB had a different conformation than WT SINV. Last, we identified two revertants, E2-H333N and E1-S247L, that restored particle growth and assembly to different degrees. We conclude the interdimer interface is critical for spike trimerization and is a novel target for potential antiviral drug design. IMPORTANCE Alphaviruses, which can cause disease when spread to humans by mosquitoes, have been classified as emerging pathogens, with infections occurring worldwide. The spikes on the surface of the alphavirus particle are absolutely required for the virus to enter a new host cell and initiate an infection. Using a structure-guided approach, we made a mutant virus that alters spike assembly in mammalian cells but not mosquito cells. This finding is important because it identifies a region in the spike that could be a target for antiviral drug design.
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22
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Tan YB, Lello LS, Liu X, Law YS, Kang C, Lescar J, Zheng J, Merits A, Luo D. Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold. Nucleic Acids Res 2022; 50:1000-1016. [PMID: 35037043 PMCID: PMC8789068 DOI: 10.1093/nar/gkab1302] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Alphaviruses such as Ross River virus (RRV), chikungunya virus (CHIKV), Sindbis virus (SINV), and Venezuelan equine encephalitis virus (VEEV) are mosquito-borne pathogens that can cause arthritis or encephalitis diseases. Nonstructural protein 4 (nsP4) of alphaviruses possesses RNA-dependent RNA polymerase (RdRp) activity essential for viral RNA replication. No 3D structure has been available for nsP4 of any alphaviruses despite its importance for understanding alphaviral RNA replication and for the design of antiviral drugs. Here, we report crystal structures of the RdRp domain of nsP4 from both RRV and SINV determined at resolutions of 2.6 Å and 1.9 Å. The structure of the alphavirus RdRp domain appears most closely related to RdRps from pestiviruses, noroviruses, and picornaviruses. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) methods showed that in solution, nsP4 is highly dynamic with an intrinsically disordered N-terminal domain. Both full-length nsP4 and the RdRp domain were capable to catalyze RNA polymerization. Structure-guided mutagenesis using a trans-replicase system identified nsP4 regions critical for viral RNA replication.
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Affiliation(s)
- Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921
| | - Laura Sandra Lello
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Xin Liu
- Shanghai Institute of Materia Medica, China Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, China
| | - Yee-Song Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Rd, #05-01/06 Chromos, Singapore138670
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
| | - Jie Zheng
- Shanghai Institute of Materia Medica, China Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, China
| | - Andres Merits
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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23
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Ciota AT. Eastern Equine Encephalitis Virus Taxonomy, Genomics, and Evolution. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:14-19. [PMID: 34734630 DOI: 10.1093/jme/tjab079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 06/13/2023]
Abstract
Eastern equine encephalitis virus (EEEV; Togaviridae, Alphavirus) is an arthropod-borne virus (arbovirus) primarily maintained in an enzootic cycle between Culiseta melanura (Coquillett) and passerine birds. EEEV, which has the highest reported case- fatality rate among arbovirus in the Americas, is responsible for sporadic outbreaks in the Eastern and Midwest United States. Infection is associated with severe neurologic disease and mortality in horses, humans, and other vertebrate hosts. Here, we review what is known about EEEV taxonomy, functional genomics, and evolution, and identify gaps in knowledge regarding the role of EEEV genetic diversity in transmission and disease.
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Affiliation(s)
- Alexander T Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Rensselaer, NY
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24
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Fourie I, Williams J, Ismail A, Jansen van Vuren P, Stoltz A, Venter M. Detection and genome characterization of Middelburg virus strains isolated from CSF and whole blood samples of humans with neurological manifestations in South Africa. PLoS Negl Trop Dis 2022; 16:e0010020. [PMID: 34979534 PMCID: PMC8722727 DOI: 10.1371/journal.pntd.0010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Old world Alphavirus, Middelburg virus (MIDV), is not well known and although a few cases associated with animal illness have previously been described from Southern Africa, there has been no investigation into the association of the virus with human illness. The current study aimed to investigate possible association of MIDV infection with febrile or neurological manifestations in hospitalized or symptomatic patients fromGauteng, South Africa. METHODS This study is a descriptive retrospective and prospective laboratory based study. Archived cerebrospinal fluid (CSF) samples submitted to the National Health Laboratory Service (NHLS), Tshwane Academic division for viral investigation from public sector hospitals in Gauteng as well as EDTA (ethylenediaminetetraacetic acid) whole blood samples from ad hoc cases of veterinary students, presenting with neurological and febrile illness, were selected and screened for the presence of alphaviruses using real-time reverse transcription(rtRT) PCR.Virus isolations from rtRT-PCR positive samples were conducted in Vero cell culture and used to obtain full genome sequences. Basic descriptive statistical analysis was conducted using EpiInfo. RESULTS MIDV was detected by rtRT-PCR in 3/187 retrospective CSF specimens obtained from the NHLS from hospitalised patients in the Tshwane region of Gauteng and 1/2 EDTA samples submitted in the same year (2017) from ad hoc query arbovirus cases from veterinary students from the Faculty of Veterinary Science University of Pretoria.Full genome sequences were obtained for virus isolates from two cases; one from an EDTA whole blood sample (ad hoc case) and another from a CSF sample (NHLS sample).Two of the four Middelburg virus positive cases,for which clinical information was available, had other comorbidities or infections at the time of infection. CONCLUSION Detection of MIDV in CSF of patients with neurological manifestations suggests that the virus should be investigated as a human pathogen with the potential of causing or contributing to neurological signs in children and adults.
