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Huston NC, Tsao LH, Brackney DE, Pyle AM. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proc Natl Acad Sci U S A 2024; 121:e2312080121. [PMID: 38985757 PMCID: PMC11260092 DOI: 10.1073/pnas.2312080121] [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: 07/16/2023] [Accepted: 05/25/2024] [Indexed: 07/12/2024] Open
Abstract
West Nile virus (WNV) is an arthropod-borne, positive-sense RNA virus that poses an increasing global threat due to warming climates and lack of effective therapeutics. Like other enzootic viruses, little is known about how host context affects the structure of the full-length RNA genome. Here, we report a complete secondary structure of the entire WNV genome within infected mammalian and arthropod cell lines. Our analysis affords structural insights into multiple, conserved aspects of flaviviral biology. We show that the WNV genome folds with minimal host dependence, and we prioritize well-folded regions for functional validation using structural homology between hosts as a guide. Using structure-disrupting, antisense locked nucleic acids, we then demonstrate that the WNV genome contains riboregulatory structures with conserved and host-specific functional roles. These results reveal promising RNA drug targets within flaviviral genomes, and they highlight the therapeutic potential of ASO-LNAs as both WNV-specific and pan-flaviviral therapeutic agents.
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Affiliation(s)
- Nicholas C. Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Lucille H. Tsao
- Department of Chemistry, Yale University, New Haven, CT06511
| | - Doug E. Brackney
- Department of Entomology, Connecticut Agricultural Experimental Station, New Haven, CT06511
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- HHMI, Chevy Chase, MD20815
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2
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Lewis J, Gallichotte EN, Randall J, Glass A, Foy BD, Ebel GD, Kading RC. Intrinsic factors driving mosquito vector competence and viral evolution: a review. Front Cell Infect Microbiol 2023; 13:1330600. [PMID: 38188633 PMCID: PMC10771300 DOI: 10.3389/fcimb.2023.1330600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/08/2023] [Indexed: 01/09/2024] Open
Abstract
Mosquitoes are responsible for the transmission of numerous viruses of global health significance. The term "vector competence" describes the intrinsic ability of an arthropod vector to transmit an infectious agent. Prior to transmission, the mosquito itself presents a complex and hostile environment through which a virus must transit to ensure propagation and transmission to the next host. Viruses imbibed in an infectious blood meal must pass in and out of the mosquito midgut, traffic through the body cavity or hemocoel, invade the salivary glands, and be expelled with the saliva when the vector takes a subsequent blood meal. Viruses encounter physical, cellular, microbial, and immunological barriers, which are influenced by the genetic background of the mosquito vector as well as environmental conditions. Collectively, these factors place significant selective pressure on the virus that impact its evolution and transmission. Here, we provide an overview of the current state of the field in understanding the mosquito-specific factors that underpin vector competence and how each of these mechanisms may influence virus evolution.
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Affiliation(s)
- Juliette Lewis
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Emily N. Gallichotte
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Jenna Randall
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Arielle Glass
- Department of Cellular and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Brian D. Foy
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Gregory D. Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Rebekah C. Kading
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
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3
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Damayo JE, McKee RC, Buchmann G, Norton AM, Ashe A, Remnant EJ. Virus replication in the honey bee parasite, Varroa destructor. J Virol 2023; 97:e0114923. [PMID: 37966226 PMCID: PMC10746231 DOI: 10.1128/jvi.01149-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.
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Affiliation(s)
- James E. Damayo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca C. McKee
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gabriele Buchmann
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Institute of Plant Genetics, Heinrich-Heine University, Duesseldorf, Germany
| | - Amanda M. Norton
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Academic Support Unit, Research and Advanced Instrumentation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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4
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Fitzmeyer EA, Gallichotte EN, Weger-Lucarelli J, Kapuscinski ML, Abdo Z, Pyron K, Young MC, Ebel GD. Loss of West Nile virus genetic diversity during mosquito infection due to species-dependent population bottlenecks. iScience 2023; 26:107711. [PMID: 37701570 PMCID: PMC10494182 DOI: 10.1016/j.isci.2023.107711] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
Vector competence (VC) refers to the efficiency of pathogen transmission by vectors. Each step in the infection of a mosquito vector constitutes a barrier to transmission that may impose bottlenecks on virus populations. West Nile virus (WNV) is maintained by multiple mosquito species with varying VC. However, the extent to which bottlenecks and VC are linked is poorly understood. Similarly, quantitative analyses of mosquito-imposed bottlenecks on virus populations are limited. We used molecularly barcoded WNV to quantify tissue-associated population bottlenecks in three variably competent WNV vectors. Our results confirm strong population bottlenecks during mosquito infection that are capable of dramatically reshaping virus population structure in a non-selective manner. In addition, we found that mosquitoes with differing VC uniquely shape WNV population structure: highly competent vectors are more likely to contribute to the maintenance of rare viral genotypes. These findings have important implications for arbovirus emergence and evolution.
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Affiliation(s)
- Emily A. Fitzmeyer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Emily N. Gallichotte
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Marylee L. Kapuscinski
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kyra Pyron
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Michael C. Young
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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5
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Caldwell HS, Kuo L, Pata JD, Dupuis AP, Arnold JJ, Yeager C, Stout J, Koetzner CA, Payne AF, Bialosuknia SM, Banker EM, Nolen TA, Cameron CE, Ciota AT. Maintenance of a host-specific minority mutation in the West Nile virus NS3. iScience 2023; 26:107468. [PMID: 37593454 PMCID: PMC10428113 DOI: 10.1016/j.isci.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
West Nile virus (WNV), the most prevalent arthropod-borne virus (arbovirus) in the United States, is maintained in a cycle between Culex spp. mosquitoes and birds. Arboviruses exist within hosts and vectors as a diverse set of closely related genotypes. In theory, this genetic diversity can facilitate adaptation to distinct environments during host cycling, yet host-specific fitness of minority genotypes has not been assessed. Utilizing WNV deep-sequencing data, we previously identified a naturally occurring, mosquito-biased substitution, NS3 P319L. Using both cell culture and experimental infection in natural hosts, we demonstrated that this substitution confers attenuation in vertebrate hosts and increased transmissibility by mosquitoes. Biochemical assays demonstrated temperature-sensitive ATPase activity consistent with host-specific phenotypes. Together these data confirm the maintenance of host-specific minority variants in arbovirus mutant swarms, suggest a unique role for NS3 in viral fitness, and demonstrate that intrahost sequence data can inform mechanisms of host-specific adaptation.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
| | - Lili Kuo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alan P. Dupuis
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Calvin Yeager
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jessica Stout
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Cheri A. Koetzner
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Anne F. Payne
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Sean M. Bialosuknia
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Elyse M. Banker
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Taylor A. Nolen
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
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6
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Viljakainen L, Fürst MA, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. Antiviral immune response reveals host-specific virus infections in natural ant populations. Front Microbiol 2023; 14:1119002. [PMID: 37007485 PMCID: PMC10060816 DOI: 10.3389/fmicb.2023.1119002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.
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Affiliation(s)
- Lumi Viljakainen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- *Correspondence: Lumi Viljakainen,
| | - Matthias A. Fürst
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Anna V. Grasse
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jaana Jurvansuu
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jinook Oh
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lassi Tolonen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Thomas Eder
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
| | - Sylvia Cremer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Sylvia Cremer,
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7
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Cable J, Denison MR, Kielian M, Jackson WT, Bartenschlager R, Ahola T, Mukhopadhyay S, Fremont DH, Kuhn RJ, Shannon A, Frazier MN, Yuen KY, Coyne CB, Wolthers KC, Ming GL, Guenther CS, Moshiri J, Best SM, Schoggins JW, Jurado KA, Ebel GD, Schäfer A, Ng LFP, Kikkert M, Sette A, Harris E, Wing PAC, Eggenberger J, Krishnamurthy SR, Mah MG, Meganck RM, Chung D, Maurer-Stroh S, Andino R, Korber B, Perlman S, Shi PY, Bárcena M, Aicher SM, Vu MN, Kenney DJ, Lindenbach BD, Nishida Y, Rénia L, Williams EP. Positive-strand RNA viruses-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1521:46-66. [PMID: 36697369 PMCID: PMC10347887 DOI: 10.1111/nyas.14957] [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] [Indexed: 01/27/2023]
Abstract
Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.
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Affiliation(s)
| | - Mark R Denison
- Department of Pediatrics and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; and Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - William T Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University and German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg, Germany
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | | | - Daved H Fremont
- Department of Pathology & Immunology; Department of Molecular Microbiology; and Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix Marseille Université, Marseille, France
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, People's Republic of China
| | - Carolyn B Coyne
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Katja C Wolthers
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jasmine Moshiri
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory D Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lisa F P Ng
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Peter A C Wing
- Nuffield Department of Medicine and Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology and NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcus G Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore City, Singapore
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Donghoon Chung
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas, USA
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore City, Singapore
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sophie-Marie Aicher
- Institut Pasteurgrid, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Devin J Kenney
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yukiko Nishida
- Chugai Pharmaceutical, Co., Tokyo, Japan
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Laurent Rénia
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
| | - Evan P Williams
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
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8
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Vector Competence of German Aedes punctor (Kirby, 1837) for West Nile Virus Lineages 1 and 2. Viruses 2022; 14:v14122787. [PMID: 36560791 PMCID: PMC9787774 DOI: 10.3390/v14122787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
West Nile virus (WNV) is a zoonotic flavivirus transmitted by mosquitoes as a biological vector. Because of its biting behavior, the widespread snow-melt mosquito Aedes punctor could be a potential bridge vector for WNV to humans and nonhuman mammals. However, little is known on its role in transmission of WNV. The aim of this study was to determine the vector competence of German Ae. punctor for WNV lineages 1 and 2. Field-collected larvae and pupae were reared to adults and offered infectious blood containing either an Italian WNV lineage 1 or a German WNV lineage 2 strain via cotton stick feeding. Engorged females were incubated for 14/15 or 21 days at 18 °C. After incubation; surviving mosquitoes were dissected and forced to salivate. Mosquito bodies with abdomens, thoraces and heads, legs plus wings and saliva samples were investigated for WNV RNA by RT-qPCR. Altogether, 2/70 (2.86%) and 5/85 (5.88%) mosquito bodies were found infected with WNV lineage 1 or 2, respectively. In two mosquitoes, viral RNA was also detected in legs and wings. No saliva sample contained viral RNA. Based on these results, we conclude that Ae. punctor does not play an important role in WNV transmission in Germany.
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9
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Cárdenas P, Corredor V, Santos-Vega M. Genomic epidemiological models describe pathogen evolution across fitness valleys. SCIENCE ADVANCES 2022; 8:eabo0173. [PMID: 35857510 PMCID: PMC9278859 DOI: 10.1126/sciadv.abo0173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Genomics is fundamentally changing epidemiological research. However, systematically exploring hypotheses in pathogen evolution requires new modeling tools. Models intertwining pathogen epidemiology and genomic evolution can help understand processes such as the emergence of novel pathogen genotypes with higher transmissibility or resistance to treatment. In this work, we present Opqua, a flexible simulation framework that explicitly links epidemiology to sequence evolution and selection. We use Opqua to study determinants of evolution across fitness valleys. We confirm that competition can limit evolution in high-transmission environments and find that low transmission, host mobility, and complex pathogen life cycles facilitate reaching new adaptive peaks through population bottlenecks and decoupling of selective pressures. The results show the potential of genomic epidemiological modeling as a tool in infectious disease research.
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Affiliation(s)
- Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Mauricio Santos-Vega
- Grupo Biología Matemática y Computacional, Departamento Ingeniería Biomédica, Universidad de los Andes, Bogotá, D.C., Colombia
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10
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Henderson C, Brustolin M, Hegde S, Dayama G, Lau N, Hughes GL, Bergey C, Rasgon JL. Transcriptomic and small RNA response to Mayaro virus infection in Anopheles stephensi mosquitoes. PLoS Negl Trop Dis 2022; 16:e0010507. [PMID: 35763539 PMCID: PMC9273063 DOI: 10.1371/journal.pntd.0010507] [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: 08/19/2021] [Revised: 07/11/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Mayaro virus (MAYV) is an arboviral pathogen in the genus Alphavirus that is circulating in South America with potential to spread to naïve regions. MAYV is also one of the few viruses with the ability to be transmitted by mosquitoes in the genus Anopheles, as well as the typical arboviral transmitting mosquitoes in the genus Aedes. Few studies have investigated the infection response of Anopheles mosquitoes. In this study we detail the transcriptomic and small RNA responses of An. stephensi to infection with MAYV via infectious bloodmeal at 2, 7, and 14 days post infection (dpi). 487 unique transcripts were significantly regulated, 78 putative novel miRNAs were identified, and an siRNA response is observed targeting the MAYV genome. Gene ontology analysis of transcripts regulated at each timepoint shows a number of proteases regulated at 2 and 7 dpi, potentially representative of Toll or melanization pathway activation, and repression of pathways related to autophagy and apoptosis at 14 dpi. These findings provide a basic understanding of the infection response of An. stephensi to MAYV and help to identify host factors which might be useful to target to inhibit viral replication in Anopheles mosquitoes. Mayaro virus (MAYV) is a mosquito-borne Alphavirus responsible for outbreaks in South America and the Caribbean. In this study we infected Anopheles stephensi with MAYV and sequenced mRNA and small RNA to understand how MAYV infection impacts gene transcription and the expression of small RNAs in the mosquito vector. Genes involved with innate immunity and signaling pathways related to cell death are regulated in response to MAYV infection of An. stephensi, we also discovered novel miRNAs and describe the expression patterns of miRNAs, siRNAs, and piRNAs following bloodmeal ingestion. These results suggest that MAYV does induce a molecular response to infection in its mosquito vector species.
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Affiliation(s)
- Cory Henderson
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Marco Brustolin
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Shivanand Hegde
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Gargi Dayama
- School of Medicine, Boston University, Boston, Massachusetts, United States of America
| | - Nelson Lau
- School of Medicine, Boston University, Boston, Massachusetts, United States of America
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Christina Bergey
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Jason L. Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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11
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Bifani AM, Siriphanitchakorn T, Choy MM. Intra-Host Diversity of Dengue Virus in Mosquito Vectors. Front Cell Infect Microbiol 2022; 12:888804. [PMID: 35811685 PMCID: PMC9256930 DOI: 10.3389/fcimb.2022.888804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Dengue virus (DENV) is the most common arbovirus, causing a significant burden on both the economy and global healthcare systems. The virus is transmitted by Aedes species of mosquitoes as a swarm of closely related virus genomes, collectively referred to as a quasispecies. The level of genomic diversity within this quasispecies varies as DENV moves through various ecological niches within its transmission cycle. Here, the factors that influence the level of DENV quasispecies diversity during the course of infection in the mosquito vectors are reviewed.