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Affiliation(s)
- Isabel Fourie
- Zoonotic Arbo-and Respiratory Virus (ZARV) program, Centre for Viral Zoonoses (CVZ), University of Pretoria, Pretoria, South Africa
| | - June Williams
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute of Communicable Diseases (NICD), Division of National Health Laboratory Service (NHLS), Sandringham, South Africa
| | - Petrus Jansen van Vuren
- Australian Centre for Disease Preparedness, CSIRO-Health and Biosecurity, Geelong, Australia
| | - Anton Stoltz
- Infectious diseases, Steve Biko Hospital, Pretoria, South Africa
| | - Marietjie Venter
- Zoonotic Arbo-and Respiratory Virus (ZARV) program, Centre for Viral Zoonoses (CVZ), University of Pretoria, Pretoria, South Africa
- * E-mail:
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25
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Lucas CJ, Morrison TE. Animal models of alphavirus infection and human disease. Adv Virus Res 2022; 113:25-88. [DOI: 10.1016/bs.aivir.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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26
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Noguera P, Klinger M, Örün H, Grunow B, Del-Pozo J. Ultrastructural insights into the replication cycle of salmon pancreas disease virus (SPDV) using salmon cardiac primary cultures (SCPCs). JOURNAL OF FISH DISEASES 2021; 44:2031-2041. [PMID: 34424537 DOI: 10.1111/jfd.13518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Salmon pancreas disease virus (SPDV) has been affecting the salmon farming industry for over 30 years, but despite the substantial amount of studies, there are still a number of recognized knowledge gaps, for example in the transmission of the virus. In this work, an ultrastructural morphological approach was used to describe observations after infection by SPDV of an ex vivo cardiac model generated from Atlantic salmon embryos. The observations in this study and those available on previous ultrastructural work on SPDV are compared and contrasted with the current knowledge on terrestrial mammalian and insect alphaviral replication cycles, which is deeper than that of SPDV both morphologically and mechanistically. Despite their limitations, morphological descriptions remain an excellent way to generate novel hypotheses, and this has been the aim of this work. This study has used a target host, ex vivo model and resulted in some previously undescribed features, including filopodial membrane projections, cytoplasmic stress granules or putative intracytoplasmic budding. The latter suggests a new hypothesis that warrants further mechanistic research: SPDV in salmon may have retained the capacity for non-cytolytic (persistent) infections by intracellular budding, similar to that noted in arthropod vectors of other alphaviruses. In the notable absence of a known intermediate host for SPDV, the presence of this pattern suggests that both cytopathic and persistent infections may coexist in the same host. It is our hope that the ultrastructural comparison presented here stimulates new research that brings the knowledge on SPDV replication cycle up to a similar level to that of terrestrial alphaviruses.
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Affiliation(s)
| | | | - Histro Örün
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
| | - Bianka Grunow
- Leibniz-Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Jorge Del-Pozo
- Royal Dick School of Veterinary Sciences, University of Edinburgh, Roslin, UK
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27
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Chaudhary S, Jain J, Kumar R, Shrinet J, Weaver SC, Auguste AJ, Sunil S. Chikungunya virus molecular evolution in India since its re-emergence in 2005. Virus Evol 2021; 7:veab074. [PMID: 34754512 PMCID: PMC8570154 DOI: 10.1093/ve/veab074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is among the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of fifty clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analysed them along with 753 genomes available on the Virus Pathogen Database and Analysis Resource sampled over fifteen years (2005-20) from a range of locations across the globe and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.
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Affiliation(s)
| | - Jaspreet Jain
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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28
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The C-Terminal Domain of Salmonid Alphavirus Nonstructural Protein 2 (nsP2) Is Essential and Sufficient To Block RIG-I Pathway Induction and Interferon-Mediated Antiviral Response. J Virol 2021; 95:e0115521. [PMID: 34523969 DOI: 10.1128/jvi.01155-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonid alphavirus (SAV) is an atypical alphavirus that has a considerable impact on salmon and trout farms. Unlike other alphaviruses, such as the chikungunya virus, SAV is transmitted without an arthropod vector, and it does not cause cell shutoff during infection. The mechanisms by which SAV escapes the host immune system remain unknown. By studying the role of SAV proteins on the RIG-I signaling cascade, the first line of defense of the immune system during infection, we demonstrated that nonstructural protein 2 (nsP2) effectively blocks the induction of type I interferon (IFN). This inhibition, independent of the protease activity carried by nsP2, occurs downstream of IRF3, which is the transcription factor allowing the activation of the IFN promoter and its expression. The inhibitory effect of nsP2 on the RIG-I pathway depends on the localization of nsP2 in the host cell nucleus, which is linked to two nuclear localization sequences (NLS) located in its C-terminal part. The C-terminal domain of nsP2 by itself is sufficient and necessary to block IFN induction. Mutation of the NLS of nsP2 is deleterious to the virus. Finally, nsP2 does not interact with IRF3, indicating that its action is possible through a targeted interaction within discrete areas of chromatin, as suggested by its punctate distribution observed in the nucleus. These results therefore demonstrate a major role for nsP2 in the control by SAV of the host cell's innate immune response. IMPORTANCE The global consumption of fish continues to rise, and the future demand cannot be met by capture fisheries alone due to limited stocks of wild fish. Aquaculture is currently the world's fastest-growing food production sector, with an annual growth rate of 6 to 8%. Recurrent outbreaks of SAV result in significant economic losses with serious environmental consequences for wild stocks. While the clinical and pathological signs of SAV infection are fairly well known, the molecular mechanisms involved are poorly described. In the present study, we focus on the nonstructural protein nsP2 and characterize a specific domain containing nuclear localization sequences that are critical for the inhibition of the host innate immune response mediated by the RIG-I pathway.
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29
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Tschá MK, Suzukawa AA, Rodrigues-Luiz GF, da Silva AM, Cataneo AHD, Mattoso Coelho G, Ferreira AC, Soares Medeiros LC, Mansur D, Zanluca C, Duarte dos Santos CN. Pirahy virus: Identification of a new and potential emerging arbovirus in South Brazil. Virus Evol 2021; 7:veab105. [PMID: 35310294 PMCID: PMC8928568 DOI: 10.1093/ve/veab105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 01/14/2023] Open
Abstract
Genomic and epidemiological surveillance are paramount for the discovery of new viruses with the potential to cross species barriers. Here, we present a new member of the genus Alphavirus found in Trichoprosopon and Wyeomia mosquitoes, tentatively named Pirahy virus (PIRAV). PIRAV was isolated from mosquito pools collected in a rural area of Piraí do Sul, South Brazil. In vitro assays revealed that PIRAV replicates and causes cytopathic effects in vertebrate cell lines such as Vero E6, SH-SY5Y, BHK-21 and UMNSAH/DF-1. Genomic signature analysis supports these results showing a dinucleotide and codon usage balance compatible with several hosts. Phylogenetic analyses placed PIRAV basal to the Venezuelan equine encephalitis complex. Genome analyses, electron microscopy, and biological characterization show findings that may alert for the emergence of a new arbovirus in South America.