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12
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Comparison of Endemic and Epidemic Vesicular Stomatitis Virus Lineages in Culicoides sonorensis Midges. Viruses 2022; 14:v14061221. [PMID: 35746691 PMCID: PMC9230599 DOI: 10.3390/v14061221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
Abstract
Vesicular stomatitis virus (VSV) primarily infects livestock and is transmitted by direct contact and vectored by Culicoides midges (Diptera: Ceratopogonidae). Endemic to Central and South America, specific VSV lineages spread northward out of endemic regions of Mexico and into the U.S. sporadically every five to ten years. In 2012, a monophyletic epidemic lineage 1.1 successfully spread northward into the U.S. In contrast, the closest endemic ancestor, lineage 1.2, remained circulating exclusively in endemic regions in Mexico. It is not clear what roles virus-animal interactions and/or virus-vector interactions play in the ability of specific viral lineages to escape endemic regions in Mexico and successfully cause outbreaks in the U.S., nor the genetic basis for such incursions. Whole-genome sequencing of epidemic VSV 1.1 and endemic VSV 1.2 revealed significant differences in just seven amino acids. Previous studies in swine showed that VSV 1.1 was more virulent than VSV 1.2. Here, we compared the efficiency of these two viral lineages to infect the vector Culicoides sonorensis (Wirth and Jones) and disseminate to salivary glands for subsequent transmission. Our results showed that midges orally infected with the epidemic VSV 1.1 lineage had significantly higher infection dissemination rates compared to those infected with the endemic VSV 1.2 lineage. Thus, in addition to affecting virus-animal interactions, as seen with higher virulence in pigs, small genetic changes may also affect virus-vector interactions, contributing to the ability of specific viral lineages to escape endemic regions via vector-borne transmission.
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13
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Vector-Borne Viral Diseases as a Current Threat for Human and Animal Health—One Health Perspective. J Clin Med 2022; 11:jcm11113026. [PMID: 35683413 PMCID: PMC9181581 DOI: 10.3390/jcm11113026] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022] Open
Abstract
Over the last decades, an increase in the emergence or re-emergence of arthropod-borne viruses has been observed in many regions. Viruses such as dengue, yellow fever, or zika are a threat for millions of people on different continents. On the other hand, some arboviruses are still described as endemic, however, they could become more important in the near future. Additionally, there is a group of arboviruses that, although important for animal breeding, are not a direct threat for human health. Those include, e.g., Schmallenberg, bluetongue, or African swine fever viruses. This review focuses on arboviruses and their major vectors: mosquitoes, ticks, biting midges, and sandflies. We discuss the current knowledge on arbovirus transmission, ecology, and methods of prevention. As arboviruses are a challenge to both human and animal health, successful prevention and control are therefore only possible through a One Health perspective.
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14
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Colmant AMG, Furlong MJ, Etebari K. Discovery of a Novel Jingmenvirus in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2022; 14:v14061140. [PMID: 35746612 PMCID: PMC9229714 DOI: 10.3390/v14061140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 02/07/2023] Open
Abstract
In Australia, soldier flies are major pests of sugarcane, and they can cause significant yield losses in some areas, possibly due to the virus’ transmission to the plants. We sequenced fly larvae salivary glands and identified a novel jingmenvirus, putatively named Inopus flavus jingmenvirus 1 (IFJV1). Phylogenetic trees confirmed that IFJV1 groups with insect-associated jingmenviruses, newly identified flavivirus-like viruses with a segmented genome. After the design and the validation of molecular detection systems for IFJV1, larval homogenates were passaged on insect and vertebrate cells, but IFJV1 could only be detected in the first two passages in insect cells and not at all in vertebrate cells. Despite this lack of consistent replication in laboratory models, this virus does replicate in its host Inopus flavus, as sequenced, small RNA from the larvae matched the IFJV1 sequences. Moreover, they were found to be predominantly 21 nucleotides long and map to the whole sequences on both strands, which is typical of an actively replicating virus. This discovery confirms the worldwide presence of jingmenviruses which, until now, had only been detected on four continents. However, the study of IFJV1 tropism and the possible pathogenicity to its host or the sugarcane it parasitizes requires the development of a stable replication model.
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Affiliation(s)
- Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), 13005 Marseille, France;
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J. Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (M.J.F.); (K.E.)
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (M.J.F.); (K.E.)
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15
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Caldwell HS, Pata JD, Ciota AT. The Role of the Flavivirus Replicase in Viral Diversity and Adaptation. Viruses 2022; 14:1076. [PMID: 35632818 PMCID: PMC9143365 DOI: 10.3390/v14051076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses readily alternate and adapt to different hosts and environments. Here, we review a subset of the different aspects of flaviviral biology which impact host switching and viral fitness. These include the mechanism of replication and structural biology of the NS3 and NS5 proteins, which reproduce the viral genome; rates of mutation resulting from this replication and the role of mutational frequency in viral fitness; and the theory of quasispecies evolution and how it contributes to our understanding of genetic and phenotypic plasticity.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
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16
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Mongelli V, Lequime S, Kousathanas A, Gausson V, Blanc H, Nigg J, Quintana-Murci L, Elena SF, Saleh MC. Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster. Nat Ecol Evol 2022; 6:565-578. [PMID: 35273366 PMCID: PMC7612704 DOI: 10.1038/s41559-022-01697-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 02/05/2023]
Abstract
Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen-sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV and the virus was serially passaged ten times via reinfection in naive flies. Viral population diversity was studied after each viral passage by high-throughput sequencing and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole and not specific antiviral defence pathways in isolation, generally constrains viral diversity and evolution.
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Affiliation(s)
- Vanesa Mongelli
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | | | - Valérie Gausson
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Hervé Blanc
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Jared Nigg
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetic Unit, Institut Pasteur, CNRS, Paris, France
- Human Genomics and Evolution, Collège de France, Paris, France
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), València, Spain.
- The Santa Fe Institute, Santa Fe, NM, USA.
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France.
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17
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Kopanke J, Carpenter M, Lee J, Reed K, Rodgers C, Burton M, Lovett K, Westrich JA, McNulty E, McDermott E, Barbera C, Cavany S, Rohr JR, Perkins TA, Mathiason CK, Stenglein M, Mayo C. Bluetongue Research at a Crossroads: Modern Genomics Tools Can Pave the Way to New Insights. Annu Rev Anim Biosci 2022; 10:303-324. [PMID: 35167317 DOI: 10.1146/annurev-animal-051721-023724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bluetongue virus (BTV) is an arthropod-borne, segmented double-stranded RNA virus that can cause severe disease in both wild and domestic ruminants. BTV evolves via several key mechanisms, including the accumulation of mutations over time and the reassortment of genome segments.Additionally, BTV must maintain fitness in two disparate hosts, the insect vector and the ruminant. The specific features of viral adaptation in each host that permit host-switching are poorly characterized. Limited field studies and experimental work have alluded to the presence of these phenomena at work, but our understanding of the factors that drive or constrain BTV's genetic diversification remains incomplete. Current research leveraging novel approaches and whole genome sequencing applications promises to improve our understanding of BTV's evolution, ultimately contributing to the development of better predictive models and management strategies to reduce future impacts of bluetongue epizootics.
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Affiliation(s)
- Jennifer Kopanke
- Office of the Campus Veterinarian, Washington State University, Spokane, Washington, USA;
| | - Molly Carpenter
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Justin Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;
| | - Kirsten Reed
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Case Rodgers
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mollie Burton
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Kierra Lovett
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Joseph A Westrich
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Erin McNulty
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Emily McDermott
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Carly Barbera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Candace K Mathiason
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
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18
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Öhlund P, Hayer J, Hesson JC, Blomström AL. Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line. Viruses 2021; 13:v13112181. [PMID: 34834988 PMCID: PMC8620693 DOI: 10.3390/v13112181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022] Open
Abstract
RNA interference (RNAi)-mediated antiviral immunity is believed to be the primary defense against viral infection in mosquitoes. The production of virus-specific small RNA has been demonstrated in mosquitoes and mosquito-derived cell lines for viruses in all of the major arbovirus families. However, many if not all mosquitoes are infected with a group of viruses known as insect-specific viruses (ISVs), and little is known about the mosquito immune response to this group of viruses. Therefore, in this study, we sequenced small RNA from an Aedes albopictus-derived cell line infected with either Lammi virus (LamV) or Hanko virus (HakV). These viruses belong to two distinct phylogenetic groups of insect-specific flaviviruses (ISFVs). The results revealed that both viruses elicited a strong virus-derived small interfering RNA (vsiRNA) response that increased over time and that targeted the whole viral genome, with a few predominant hotspots observed. Furthermore, only the LamV-infected cells produced virus-derived Piwi-like RNAs (vpiRNAs); however, they were mainly derived from the antisense genome and did not show the typical ping-pong signatures. HakV, which is more distantly related to the dual-host flaviviruses than LamV, may lack certain unknown sequence elements or structures required for vpiRNA production. Our findings increase the understanding of mosquito innate immunity and ISFVs' effects on their host.