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Affiliation(s)
- Marcel Kruchelski Tschá
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Andreia A Suzukawa
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Gabriela Flavia Rodrigues-Luiz
- Departamento de Microbiologia, Imunologia e
Parasitologia, Centro de Ciências Biológicas (CCB), Universidade Federal de Santa
Catarina (UFSC), Av. Prof. Henrique da Silva Fontes 2754, Florianópolis,
SC 88040-900, Brazil
| | - Allan Martins da Silva
- Laboratório Central, Secretaria de Estado da
Saúde do Paraná, Rua Sebastiana Santana Fraga 1001, São José dos
Pinhais, PR 83060-500, Brazil
| | - Allan Henrique Depieri Cataneo
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Gabriela Mattoso Coelho
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Adão Celestino Ferreira
- Núcleo de Entomologia de Foz do Iguaçu,
Secretaria de Estado da Saúde do Paraná, R. Santos Dumont 460, Foz do
Iguaçu, PR 85851-040, Brazil
| | - Lia Carolina Soares Medeiros
- Laboratório de Biologia Celular, Instituto Carlos
Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba, PR
81350-010, Brazil
| | - Daniel Mansur
- Departamento de Microbiologia, Imunologia e
Parasitologia, Centro de Ciências Biológicas (CCB), Universidade Federal de Santa
Catarina (UFSC), Av. Prof. Henrique da Silva Fontes 2754, Florianópolis,
SC 88040-900, Brazil
| | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Claudia N Duarte dos Santos
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
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30
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Steyn J, Fourie I, Steyl J, Williams J, Stivaktas V, Botha E, van Niekerk S, Reininghaus B, Venter M. Zoonotic Alphaviruses in Fatal and Neurologic Infections in Wildlife and Nonequine Domestic Animals, South Africa. Emerg Infect Dis 2021; 26:1182-1191. [PMID: 32441633 PMCID: PMC7258481 DOI: 10.3201/eid2606.191179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Alphaviruses from Africa, such as Middelburg virus (MIDV), and Sindbis virus (SINV), were detected in horses with neurologic disease in South Africa, but their host ranges remain unknown. We investigated the contribution of alphaviruses to neurologic infections and death in wildlife and domestic animals in this country. During 2010-2018, a total of 608 clinical samples from wildlife and nonequine domestic animals that had febrile, neurologic signs or unexplained deaths were tested for alphaviruses. We identified 32 (5.5%) of 608 alphavirus infections (9 SINV and 23 MIDV), mostly in neurotissue of wildlife, domestic animals, and birds. Phylogenetic analysis of the RNA-dependent RNA polymerase gene confirmed either SINV or MIDV. This study implicates MIDV and SINV as potential causes of neurologic disease in wildlife and nonequine domestic species in Africa and suggests a wide host range and pathogenic potential.
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31
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The utilization of advance telemetry to investigate critical physiological parameters including electroencephalography in cynomolgus macaques following aerosol challenge with eastern equine encephalitis virus. PLoS Negl Trop Dis 2021; 15:e0009424. [PMID: 34138849 PMCID: PMC8259972 DOI: 10.1371/journal.pntd.0009424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/06/2021] [Accepted: 04/29/2021] [Indexed: 11/19/2022] Open
Abstract
Most alphaviruses are mosquito-borne and can cause severe disease in humans and domesticated animals. In North America, eastern equine encephalitis virus (EEEV) is an important human pathogen with case fatality rates of 30–90%. Currently, there are no therapeutics or vaccines to treat and/or prevent human infection. One critical impediment in countermeasure development is the lack of insight into clinically relevant parameters in a susceptible animal model. This study examined the disease course of EEEV in a cynomolgus macaque model utilizing advanced telemetry technology to continuously and simultaneously measure temperature, respiration, activity, heart rate, blood pressure, electrocardiogram (ECG), and electroencephalography (EEG) following an aerosol challenge at 7.0 log10 PFU. Following challenge, all parameters were rapidly and substantially altered with peak alterations from baseline ranged as follows: temperature (+3.0–4.2°C), respiration rate (+56–128%), activity (-15-76% daytime and +5–22% nighttime), heart rate (+67–190%), systolic (+44–67%) and diastolic blood pressure (+45–80%). Cardiac abnormalities comprised of alterations in QRS and PR duration, QTc Bazett, T wave morphology, amplitude of the QRS complex, and sinoatrial arrest. An unexpected finding of the study was the first documented evidence of a critical cardiac event as an immediate cause of euthanasia in one NHP. All brain waves were rapidly (~12–24 hpi) and profoundly altered with increases of up to 6,800% and severe diffuse slowing of all waves with decreases of ~99%. Lastly, all NHPs exhibited disruption of the circadian rhythm, sleep, and food/fluid intake. Accordingly, all NHPs met the euthanasia criteria by ~106–140 hpi. This is the first of its kind study utilizing state of the art telemetry to investigate multiple clinical parameters relevant to human EEEV infection in a susceptible cynomolgus macaque model. The study provides critical insights into EEEV pathogenesis and the parameters identified will improve animal model development to facilitate rapid evaluation of vaccines and therapeutics. In North America, EEEV causes the most severe mosquito-borne disease in humans highlighted by fatal encephalitis and permeant debilitating neurological sequelae in survivors. The first confirmed human cases were reported more than 80 years ago and since then multiple sporadic outbreaks have occurred including one of the largest in 2019. Unfortunately, most human infections are diagnosed at the on-set of severe neurological symptoms and consequently a detailed disease course in humans is lacking. This gap in knowledge is a significant obstacle in the development of appropriate animal models to evaluate countermeasures. Here, we performed a cutting-edge study by utilizing a new telemetry technology to understand the course of EEEV infection in a susceptible macaque model by measuring multiple physiological parameters relevant to human disease. Our study demonstrates that the infection rapidly produces considerable alterations in many critical parameters including the electrical activity of the heart and the brain leading to severe disease. The study also highlights the extraordinary potential of new telemetry technology to develop the next generation of animal models to comprehensively investigate pathogenesis as well as evaluate countermeasures to treat and/or prevent EEEV disease.
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32
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Wichit S, Gumpangseth N, Hamel R, Yainoy S, Arikit S, Punsawad C, Missé D. Chikungunya and Zika Viruses: Co-Circulation and the Interplay between Viral Proteins and Host Factors. Pathogens 2021; 10:448. [PMID: 33918691 PMCID: PMC8068860 DOI: 10.3390/pathogens10040448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Chikungunya and Zika viruses, both transmitted by mosquito vectors, have globally re-emerged over for the last 60 years and resulted in crucial social and economic concerns. Presently, there is no specific antiviral agent or vaccine against these debilitating viruses. Understanding viral-host interactions is needed to develop targeted therapeutics. However, there is presently limited information in this area. In this review, we start with the updated virology and replication cycle of each virus. Transmission by similar mosquito vectors, frequent co-circulation, and occurrence of co-infection are summarized. Finally, the targeted host proteins/factors used by the viruses are discussed. There is an urgent need to better understand the virus-host interactions that will facilitate antiviral drug development and thus reduce the global burden of infections caused by arboviruses.
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Affiliation(s)
- Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; (N.G.); (S.Y.)
- School of Medicine, Walailak University, Nakhon Si Thammarat 80160, Thailand;
| | - Nuttamonpat Gumpangseth
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; (N.G.); (S.Y.)
| | - Rodolphe Hamel
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France; (R.H.); (D.M.)
| | - Sakda Yainoy
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; (N.G.); (S.Y.)
| | - Siwaret Arikit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
| | - Chuchard Punsawad
- School of Medicine, Walailak University, Nakhon Si Thammarat 80160, Thailand;
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France; (R.H.); (D.M.)
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33
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De Caluwé L, Coppens S, Vereecken K, Daled S, Dhaenens M, Van Ostade X, Deforce D, Ariën KK, Bartholomeeusen K. The CD147 Protein Complex Is Involved in Entry of Chikungunya Virus and Related Alphaviruses in Human Cells. Front Microbiol 2021; 12:615165. [PMID: 33717005 PMCID: PMC7946996 DOI: 10.3389/fmicb.2021.615165] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/05/2021] [Indexed: 01/22/2023] Open
Abstract
Chikungunya virus (CHIKV) is an arbovirus with a global spread and significant public health impact. It is a positive stranded RNA alphavirus belonging to the Togaviridae family. However, many questions about the replication cycle of CHIKV remain unanswered. The entry process of CHIKV is not completely understood nor are the associated virus-receptor interactions fully identified. Here, we designed an affinity purification mass spectrometry coupled approach that allowed the identification of factors that facilitate entry of CHIKV in human cells. The identified entry factors were further validated using CRISPR/Cas9. In HEK293T cells we identified the CD147 protein complex as an entry factor for CHIKV. We further showed the involvement of the CD147 protein complex in the replication cycle of related alphaviruses. Interestingly, CD147 contains similar protein domains as the previously identified alphavirus entry factor MXRA8.
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Affiliation(s)
- Lien De Caluwé
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Sandra Coppens
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Katleen Vereecken
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Simon Daled
- Laboratory for Pharmaceutical Biotechnology, University of Ghent, Ghent, Belgium.,ProGenTomics, Ghent, Belgium
| | - Maarten Dhaenens
- Laboratory for Pharmaceutical Biotechnology, University of Ghent, Ghent, Belgium.,ProGenTomics, Ghent, Belgium
| | - Xaveer Van Ostade
- Laboratory of Proteinscience, Proteomics and Epigenetic Signaling, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, University of Ghent, Ghent, Belgium.,ProGenTomics, Ghent, Belgium
| | - Kevin K Ariën
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Koen Bartholomeeusen
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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34
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Libbey JE, Fujinami RS. Viral mouse models used to study multiple sclerosis: past and present. Arch Virol 2021; 166:1015-1033. [PMID: 33582855 PMCID: PMC7882042 DOI: 10.1007/s00705-021-04968-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/06/2020] [Indexed: 12/19/2022]
Abstract
Multiple sclerosis (MS) is a common inflammatory demyelinating disease of the central nervous system. Although the etiology of MS is unknown, genetics and environmental factors, such as infections, play a role. Viral infections of mice have been used as model systems to study this demyelinating disease of humans. Three viruses that have long been studied in this capacity are Theiler’s murine encephalomyelitis virus, mouse hepatitis virus, and Semliki Forest virus. This review describes the viruses themselves, the infection process, the disease caused by infection and its accompanying pathology, and the model systems and their usefulness in studying MS.
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Affiliation(s)
- J E Libbey
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, 2600 EEJMRB, Salt Lake City, UT, 84112, USA
| | - R S Fujinami
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, 2600 EEJMRB, Salt Lake City, UT, 84112, USA.
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35
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Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus. Genes (Basel) 2021; 12:genes12020239. [PMID: 33567556 PMCID: PMC7914560 DOI: 10.3390/genes12020239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/29/2021] [Accepted: 02/04/2021] [Indexed: 01/21/2023] Open
Abstract
Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.
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36
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Visualization of the Oncolytic Alphavirus M1 Life Cycle in Cancer Cells. Virol Sin 2021; 36:655-666. [PMID: 33481190 DOI: 10.1007/s12250-020-00339-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/26/2020] [Indexed: 01/16/2023] Open
Abstract
Oncolytic alphavirus M1 has been shown to selectively target and kill cancer cells, but cytopathic morphologies induced by M1 virus and the life cycle of the M1 strain in cancer cells remain unclear. Here, we study the key stages of M1 virus infection and replication in the M1 virus-sensitive HepG2 liver cancer cell line by transmission electron microscopy, specifically examining viral entry, assembly, maturation and release. We found that M1 virus induces vacuolization of cancer cells during infection and ultimately nuclear marginalization, a typical indicator of apoptosis. Specifically, our results suggest that the endoplasmic reticulum participates in the assembly of nucleocapsids. In the early and late stage of infection, three kinds of special cytopathic vacuoles are formed and appear to be involved in the replication, maturation and release of the virus. Taken together, our data displayed the process of M1 virus infection of tumor cells and provide the structural basis for the study of M1 virus-host interactions.