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Affiliation(s)
- Pontus Öhlund
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P.O. Box 7028, 750 07 Uppsala, Sweden;
- Correspondence: ; Tel.: +46-18-672-409
| | - Juliette Hayer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre, P.O. Box 7023, 750 07 Uppsala, Sweden;
| | - Jenny C. Hesson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, P.O. Box 582, 751 23 Uppsala, Sweden;
| | - Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P.O. Box 7028, 750 07 Uppsala, Sweden;
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19
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An Aedes aegypti-Derived Ago2 Knockout Cell Line to Investigate Arbovirus Infections. Viruses 2021; 13:v13061066. [PMID: 34205194 PMCID: PMC8227176 DOI: 10.3390/v13061066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/19/2021] [Accepted: 05/30/2021] [Indexed: 11/19/2022] Open
Abstract
Mosquitoes are known as important vectors of many arthropod-borne (arbo)viruses causing disease in humans. These include dengue (DENV) and Zika (ZIKV) viruses. The exogenous small interfering (si)RNA (exo-siRNA) pathway is believed to be the main antiviral defense in arthropods, including mosquitoes. During infection, double-stranded RNAs that form during viral replication and infection are cleaved by the enzyme Dicer 2 (Dcr2) into virus-specific 21 nt vsiRNAs, which are subsequently loaded into Argonaute 2 (Ago2). Ago2 then targets and subsequently cleaves complementary RNA sequences, resulting in degradation of the target viral RNA. Although various studies using silencing approaches have supported the antiviral activity of the exo-siRNA pathway in mosquitoes, and despite strong similarities between the siRNA pathway in the Drosophila melanogaster model and mosquitoes, important questions remain unanswered. The antiviral activity of Ago2 against different arboviruses has been previously demonstrated. However, silencing of Ago2 had no effect on ZIKV replication, whereas Dcr2 knockout enhanced its replication. These findings raise the question as to the role of Ago2 and Dcr2 in the control of arboviruses from different viral families in mosquitoes. Using a newly established Ago2 knockout cell line, alongside the previously reported Dcr2 knockout cell line, we investigated the impact these proteins have on the modulation of different arboviral infections. Infection of Ago2 knockout cell line with alpha- and bunyaviruses resulted in an increase of viral replication, but not in the case of ZIKV. Analysis of small RNA sequencing data in the Ago2 knockout cells revealed a lack of methylated siRNAs from different sources, such as acute and persistently infecting viruses-, TE- and transcriptome-derived RNAs. The results confirmed the importance of the exo-siRNA pathway in the defense against arboviruses, but highlights variability in its response to different viruses and the impact the siRNA pathway proteins have in controlling viral replication. Moreover, this established Ago2 knockout cell line can be used for functional Ago2 studies, as well as research on the interplay between the RNAi pathways.
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20
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Trammell CE, Goodman AG. Host Factors That Control Mosquito-Borne Viral Infections in Humans and Their Vector. Viruses 2021; 13:748. [PMID: 33923307 PMCID: PMC8145797 DOI: 10.3390/v13050748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Mosquito-borne viral infections are responsible for a significant degree of morbidity and mortality across the globe due to the severe diseases these infections cause, and they continue to increase each year. These viruses are dependent on the mosquito vector as the primary means of transmission to new vertebrate hosts including avian, livestock, and human populations. Due to the dynamic host environments that mosquito-borne viruses pass through as they are transmitted between vector and vertebrate hosts, there are various host factors that control the response to infection over the course of the pathogen's life cycle. In this review, we discuss these host factors that are present in either vector or vertebrate models during infection, how they vary or are conserved between hosts, and their implications in future research pertaining to disease prevention and treatment.
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Affiliation(s)
- Chasity E. Trammell
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA;
- NIH Protein Biotechnology Training Program, Washington State University, Pullman, WA 99164-6240, USA
| | - Alan G. Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA;
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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21
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Pontremoli C, Forni D, Clerici M, Cagliani R, Sironi M. Alternation between taxonomically divergent hosts is not the major determinant of flavivirus evolution. Virus Evol 2021; 7:veab040. [PMID: 33976907 PMCID: PMC8093920 DOI: 10.1093/ve/veab040] [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] [Indexed: 01/21/2023] Open
Abstract
Flaviviruses display diverse epidemiological and ecological features. Tick-borne and mosquito-borne flaviviruses (TBFV and MBFV, respectively) are important human pathogens that alternate replication in invertebrate vectors and vertebrate hosts. The Flavivirus genus also includes insect-specific viruses (ISFVs) and viruses with unknown invertebrate hosts. It is generally accepted that viruses that alternate between taxonomically different hosts evolve slowly and that the evolution of MBFVs and TBFVs is dominated by strong constraints, with limited episodes of positive selection. We exploited the availability of flavivirus genomes to test these hypotheses and to compare their rates and patterns of evolution. We estimated the substitution rates of CFAV and CxFV (two ISFVs) and, by taking into account the time-frame of measurement, compared them with those of other flaviviruses. Results indicated that CFAV and CxFV display relatively different substitution rates. However, these data, together with estimates for single-host members of the Flaviviridae family, indicated that MBFVs do not display relatively slower evolution. Conversely, TBFVs displayed some of lowest substitution rates among flaviviruses. Analysis of selective patterns over longer evolutionary time-frames confirmed that MBFVs evolve under strong purifying selection. Interestingly, TBFVs and ISFVs did not show extremely different levels of constraint, although TBFVs alternate among hosts, whereas ISFVs do not. Additional results showed that episodic positive selection drove the evolution of MBFVs, despite their high constraint. Positive selection was also detected on two branches of the TBFVs phylogeny that define the seabird clade. Thus, positive selection was much more common during the evolution of arthropod-borne flaviviruses than previously thought. Overall, our data indicate that flavivirus evolutionary patterns are complex and most likely determined by multiple factors, not limited to the alternation between taxonomically divergent hosts. The frequency of both positive and purifying selection, especially in MBFVs, suggests that a minority of sites in the viral polyprotein experience weak constraint and can evolve to generate new viral phenotypes and possibly promote adaptation to new hosts.
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Affiliation(s)
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan 20122, Italy,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan 20121, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
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22
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Saiz JC, Martín-Acebes MA, Blázquez AB, Escribano-Romero E, Poderoso T, Jiménez de Oya N. Pathogenicity and virulence of West Nile virus revisited eight decades after its first isolation. Virulence 2021; 12:1145-1173. [PMID: 33843445 PMCID: PMC8043182 DOI: 10.1080/21505594.2021.1908740] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
West Nile virus (WNV) is a flavivirus which transmission cycle is maintained between mosquitoes and birds, although it occasionally causes sporadic outbreaks in horses and humans that can result in serious diseases and even death. Since its first isolation in Africa in 1937, WNV had been considered a neglected pathogen until its recent spread throughout Europe and the colonization of America, regions where it continues to cause outbreaks with severe neurological consequences in humans and horses. Although our knowledge about the characteristics and consequences of the virus has increased enormously lately, many questions remain to be resolved. Here, we thoroughly update our knowledge of different aspects of the WNV life cycle: virology and molecular classification, host cell interactions, transmission dynamics, host range, epidemiology and surveillance, immune response, clinical presentations, pathogenesis, diagnosis, prophylaxis (antivirals and vaccines), and prevention, and we highlight those aspects that are still unknown and that undoubtedly require further investigation.