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37
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Madden EA, Plante KS, Morrison CR, Kutchko KM, Sanders W, Long KM, Taft-Benz S, Cruz Cisneros MC, White AM, Sarkar S, Reynolds G, Vincent HA, Laederach A, Moorman NJ, Heise MT. Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus. J Virol 2020; 94:e00701-20. [PMID: 32999019 PMCID: PMC7925192 DOI: 10.1128/jvi.00701-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3'UTR variants. A duplication in the 3'UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3'UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis.IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes febrile illness and debilitating arthralgia in humans. CHIKV causes explosive outbreaks but there are no approved therapies to treat or prevent CHIKV infection. The CHIKV genome contains functional RNA secondary structures that are essential for proper virus replication. Since RNA secondary structures have only been defined for a small portion of the CHIKV genome, we used a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA. We identified 23 highly specific structured regions of the genome, and confirmed the functional importance of one structure using mutagenesis. Furthermore, we defined the RNA secondary structure of three CHIKV 3'UTR variants that differ in their ability to replicate in mosquito cells. Our study highlights the complexity of the CHIKV genome and describes new systems for designing compensatory mutations to test the functional relevance of viral RNA secondary structures.
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Affiliation(s)
- Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth S Plante
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Clayton R Morrison
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrina M Kutchko
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristin M Long
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon Taft-Benz
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Sanjay Sarkar
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Grace Reynolds
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather A Vincent
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alain Laederach
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathanial J Moorman
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
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38
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De Caluwé L, Ariën KK, Bartholomeeusen K. Host Factors and Pathways Involved in the Entry of Mosquito-Borne Alphaviruses. Trends Microbiol 2020; 29:634-647. [PMID: 33208275 DOI: 10.1016/j.tim.2020.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/17/2022]
Abstract
Chikungunya virus (CHIKV) is an arthropod-borne virus that has re-emerged recently and has spread to previously unaffected regions, resulting in millions of infections worldwide. The genus Alphavirus, in the family Togaviridae, contains several members with a similar potential for epidemic emergence. In order for CHIKV to replicate in targeted cell types it is essential for the virus to enter these cells. In this review, we summarize our current understanding of the versatile and promiscuous steps in CHIKV binding and entry into human and mosquito host cells. We describe the different entry pathways, receptors, and attachment factors so far described for CHIKV and other mosquito-borne alphaviruses and discuss them in the context of tissue tropism and potential therapeutic targeting.
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Affiliation(s)
- Lien De Caluwé
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Kevin K Ariën
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Koen Bartholomeeusen
- Virology Unit, Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
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39
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Rack JGM, Zorzini V, Zhu Z, Schuller M, Ahel D, Ahel I. Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential. Open Biol 2020; 10:200237. [PMID: 33202171 PMCID: PMC7729036 DOI: 10.1098/rsob.200237] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Viral macrodomains possess the ability to counteract host ADP-ribosylation, a post-translational modification implicated in the creation of an antiviral environment via immune response regulation. This brought them into focus as promising therapeutic targets, albeit the close homology to some of the human macrodomains raised concerns regarding potential cross-reactivity and adverse effects for the host. Here, we evaluate the structure and function of the macrodomain of SARS-CoV-2, the causative agent of COVID-19. We show that it can antagonize ADP-ribosylation by PARP14, a cellular (ADP-ribosyl)transferase necessary for the restriction of coronaviral infections. Furthermore, our structural studies together with ligand modelling revealed the structural basis for poly(ADP-ribose) binding and hydrolysis, an emerging new aspect of viral macrodomain biology. These new insights were used in an extensive evolutionary analysis aimed at evaluating the druggability of viral macrodomains not only from the Coronaviridae but also Togaviridae and Iridoviridae genera (causing diseases such as Chikungunya and infectious spleen and kidney necrosis virus disease, respectively). We found that they contain conserved features, distinct from their human counterparts, which may be exploited during drug design.
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Affiliation(s)
| | | | | | | | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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40
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Rodrigues TCS, Nielsen O, Popov VL, Burek-Huntington KA, Rotstein D, Subramaniam K, Waltzek TB. Characterization of an alphavirus isolated from a stranded harbor porpoise (Phocoena phocoena) from Alaska. Virus Res 2020; 291:198187. [PMID: 33075445 DOI: 10.1016/j.virusres.2020.198187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 10/23/2022]
Abstract
The family Togaviridae comprises several significant human and veterinary mosquito-borne pathogens. Two togaviruses (genus Alphavirus) have been previously identified in association with marine mammals, the southern elephant seal virus (SESV) and Eastern equine encephalitis virus (EEEV) from a fatal captive harbor seal infection. Herein we report the ultrastructural and phylogenomic characterization of a novel marine togavirus, the first isolated from a cetacean, an Alaskan harbor porpoise (Phocoena phocoena) displaying ulcerative dermatitis. A skin sample was processed for virus isolation on Vero.DogSLAMtag cells and cytopathic effects (CPE) were observed on primary isolation approximately 20 days post-infection. Transmission electron microscopy of the infected Vero.DogSLAMtag cells revealed typical alphavirus particles budding from both plasma and vacuolar membranes of infected cells. A next-generation sequencing approach was used to determine the near complete genome of the Alaskan harbor porpoise alphavirus (AHPV). Phylogenetic analysis supported the AHPV as the sister species to the SESV, forming a marine mammal alphavirus clade separate from the recognized alphavirus antigenic complexes. Genetic comparison of the protein coding sequence of the AHPV to other alphaviruses demonstrated amino acid identities ranging from 42.1-67.1%, with the highest identity to the SESV. Based on its genetic divergence, we propose the AHPV represents a novel alphavirus species, pending formal proposal to and ratification by the International Committee on Taxonomy of Viruses. The ecological and genetic characteristics of the AHPV and the SESV also suggest they represent a novel antigenic complex within the genus Alphavirus, which we propose to be named the Marine Mammal Virus Complex. The role of the AHPV in the associated harbor porpoise cutaneous pathology, if any, remains unclear. Further research is needed to determine AHPV's route(s) of transmission and potential vectors, host range, prevalence, and pathogenicity in cetaceans including harbour porpoises.