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Affiliation(s)
- Juan-Carlos Saiz
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Miguel A Martín-Acebes
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Ana B Blázquez
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Estela Escribano-Romero
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Teresa Poderoso
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nereida Jiménez de Oya
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
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23
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Tikhe CV, Dimopoulos G. Mosquito antiviral immune pathways. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103964. [PMID: 33301792 DOI: 10.1016/j.dci.2020.103964] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Mosquitoes are vectors of a large number of viral pathogens. In recent years, increased urbanization and climate change has expanded the range of many vector mosquitoes. The lack of effective medical interventions has made the control of mosquito-borne viral diseases very difficult. Understanding the interactions between the mosquito immune system and viruses is critical if we are to develop effective control strategies against these diseases. Mosquitoes harbor multiple conserved immune pathways that curb invading viral pathogens. Despite the conservation of these pathways, the activation and intensity of the mosquito immune response varies with the mosquito species, tissue, and the infecting virus. This article reviews major conserved antiviral immune pathways in vector mosquitoes, their interactions with invading viral pathogens, and how these interactions restrict or promote infection of these medically important viruses.
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Affiliation(s)
- Chinmay V Tikhe
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States; Johns Hopkins Malaria Research Institute, United States.
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States; Johns Hopkins Malaria Research Institute, United States.
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24
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Scroggs SLP, Gass JT, Chinnasamy R, Widen SG, Azar SR, Rossi SL, Arterburn JB, Vasilakis N, Hanley KA. Evolution of resistance to fluoroquinolones by dengue virus serotype 4 provides insight into mechanism of action and consequences for viral fitness. Virology 2021; 552:94-106. [PMID: 33120225 PMCID: PMC7528753 DOI: 10.1016/j.virol.2020.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/30/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
Drugs against flaviviruses such as dengue (DENV) and Zika (ZIKV) virus are urgently needed. We previously demonstrated that three fluoroquinolones, ciprofloxacin, enoxacin, and difloxacin, suppress replication of six flaviviruses. To investigate the barrier to resistance and mechanism(s) of action of these drugs, DENV-4 was passaged in triplicate in HEK-293 cells in the presence or absence of each drug. Resistance to ciprofloxacin was detected by the seventh passage and to difloxacin by the tenth, whereas resistance to enoxacin did not occur within ten passages. Two putative resistance-conferring mutations were detected in the envelope gene of ciprofloxacin and difloxacin-resistant DENV-4. In the absence of ciprofloxacin, ciprofloxacin-resistant viruses sustained a significantly higher viral titer than control viruses in HEK-293 and HuH-7 cells and resistant viruses were more stable than control viruses at 37 °C. These results suggest that the mechanism of action of ciprofloxacin and difloxacin involves interference with virus binding or entry.
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Affiliation(s)
- Stacey L P Scroggs
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - Jordan T Gass
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Ramesh Chinnasamy
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Steven G Widen
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Sasha R Azar
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Shannan L Rossi
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Jeffrey B Arterburn
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Nikos Vasilakis
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA; Center for Biodefense and Emerging Infectious Diseases, The University of University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, The University of University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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25
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Núñez AI, Esteve-Codina A, Gómez-Garrido J, Brustolin M, Talavera S, Berdugo M, Dabad M, Alioto T, Bensaid A, Busquets N. Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure. PLoS Negl Trop Dis 2020; 14:e0008870. [PMID: 33301456 PMCID: PMC7755283 DOI: 10.1371/journal.pntd.0008870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 12/22/2020] [Accepted: 10/10/2020] [Indexed: 01/02/2023] Open
Abstract
Rift Valley fever phlebovirus (RVFV) causes an emerging zoonotic disease and is mainly transmitted by Culex and Aedes mosquitoes. While Aedes aegypti-dengue virus (DENV) is the most studied model, less is known about the genes involved in infection-responses in other mosquito-arboviruses pairing. The main objective was to investigate the molecular responses of Cx. pipiens to RVFV exposure focusing mainly on genes implicated in innate immune responses. Mosquitoes were fed with blood spiked with RVFV. The fully-engorged females were pooled at 3 different time points: 2 hours post-exposure (hpe), 3- and 14-days post-exposure (dpe). Pools of mosquitoes fed with non-infected blood were also collected for comparisons. Total RNA from each mosquito pool was subjected to RNA-seq analysis and a de novo transcriptome was constructed. A total of 451 differentially expressed genes (DEG) were identified. Most of the transcriptomic alterations were found at an early infection stage after RVFV exposure. Forty-eight DEG related to immune infection-response were characterized. Most of them were related with the RNAi system, Toll and IMD pathways, ubiquitination pathway and apoptosis. Our findings provide for the first time a comprehensive view on Cx. pipiens-RVFV interactions at the molecular level. The early depletion of RNAi pathway genes at the onset of the RVFV infection would allow viral replication in mosquitoes. While genes from the Toll and IMD immune pathways were altered in response to RVFV none of the DEG were related to the JAK/STAT pathway. The fact that most of the DEG involved in the Ubiquitin-proteasome pathway (UPP) or apoptosis were found at an early stage of infection would suggest that apoptosis plays a regulatory role in infected Cx. pipiens midguts. This study provides a number of target genes that could be used to identify new molecular targets for vector control.
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Affiliation(s)
- Ana I. Núñez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marco Brustolin
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sandra Talavera
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Miguel Berdugo
- Instituto de Biología Evolutiva, Universitat Pompeu i Fabra-CSIC, Dr. Aigüader 88, Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu i Fabra (UPF), Barcelona, Catalonia, Spain
| | - Albert Bensaid
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Núria Busquets
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
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26
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The Genetic Diversification of a Single Bluetongue Virus Strain Using an In Vitro Model of Alternating-Host Transmission. Viruses 2020; 12:v12091038. [PMID: 32961886 PMCID: PMC7551957 DOI: 10.3390/v12091038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Bluetongue virus (BTV) is an arbovirus that has been associated with dramatic epizootics in both wild and domestic ruminants in recent decades. As a segmented, double-stranded RNA virus, BTV can evolve via several mechanisms due to its genomic structure. However, the effect of BTV’s alternating-host transmission cycle on the virus’s genetic diversification remains poorly understood. Whole genome sequencing approaches offer a platform for investigating the effect of host-alternation across all ten segments of BTV’s genome. To understand the role of alternating hosts in BTV’s genetic diversification, a field isolate was passaged under three different conditions: (i) serial passages in Culicoides sonorensis cells, (ii) serial passages in bovine pulmonary artery endothelial cells, or (iii) alternating passages between insect and bovine cells. Aliquots of virus were sequenced, and single nucleotide variants were identified. Measures of viral population genetics were used to quantify the genetic diversification that occurred. Two consensus variants in segments 5 and 10 occurred in virus from all three conditions. While variants arose across all passages, measures of genetic diversity remained largely similar across cell culture conditions. Despite passage in a relaxed in vitro system, we found that this BTV isolate exhibited genetic stability across passages and conditions. Our findings underscore the valuable role that whole genome sequencing may play in improving understanding of viral evolution and highlight the genetic stability of BTV.
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27
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Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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28
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Ko HY, Salem GM, Chang GJJ, Chao DY. Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology. Front Microbiol 2020; 11:1371. [PMID: 32636827 PMCID: PMC7318875 DOI: 10.3389/fmicb.2020.01371] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue viral (DENV) infection results in a wide spectrum of clinical manifestations from asymptomatic, mild fever to severe hemorrhage diseases upon infection. Severe dengue is the leading cause of pediatric deaths and/or hospitalizations, which are a major public health burden in dengue-endemic or hyperendemic countries. Like other RNA viruses, DENV continues to evolve. Adaptive mutations are obscured by the major consensus sequence (so-called wild-type sequences) and can only be identified once they become the dominant viruses in the virus population, a process that can take months or years. Traditional surveillance systems still rely on Sanger consensus sequencing. However, with the recent advancement of high-throughput next-generation sequencing (NGS) technologies, the genome-wide investigation of virus population within-host and between-hosts becomes achievable. Thus, viral population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of viral genomics at the molecular level. This review focuses on the studies within the recent decade utilizing NGS in different experimental and epidemiological settings to understand how the adaptive evolution of dengue variants shapes the dengue epidemic and disease severity through its transmission. We propose three types of studies that can be pursued in the future to enhance our surveillance for epidemic prediction and better medical management.