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Affiliation(s)
- Thaís C S Rodrigues
- Department of Infectious Diseases and Immunology, University of Florida, 2187 Mowry Road, 32611, Gainesville, FL, USA
| | - Ole Nielsen
- Department of Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6 Canada.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609 USA
| | | | | | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, University of Florida, 2187 Mowry Road, 32611, Gainesville, FL, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, University of Florida, 2187 Mowry Road, 32611, Gainesville, FL, USA
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41
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Hermanns K, Marklewitz M, Zirkel F, Overheul GJ, Page RA, Loaiza JR, Drosten C, van Rij RP, Junglen S. Agua Salud alphavirus defines a novel lineage of insect-specific alphaviruses discovered in the New World. J Gen Virol 2020; 101:96-104. [PMID: 31674898 PMCID: PMC7414432 DOI: 10.1099/jgv.0.001344] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genus Alphavirus harbours mostly insect-transmitted viruses that cause severe disease in humans, livestock and wildlife. Thus far, only three alphaviruses with a host range restricted to insects have been found in mosquitoes from the Old World, namely Eilat virus (EILV), Taï Forest alphavirus (TALV) and Mwinilunga alphavirus (MWAV). In this study, we found a novel alphavirus in one Culex declarator mosquito sampled in Panama. The virus was isolated in C6/36 mosquito cells, and full genome sequencing revealed an 11 468 nt long genome with maximum pairwise nucleotide identity of 62.7 % to Sindbis virus. Phylogenetic analyses placed the virus as a solitary deep rooting lineage in a basal relationship to the Western equine encephalitis antigenic complex and to the clade comprising EILV, TALV and MWAV, indicating the detection of a novel alphavirus, tentatively named Agua Salud alphavirus (ASALV). No growth of ASALV was detected in vertebrate cell lines, including cell lines derived from ectothermic animals, and replication of ASALV was strongly impaired above 31 °C, suggesting that ASALV represents the first insect-restricted alphavirus of the New World.
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Affiliation(s)
- Kyra Hermanns
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marco Marklewitz
- German Center for Infection Research (DZIF), Berlin, Germany.,Smithsonian Tropical Research Institute, Panama City, Republic of Panama.,Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Florian Zirkel
- Present address: Biotest AG, Dreieich, Germany.,Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rachel A Page
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Jose R Loaiza
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama.,Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Panama City, Republic of Panama.,Programa Centroamericano de Maestría en Entomología, Vicerrectoría de Investigación y Postgrado, Universidad de Panamá, Panama, Republic of Panama
| | - Christian Drosten
- German Center for Infection Research (DZIF), Berlin, Germany.,Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Sandra Junglen
- German Center for Infection Research (DZIF), Berlin, Germany.,Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
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42
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Filomatori CV, Merwaiss F, Bardossy ES, Alvarez DE. Impact of alphavirus 3'UTR plasticity on mosquito transmission. Semin Cell Dev Biol 2020; 111:148-155. [PMID: 32665176 DOI: 10.1016/j.semcdb.2020.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
Alphaviruses such as chikungunya and western equine encephalitis viruses are important human pathogens transmitted by mosquitoes that have recently caused large epidemic and epizootic outbreaks. The epidemic potential of alphaviruses is often related to enhanced mosquito transmission. Tissue barriers and antiviral responses impose bottlenecks to viral populations in mosquitoes. Substitutions in the envelope proteins and the presence of repeated sequence elements (RSEs) in the 3'UTR of epidemic viruses were proposed to be specifically associated to efficient replication in mosquito vectors. Here, we discuss the molecular mechanisms that originated RSEs, the evolutionary forces that shape the 3'UTR of alphaviruses, and the significance of RSEs for mosquito transmission. Finally, the presence of RSEs in the 3'UTR of viral genomes appears as evolutionary trait associated to mosquito adaptation and emerges as a common feature among viruses from the alphavirus and flavivirus genera.
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Affiliation(s)
- Claudia V Filomatori
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Fernando Merwaiss
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Eugenia S Bardossy
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina.
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Abstract
Alphaviruses, members of the enveloped, positive-sense, single-stranded RNA Togaviridae family, represent a reemerging public health threat as mosquito vectors expand into new geographic territories. The Old World alphaviruses, which include chikungunya virus, Ross River virus, and Sindbis virus, tend to cause a clinical syndrome characterized by fever, rash, and arthritis, whereas the New World alphaviruses, which consist of Venezuelan equine encephalitis virus, eastern equine encephalitis virus, and western equine encephalitis virus, induce encephalomyelitis. Following recovery from the acute phase of infection, many patients are left with debilitating persistent joint and neurological complications that can last for years. Clues from human cases and studies using animal models strongly suggest that much of the disease and pathology induced by alphavirus infection, particularly atypical and chronic manifestations, is mediated by the immune system rather than directly by the virus. This review discusses the current understanding of the immunopathogenesis of the arthritogenic and neurotropic alphaviruses accumulated through both natural infection of humans and experimental infection of animals, particularly mice. As treatment following alphavirus infection is currently limited to supportive care, understanding the contribution of the immune system to the disease process is critical to developing safe and effective therapies.
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Affiliation(s)
- Victoria K Baxter
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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Michie A, Ernst T, Chua ILJ, Lindsay MDA, Neville PJ, Nicholson J, Jardine A, Mackenzie JS, Smith DW, Imrie A. Phylogenetic and Timescale Analysis of Barmah Forest Virus as Inferred from Genome Sequence Analysis. Viruses 2020; 12:E732. [PMID: 32640629 PMCID: PMC7412159 DOI: 10.3390/v12070732] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 11/17/2022] Open
Abstract
Barmah Forest virus (BFV) is a medically important mosquito-borne alphavirus endemic to Australia. Symptomatic disease can be a major cause of morbidity, associated with fever, rash, and debilitating arthralgia. BFV disease is similar to that caused by Ross River virus (RRV), the other major Australian alphavirus. Currently, just four BFV whole-genome sequences are available with no genome-scale phylogeny in existence to robustly characterise genetic diversity. Thirty novel genome sequences were derived for this study, for a final 34-taxon dataset sampled over a 44 year period. Three distinct BFV genotypes were characterised (G1-3) that have circulated in Australia and Papua New Guinea (PNG). Evidence of spatio-temporal co-circulation of G2 and G3 within regions of Australia was noted, including in the South West region of Western Australia (WA) during the first reported disease outbreaks in the state's history. Compared with RRV, the BFV population appeared more stable with less frequent emergence of novel lineages. Preliminary in vitro assessment of RRV and BFV replication kinetics found that RRV replicates at a significantly faster rate and to a higher, more persistent titre compared with BFV, perhaps indicating mosquitoes may be infectious with RRV for longer than with BFV. This investigation resolved a greater diversity of BFV, and a greater understanding of the evolutionary dynamics and history was attained.
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Affiliation(s)
- Alice Michie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
| | - Timo Ernst
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
| | - I-Ly Joanna Chua
- PathWest Laboratory Medicine Western Australia, Perth, WA 6000, Australia; (I-L.J.C.); (J.S.M.); (D.W.S.)
| | - Michael D. A. Lindsay
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - Peter J. Neville
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - Jay Nicholson
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - Andrew Jardine
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - John S. Mackenzie
- PathWest Laboratory Medicine Western Australia, Perth, WA 6000, Australia; (I-L.J.C.); (J.S.M.); (D.W.S.)
- Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4067, Australia
| | - David W. Smith
- PathWest Laboratory Medicine Western Australia, Perth, WA 6000, Australia; (I-L.J.C.); (J.S.M.); (D.W.S.)
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
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45
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Julia da Silva Pessoa Vieira C, José Ferreira da Silva D, Rigotti Kubiszeski J, Ceschini Machado L, Pena LJ, Vieira de Morais Bronzoni R, da Luz Wallau G. The Emergence of Chikungunya ECSA Lineage in a Mayaro Endemic Region on the Southern Border of the Amazon Forest. Trop Med Infect Dis 2020; 5:E105. [PMID: 32604785 PMCID: PMC7345197 DOI: 10.3390/tropicalmed5020105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Anthropic changes on the edges of the tropical forests may facilitate the emergence of new viruses from the sylvatic environment and the simultaneous circulation of sylvatic and urban viruses in the human population. In this study, we investigated the presence of arboviruses (arthropod-borne viruses) in the sera of 354 patients, sampled from February 2014 to October 2018 in Sinop city. We sequenced the complete genomes of one chikungunya virus (CHIKV)-positive and one out of the 33 Mayaro virus (MAYV)-positive samples. The CHIKV genome obtained here belongs to the East/Central/South African (ECSA) genotype and the MAYV genome belongs to the L genotype. These genomes clustered with other viral strains from different Brazilian states, but the CHIKV strain circulating in Sinop did not cluster with other genomes from the Mato Grosso state, suggesting that at least two independent introductions of this virus occurred in Mato Grosso. Interestingly, the arrival of CHIKV in Sinop seems to not have caused a surge in human cases in the following years, as observed in the rest of the state, suggesting that cross immunity from MAYV infection might be protecting the population from CHIKV infection. These findings reinforce the need for continued genomic surveillance in order to evaluate how simultaneously circulating alphaviruses infecting the human population will unfold.
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Affiliation(s)
- Carla Julia da Silva Pessoa Vieira
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - David José Ferreira da Silva
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - Janaína Rigotti Kubiszeski
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - Laís Ceschini Machado
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife 50670-420, PE, Brazil; (L.C.M.); (L.J.P.)
| | - Lindomar José Pena
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife 50670-420, PE, Brazil; (L.C.M.); (L.J.P.)
| | - Roberta Vieira de Morais Bronzoni
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - Gabriel da Luz Wallau
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife 50670-420, PE, Brazil; (L.C.M.); (L.J.P.)
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46
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Bugert JJ, Hucke F, Zanetta P, Bassetto M, Brancale A. Antivirals in medical biodefense. Virus Genes 2020; 56:150-167. [PMID: 32076918 PMCID: PMC7089181 DOI: 10.1007/s11262-020-01737-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
The viruses historically implicated or currently considered as candidates for misuse in bioterrorist events are poxviruses, filoviruses, bunyaviruses, orthomyxoviruses, paramyxoviruses and a number of arboviruses causing encephalitis, including alpha- and flaviviruses. All these viruses are of concern for public health services when they occur in natural outbreaks or emerge in unvaccinated populations. Recent events and intelligence reports point to a growing risk of dangerous biological agents being used for nefarious purposes. Public health responses effective in natural outbreaks of infectious disease may not be sufficient to deal with the severe consequences of a deliberate release of such agents. One important aspect of countermeasures against viral biothreat agents are the antiviral treatment options available for use in post-exposure prophylaxis. These issues were adressed by the organizers of the 16th Medical Biodefense Conference, held in Munich in 2018, in a special session on the development of drugs to treat infections with viruses currently perceived as a threat to societies or associated with a potential for misuse as biothreat agents. This review will outline the state-of-the-art methods in antivirals research discussed and provide an overview of antiviral compounds in the pipeline that are already approved for use or still under development.
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Affiliation(s)
- J J Bugert
- Bundeswehr Institute for Microbiology, Neuherbergstraße 11, 80937, Munich, Germany.
| | - F Hucke
- Bundeswehr Institute for Microbiology, Neuherbergstraße 11, 80937, Munich, Germany
| | - P Zanetta
- Bundeswehr Institute for Microbiology, Neuherbergstraße 11, 80937, Munich, Germany
| | - M Bassetto
- Department of Chemistry, Swansea University, Swansea, SA2 8PP, UK
| | - A Brancale
- Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
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47
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Skidmore AM, Adcock RS, Jonsson CB, Golden JE, Chung DH. Benzamidine ML336 inhibits plus and minus strand RNA synthesis of Venezuelan equine encephalitis virus without affecting host RNA production. Antiviral Res 2020; 174:104674. [PMID: 31816348 PMCID: PMC6935354 DOI: 10.1016/j.antiviral.2019.104674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Venezuelan equine encephalitis virus (VEEV) is an alphavirus that is endemic to the Americas. VEEV outbreaks occur periodically and cause encephalitis in both humans and equids. There are currently no therapeutics or vaccines for treatment of VEEV in humans. Our group has previously reported on the development of a benzamidine VEEV inhibitor, ML336, which shows potent antiviral activity in both in vitro and in vivo models of infection. In cell culture experiments, ML336 inhibits viral RNA synthesis when added 2-4 h post-infection, and mutations conferring resistance occur within the viral nonstructural proteins (nsP2 and nsP4). We hypothesized that ML336 targets an activity of the viral replicase complex and inhibits viral RNA synthesis. To test this hypothesis, we employed various biochemical and cellular assays. Using structural analogues of ML336, we demonstrate that the cellular antiviral activity of these compounds correlates with their inhibition of viral RNA synthesis. For instance, the IC50 of ML336 for VEEV RNA synthesis inhibition was determined as 1.1 nM, indicating potent anti-RNA synthesis activity in the low nanomolar range. While ML336 efficiently inhibited VEEV RNA synthesis, a much weaker effect was observed against the Old World alphavirus Chikungunya virus (IC50 > 4 μM), agreeing with previous data from a cell based assay. Using a tritium incorporation assay, we demonstrated that there was no significant inhibition of cellular transcription. With a combination of fluorography, strand-specific qRT-PCR, and tritium incorporation, we demonstrated that ML336 inhibits the synthesis of the positive sense genomic, negative sense template, and subgenomic RNAs of VEEV. Based on these results, we propose that the mechanism of action for this class of antiviral compounds is inhibition of viral RNA synthesis through interaction with the viral replicase complex.