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Affiliation(s)
- Hui-Ying Ko
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gwong-Jen J Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
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29
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Patterson EI, Khanipov K, Swetnam DM, Walsdorf S, Kautz TF, Thangamani S, Fofanov Y, Forrester NL. Measuring Alphavirus Fidelity Using Non-Infectious Virus Particles. Viruses 2020; 12:v12050546. [PMID: 32429270 PMCID: PMC7291308 DOI: 10.3390/v12050546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 01/17/2023] Open
Abstract
Mutations are incorporated into the genomes of RNA viruses at an optimal frequency and altering this precise frequency has been proposed as a strategy to create live-attenuated vaccines. However, determining the effect of specific mutations that alter fidelity has been difficult because of the rapid selection of the virus population during replication. By deleting residues of the structural polyprotein PE2 cleavage site, E3Δ56-59, in Venezuelan equine encephalitis virus (VEEV) TC-83 vaccine strain, non-infectious virus particles were used to assess the effect of single mutations on mutation frequency without the interference of selection that results from multiple replication cycles. Next-generation sequencing analysis revealed a significantly lower frequency of transversion mutations and overall mutation frequency for the fidelity mutants compared to VEEV TC-83 E3Δ56-59. We demonstrate that deletion of the PE2 cleavage site halts virus infection while making the virus particles available for downstream sequencing. The conservation of the site will allow the evaluation of suspected fidelity mutants across alphaviruses of medical importance.
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Affiliation(s)
- Edward I. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Correspondence:
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; (K.K.); (Y.F.)
| | - Daniele M. Swetnam
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA;
| | - Samantha Walsdorf
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
| | - Tiffany F. Kautz
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Saravanan Thangamani
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; (K.K.); (Y.F.)
| | - Naomi L. Forrester
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
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30
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McMenamin AJ, Daughenbaugh KF, Flenniken ML. The Heat Shock Response in the Western Honey Bee (Apis mellifera) is Antiviral. Viruses 2020; 12:E245. [PMID: 32098425 PMCID: PMC7077298 DOI: 10.3390/v12020245] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022] Open
Abstract
Honey bees (Apismellifera) are an agriculturally important pollinator species that live in easily managed social groups (i.e., colonies). Unfortunately, annual losses of honey bee colonies in many parts of the world have reached unsustainable levels. Multiple abiotic and biotic stressors, including viruses, are associated with individual honey bee and colony mortality. Honey bees have evolved several antiviral defense mechanisms including conserved immune pathways (e.g., Toll, Imd, JAK/STAT) and dsRNA-triggered responses including RNA interference and a non-sequence specific dsRNA-mediated response. In addition, transcriptome analyses of virus-infected honey bees implicate an antiviral role of stress response pathways, including the heat shock response. Herein, we demonstrate that the heat shock response is antiviral in honey bees. Specifically, heat-shocked honey bees (i.e., 42 °C for 4 h) had reduced levels of the model virus, Sindbis-GFP, compared with bees maintained at a constant temperature. Virus-infection and/or heat shock resulted in differential expression of six heat shock protein encoding genes and three immune genes, many of which are positively correlated. The heat shock protein encoding and immune gene transcriptional responses observed in virus-infected bees were not completely recapitulated by administration of double stranded RNA (dsRNA), a virus-associated molecular pattern, indicating that additional virus-host interactions are involved in triggering antiviral stress response pathways.
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Affiliation(s)
- Alexander J. McMenamin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Katie F. Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Michelle L. Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
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31
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Caldwell HS, Ngo K, Pata JD, Kramer LD, Ciota AT. West Nile Virus fidelity modulates the capacity for host cycling and adaptation. J Gen Virol 2020; 101:410-419. [PMID: 32068528 DOI: 10.1099/jgv.0.001393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The fidelity of flaviviruses is thought to be tightly regulated for optimal fitness within and between hosts. West Nile virus (WNV) high-fidelity (HiFi) mutations V793I and G806R within the RNA-dependent RNA polymerase, and low-fidelity (LoFi) mutation T248I within the methyltransferase, were previously shown to attenuate infectivity and replicative fitness in Culex mosquitoes and Culex tarsalis (CXT) cells but not in mammalian cells. We hypothesized that fidelity alterations would modify adaptation and maintenance in a host-specific manner. To test this hypothesis, wild-type (WT), HiFi (V793I/G806R) and LoFi (T248I) variants were sequentially passaged eight times in avian (PDE) or mosquito cells, or alternately between the two. Initial characterization confirmed that fidelity mutants are attenuated in mosquito, but not avian, cells. Deep sequencing revealed mutations unique to both cell lines and fidelity mutants, including ENV G1378A, a mutation associated with avian cell adaptation. To characterize maintenance and adaptation, viral outputs were monitored throughout passaging and viral fitness was assessed. The results indicate that fidelity mutants can at times recover fitness during mosquito cell passage, but remain attenuated relative to WT. Despite similar initial fitness, LoFi mutants were impaired during sequential passage in avian cells. Conversely, HiFi mutants passaged in avian cells showed increased adaptation, suggesting that increased fidelity may be advantageous in avian hosts. Although some adaptation occurred with individual mutants, the output titres of fidelity mutants were on average lower and were often lost during host switching. These data confirm that arbovirus fidelity is likely fine-tuned to maximize survival in disparate hosts.
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Affiliation(s)
- Haley S Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Kiet Ngo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | - Janice D Pata
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Laura D Kramer
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Alexander T Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
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32
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An RNA Thermometer Activity of the West Nile Virus Genomic 3'-Terminal Stem-Loop Element Modulates Viral Replication Efficiency during Host Switching. Viruses 2020; 12:v12010104. [PMID: 31952291 PMCID: PMC7019923 DOI: 10.3390/v12010104] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/20/2019] [Accepted: 01/12/2020] [Indexed: 02/07/2023] Open
Abstract
The 3′-terminal stem-loop (3′SL) of the RNA genome of the flavivirus West Nile (WNV) harbors, in its stem, one of the sequence elements that are required for genome cyclization. As cyclization is a prerequisite for the initiation of viral replication, the 3′SL was proposed to act as a replication silencer. The lower part of the 3′SL is metastable and confers a structural flexibility that may regulate the switch from the linear to the circular conformation of the viral RNA. In the human system, we previously demonstrated that a cellular RNA-binding protein, AUF1 p45, destabilizes the 3′SL, exposes the cyclization sequence, and thus promotes flaviviral genome cyclization and RNA replication. By investigating mutant RNAs with increased 3′SL stabilities, we showed the specific conformation of the metastable element to be a critical determinant of the helix-destabilizing RNA chaperone activity of AUF1 p45 and of the precision and efficiency of the AUF1 p45-supported initiation of RNA replication. Studies of stability-increasing mutant WNV replicons in human and mosquito cells revealed that the cultivation temperature considerably affected the replication efficiencies of the viral RNA variants and demonstrated the silencing effect of the 3′SL to be temperature dependent. Furthermore, we identified and characterized mosquito proteins displaying similar activities as AUF1 p45. However, as the RNA remodeling activities of the mosquito proteins were found to be considerably lower than those of the human protein, a potential cell protein-mediated destabilization of the 3′SL was suggested to be less efficient in mosquito cells. In summary, our data support a model in which the 3′SL acts as an RNA thermometer that modulates flavivirus replication during host switching.