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Affiliation(s)
- Andrew M Skidmore
- Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Room 642 C, Louisville, KY, USA.
| | - Robert S Adcock
- Center of Predictive Medicine, University of Louisville, 505 South Hancock St, Room 617, Louisville, KY, USA.
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave, Room 810 B, Memphis, TN, USA.
| | - Jennifer E Golden
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Dr, Room 7123, Madison, WI, USA.
| | - Dong-Hoon Chung
- Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Room 642 C, Louisville, KY, USA; Center of Predictive Medicine, University of Louisville, 505 South Hancock St, Room 617, Louisville, KY, USA.
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48
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Naturally Occurring and Engineered Alphaviruses Sensitive to Double-Stranded-RNA-Activated Protein Kinase Show Restricted Translation in Mammalian Cells, Increased Sensitivity to Interferon, and Marked Oncotropism. J Virol 2020; 94:JVI.01630-19. [PMID: 31723025 DOI: 10.1128/jvi.01630-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
Alphaviruses are insect-borne viruses that alternate between replication in mosquitoes and vertebrate species. Adaptation of some alphaviruses to vertebrate hosts has involved the acquisition of an RNA structure (downstream loop [DLP]) in viral subgenomic mRNAs that confers translational resistance to protein kinase (PKR)-mediated eIF2α phosphorylation. Here, we found that, in addition to promoting eIF2-independent translation of viral subgenomic mRNAs, presence of the DLP structure also increased the resistance of alphavirus to type I interferon (IFN). Aura virus (AURAV), an ecologically isolated relative of Sindbis virus (SV) that is poorly adapted to replication in vertebrate cells, displayed a nonfunctional DLP structure and dramatic sensitivity to type I IFN. Our data suggest that an increased resistance to IFN emerged during translational adaptation of alphavirus mRNA to vertebrate hosts, reinforcing the role that double-stranded RNA (dsRNA)-activated protein kinase (PKR) plays as both a constitutive and IFN-induced antiviral effector. Interestingly, a mutant SV lacking the DLP structure (SV-ΔDLP) and AURAV both showed a marked oncotropism for certain tumor cell lines that have defects in PKR expression and/or activation. AURAV selectively replicated in and killed some cell lines derived from human hepatocarcinoma (HCC) that lacked PKR response to infection or poly(I·C) transfection. The oncolytic activities of SV-ΔDLP and AURAV were also confirmed using tumor xenografts in mice, showing tumor regression activities comparable to wild-type SV. Our data show that translation of alphavirus subgenomic mRNAs plays a central role in IFN susceptibility and cell tropism, suggesting an unanticipated oncolytic potential that some naive arboviruses may have in virotherapy.IMPORTANCE Interferons (IFNs) induce the expression of a number of antiviral genes that protect the cells of vertebrates against viruses and other microbes. The susceptibility of cells to viruses greatly depends on the level and activity of these antiviral effectors but also on the ability of viruses to counteract this antiviral response. Here, we found that the level of one of the main IFN effectors in the cell, the dsRNA-activated protein kinase (PKR), greatly determines the permissiveness of cells to alphaviruses that lack mechanisms to counteract its activation. These naive viruses also showed a hypersensitivity to IFN, suggesting that acquisition of IFN resistance (even partial) has probably been involved in expanding the host range of alphaviruses in the past. Interestingly, some of these naive viruses showed a marked oncotropism for some tumor cell lines derived from human hepatocarcinoma (HCC), opening the possibility of their use in oncolytic therapy to treat human tumors.
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49
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Barik S. In silico structure analysis of alphaviral RNA genomes shows diversity in the evasion of IFIT1-mediated innate immunity. J Biosci 2019; 44:79. [PMID: 31502557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The IFIT (interferon-induced proteins with tetratricopeptide repeats) family constitutes a major arm of the antiviral function of type I interferon (IFN). Human IFIT1, the earliest discovered member of this family, inhibits several viruses of positivestrand RNA genome. IFIT1 specifically recognizes single-stranded RNAwith canonical 7-methylguanylate cap at the 50 end (Cap0), and inhibits their translation by competing with eIF4E (eukaryotic initiation factor 4E), an essential factor for 50Cap recognition. Recently, a novel viral mechanism of IFIT1 suppression was reported, in which an RNA hairpin in the 50 untranslated region (50UTR) of the viral genome prevented recognition by IFIT1 and enhanced virus growth. Here, I have analyzed the in silico predicted structures in the 50UTR of the genomes of the Alphaviruses, a large group of enveloped RNA virus with positive-sense single-stranded genome. The results uncovered a large ensemble of RNA secondary structures of diverse size and shape in the different viruses, which showed little correspondence to the phylogeny of the viruses. Unexpectedly, the 50UTR of several viral genomes in this family did not fold into any structure, suggesting either their extreme sensitivity to IFIT1 or the existence of alternative viral mechanisms of subverting IFIT1 function.
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50
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Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture. Viruses 2019; 11:v11090798. [PMID: 31470643 PMCID: PMC6784101 DOI: 10.3390/v11090798] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3'UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3'UTR architecture among different CHIKV lineages.
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