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33
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Blair CD. Deducing the Role of Virus Genome-Derived PIWI-Associated RNAs in the Mosquito-Arbovirus Arms Race. Front Genet 2019; 10:1114. [PMID: 31850054 PMCID: PMC6901949 DOI: 10.3389/fgene.2019.01114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/16/2019] [Indexed: 01/26/2023] Open
Abstract
The P-element-induced wimpy testis (PIWI)-associated RNA (piRNA) pathway is known for its role in the protection of genome integrity in the germline of Drosophila melanogaster by silencing transposable elements. The piRNAs that target transposons originate from piRNA clusters in transposon-rich regions of the Drosophila genome and are processed by three PIWI family proteins. In Aedes aegypti and Aedes albopictus mosquitoes, which are two of the most important vectors of arthropod-borne viruses (arboviruses), the number of PIWI family genes has expanded and some are expressed in somatic, as well as germline, tissues. These discoveries have led to active research to explore the possible expanded functional roles of the piRNA pathway in vector mosquitoes. Virus genome-derived piRNAs (which will be referred to as (virus name) vpiRNAs) have been demonstrated in Aedes spp. cultured cells and mosquitoes after infection by arthropod-borne alpha-, bunya-, and flaviviruses. However, although Culex quinquefasciatus also is an important arbovirus vector and has an expansion of PIWI family genes, vpiRNAs have seldom been documented in this genus after arbovirus infection. Generation of complementary DNA (cDNA) fragments from RNA genomes of alpha-, bunya-, and flaviviruses (viral-derived cDNAs, vDNAs) has been demonstrated in cultured Aedes spp. cells and mosquitoes, and endogenous viral elements (EVEs), cDNA fragments of non-retroviral RNA virus genomes, are found more abundantly in genomes of Ae. aegypti and Ae. albopictus than other vector mosquitoes. These observations have led to speculation that vDNAs are integrated into vector genomes to form EVEs, which serve as templates for the transcription of antiviral vpiRNA precursors. However, no EVEs derived from alphavirus genomes have been demonstrated in genomes of any vector mosquito. In addition, although EVEs have been shown to be a source of piRNAs, the preponderance of EVEs described in Aedes spp. vectors are more closely related to the genomes of persistently infecting insect-specific viruses than to acutely infecting arboviruses. Furthermore, the signature patterns of the “ping-pong” amplification cycle that maintains transposon-targeting piRNAs in Drosophila are also evident in alphavirus and bunyavirus vpiRNAs, but not in vpiRNAs of flaviviruses. These divergent observations have rendered deciphering the mechanism(s) of biogenesis and potential role of vpiRNAs in the mosquito–arbovirus arms race difficult, and the focus of this review will be to assemble major findings regarding vpiRNAs and antiviral immunity in the important arbovirus vectors from Aedes and Culex genera.
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Affiliation(s)
- Carol D Blair
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
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Marshall JM, Raban RR, Kandul NP, Edula JR, León TM, Akbari OS. Winning the Tug-of-War Between Effector Gene Design and Pathogen Evolution in Vector Population Replacement Strategies. Front Genet 2019; 10:1072. [PMID: 31737050 PMCID: PMC6831721 DOI: 10.3389/fgene.2019.01072] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/07/2019] [Indexed: 12/19/2022] Open
Abstract
While efforts to control malaria with available tools have stagnated, and arbovirus outbreaks persist around the globe, the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-based gene editing has provided exciting new opportunities for genetics-based strategies to control these diseases. In one such strategy, called "population replacement", mosquitoes, and other disease vectors are engineered with effector genes that render them unable to transmit pathogens. These effector genes can be linked to "gene drive" systems that can bias inheritance in their favor, providing novel opportunities to replace disease-susceptible vector populations with disease-refractory ones over the course of several generations. While promising for the control of vector-borne diseases on a wide scale, this sets up an evolutionary tug-of-war between the introduced effector genes and the pathogen. Here, we review the disease-refractory genes designed to date to target Plasmodium falciparum malaria transmitted by Anopheles gambiae, and arboviruses transmitted by Aedes aegypti, including dengue serotypes 2 and 3, chikungunya, and Zika viruses. We discuss resistance concerns for these effector genes, and genetic approaches to prevent parasite and viral escape variants. One general approach is to increase the evolutionary hurdle required for the pathogen to evolve resistance by attacking it at multiple sites in its genome and/or multiple stages of development. Another is to reduce the size of the pathogen population by other means, such as with vector control and antimalarial drugs. We discuss lessons learned from the evolution of resistance to antimalarial and antiviral drugs and implications for the management of resistance after its emergence. Finally, we discuss the target product profile for population replacement strategies for vector-borne disease control. This differs between early phase field trials and wide-scale disease control. In the latter case, the demands on effector gene efficacy are great; however, with new possibilities ushered in by CRISPR-based gene editing, and when combined with surveillance, monitoring, and rapid management of pathogen resistance, the odds are increasingly favoring effector genes in the upcoming evolutionary tug-of-war.
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Affiliation(s)
- John M. Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, United States
- Innovative Genomics Institute, Berkeley, CA, United States
| | - Robyn R. Raban
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
| | - Nikolay P. Kandul
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
| | - Jyotheeswara R. Edula
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
| | - Tomás M. León
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, United States
| | - Omar S. Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
- Tata Institute for Genetics and Society, University of California, San Diego, CA, United States
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Duggal NK, Langwig KE, Ebel GD, Brault AC. On the Fly: Interactions Between Birds, Mosquitoes, and Environment That Have Molded West Nile Virus Genomic Structure Over Two Decades. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:1467-1474. [PMID: 31549720 PMCID: PMC7182917 DOI: 10.1093/jme/tjz112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 05/15/2023]
Abstract
West Nile virus (WNV) was first identified in North America almost 20 yr ago. In that time, WNV has crossed the continent and established enzootic transmission cycles, resulting in intermittent outbreaks of human disease that have largely been linked with climatic variables and waning avian seroprevalence. During the transcontinental dissemination of WNV, the original genotype has been displaced by two principal extant genotypes which contain an envelope mutation that has been associated with enhanced vector competence by Culex pipiens L. (Diptera: Culicidae) and Culex tarsalis Coquillett vectors. Analyses of retrospective avian host competence data generated using the founding NY99 genotype strain have demonstrated a steady reduction in viremias of house sparrows over time. Reciprocally, the current genotype strains WN02 and SW03 have demonstrated an inverse correlation between house sparrow viremia magnitude and the time since isolation. These data collectively indicate that WNV has evolved for increased avian viremia while house sparrows have evolved resistance to the virus such that the relative host competence has remained constant. Intrahost analyses of WNV evolution demonstrate that selection pressures are avian species-specific and purifying selection is greater in individual birds compared with individual mosquitoes, suggesting that the avian adaptive and/or innate immune response may impose a selection pressure on WNV. Phylogenomic, experimental evolutionary systems, and models that link viral evolution with climate, host, and vector competence studies will be needed to identify the relative effect of different selective and stochastic mechanisms on viral phenotypes and the capacity of newly evolved WNV genotypes for transmission in continuously changing landscapes.
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Affiliation(s)
- Nisha K Duggal
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO
| | - Aaron C Brault
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO
- Corresponding author, e-mail:
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Ryabov EV, Childers AK, Lopez D, Grubbs K, Posada-Florez F, Weaver D, Girten W, vanEngelsdorp D, Chen Y, Evans JD. Dynamic evolution in the key honey bee pathogen deformed wing virus: Novel insights into virulence and competition using reverse genetics. PLoS Biol 2019; 17:e3000502. [PMID: 31600204 PMCID: PMC6805011 DOI: 10.1371/journal.pbio.3000502] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/22/2019] [Accepted: 09/20/2019] [Indexed: 12/23/2022] Open
Abstract
The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health, which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States honey bee colonies. Phylogenetic analysis showed that divergent US DWV genotypes are of monophyletic origin and were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to coexisting DWV genotypes, thereby devising a reverse-genetics system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone–derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to coexist. Mutational and recombination events were observed across clone progeny, providing new insights into the forces that drive and constrain virus diversification. Accordingly, our results suggest that Varroa influences DWV dynamics by causing an initial selective sweep, which is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. We suggest that this selection might reflect the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this hypothesis, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population. Deformed wing virus, a key pathogen of honey bees, shows rapid diversification after genetic bottlenecks; a novel reverse-genetic system provides insights into the forces that shape virus diversity, suggesting that virus quasi-species diversification may be driven by selection of genotypes capable of evading host RNAi defences.
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Affiliation(s)
- Eugene V. Ryabov
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- * E-mail: ,
| | - Anna K. Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Dawn Lopez
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Kyle Grubbs
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Francisco Posada-Florez
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Daniel Weaver
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- Beeweaver Apiaries, Navasota, Texas, United States of America
| | - William Girten
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- Department of Chemistry, Fort Lewis College, Durango, Colorado, United States of America
| | - Dennis vanEngelsdorp
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Yanping Chen
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Jay D. Evans
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
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Sexton NR, Ebel GD. Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns. Viruses 2019; 11:v11070643. [PMID: 31336898 PMCID: PMC6669465 DOI: 10.3390/v11070643] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Arthropod-borne viruses (arboviruses) of vertebrates including dengue, zika, chikungunya, Rift Valley fever, and blue tongue viruses cause extensive morbidity and mortality in humans, agricultural animals, and wildlife across the globe. As obligate intercellular pathogens, arboviruses must be well adapted to the cellular and molecular environment of both their arthropod (invertebrate) and vertebrate hosts, which are vastly different due to hundreds of millions of years of separate evolution. Here we discuss the comparative pressures on arbovirus RNA genomes as a result of a dual host life cycle, focusing on pressures that do not alter amino acids. We summarize what is currently known about arboviral genetic composition, such as dinucleotide and codon usage, and how cyclical infection of vertebrate and invertebrate hosts results in different genetic profiles compared with single-host viruses. To serve as a comparison, we compile what is known about arthropod tRNA, dinucleotide, and codon usages and compare this with vertebrates. Additionally, we discuss the potential roles of genetic robustness in arboviral evolution and how it may vary from other viruses. Overall, both arthropod and vertebrate hosts influence the resulting genetic composition of arboviruses, but a great deal remains to be investigated.
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Affiliation(s)
- Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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Liu J, Swevers L, Kolliopoulou A, Smagghe G. Arboviruses and the Challenge to Establish Systemic and Persistent Infections in Competent Mosquito Vectors: The Interaction With the RNAi Mechanism. Front Physiol 2019; 10:890. [PMID: 31354527 PMCID: PMC6638189 DOI: 10.3389/fphys.2019.00890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/27/2019] [Indexed: 12/15/2022] Open
Abstract
Arboviruses are capable to establish long-term persistent infections in mosquitoes that do not affect significantly the physiology of the insect vectors. Arbovirus infections are controlled by the RNAi machinery via the production of viral siRNAs and the formation of RISC complexes targeting viral genomes and mRNAs. Engineered arboviruses that contain cellular gene sequences can therefore be transformed to "viral silencing vectors" for studies of gene function in reverse genetics approaches. More specifically, "ideal" viral silencing vectors must be competent to induce robust RNAi effects while other interactions with the host immune system should be kept at a minimum to reduce non-specific effects. Because of their inconspicuous nature, arboviruses may approach the "ideal" viral silencing vectors in insects and it is therefore worthwhile to study the mechanisms by which the interactions with the RNAi machinery occur. In this review, an analysis is presented of the antiviral RNAi response in mosquito vectors with respect to the major types of arboviruses (alphaviruses, flaviviruses, bunyaviruses, and others). With respect to antiviral defense, the exo-RNAi pathway constitutes the major mechanism while the contribution of both miRNAs and viral piRNAs remains a contentious issue. However, additional mechanisms exist in mosquitoes that are capable to enhance or restrict the efficiency of viral silencing vectors such as the amplification of RNAi effects by DNA forms, the existence of incorporated viral elements in the genome and the induction of a non-specific systemic response by Dicer-2. Of significance is the observation that no major "viral suppressors of RNAi" (VSRs) seem to be encoded by arboviral genomes, indicating that relatively tight control of the activity of the RNA-dependent RNA polymerase (RdRp) may be sufficient to maintain the persistent character of arbovirus infections. Major strategies for improvement of viral silencing vectors therefore are proposed to involve engineering of VSRs and modifying of the properties of the RdRp. Because of safety issues (pathogen status), however, arbovirus-based silencing vectors are not well suited for practical applications, such as RNAi-based mosquito control. In that case, related mosquito-specific viruses that also establish persistent infections and may cause similar RNAi responses may represent a valuable alternative solution.
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Affiliation(s)
- Jisheng Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Luc Swevers
- Institute of Biosciences and Applications, National Centre of Scientific Research “Demokritos”, Athens, Greece
| | - Anna Kolliopoulou
- Institute of Biosciences and Applications, National Centre of Scientific Research “Demokritos”, Athens, Greece
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts. mSphere 2019; 4:4/3/e00291-19. [PMID: 31243074 PMCID: PMC6595145 DOI: 10.1128/msphere.00291-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The enzymes that copy RNA genomes lack proofreading, and viruses that possess RNA genomes, such as West Nile virus, rapidly diversify into swarms of mutant lineages within a host. Intrahost variation of the primary genomic sequence of RNA viruses has been studied extensively because the extent of this variation shapes key virus phenotypes. However, RNA genomes also form complex secondary structures based on within-genome nucleotide complementarity, which are critical regulators of the cyclization of the virus genome that is necessary for efficient replication and translation. We sought to characterize variation in these secondary structures within populations of West Nile virus during serial passage in three bird species. Our study indicates that the intrahost population of West Nile virus is a diverse assortment of RNA secondary structures that should be considered in future analyses of intrahost viral diversity, but some regions that are critical for genome cyclization are conserved within hosts. Besides potential impacts on viral replication, structural diversity can influence the efficacy of small RNA antiviral therapies. RNA viruses are infamous for their high rates of mutation, which produce swarms of genetic variants within individual hosts. To date, analyses of intrahost genetic diversity have focused on the primary genome sequence. However, virus phenotypes are shaped not only by primary sequence but also by the secondary structures into which this sequence folds. Such structures enable viral replication, translation, and binding of small RNAs, yet within-host variation at the structural level has not been adequately explored. We characterized the structural diversity of the 5′ untranslated region (UTR) of populations of West Nile virus (WNV) that had been subject to five serial passages in triplicate in each of three bird species. Viral genomes were sampled from host serum samples at each passage (n = 45 populations) and subjected to next-generation sequencing. For populations derived from passages 1, 3, and 5 (n = 9 populations), we predicted the impact of each mutation occurring at a frequency of ≥1% on the secondary structure of the 5′ UTR. As expected, mutations in double-stranded (DS) regions of the 5′ UTR stem structures caused structural changes of significantly greater magnitude than did mutations in single-stranded (SS) regions. Despite the greater impact of mutations in DS regions, mutations in DS and SS regions occurred at similar frequencies, with no evidence of enhanced selection against mutation in DS regions. In contrast, mutations in two regions that mediate genome cyclization and thereby regulate replication and translation, the 5′ cyclization sequence and the UAR flanking stem (UFS), were suppressed in all three hosts. IMPORTANCE The enzymes that copy RNA genomes lack proofreading, and viruses that possess RNA genomes, such as West Nile virus, rapidly diversify into swarms of mutant lineages within a host. Intrahost variation of the primary genomic sequence of RNA viruses has been studied extensively because the extent of this variation shapes key virus phenotypes. However, RNA genomes also form complex secondary structures based on within-genome nucleotide complementarity, which are critical regulators of the cyclization of the virus genome that is necessary for efficient replication and translation. We sought to characterize variation in these secondary structures within populations of West Nile virus during serial passage in three bird species. Our study indicates that the intrahost population of West Nile virus is a diverse assortment of RNA secondary structures that should be considered in future analyses of intrahost viral diversity, but some regions that are critical for genome cyclization are conserved within hosts. Besides potential impacts on viral replication, structural diversity can influence the efficacy of small RNA antiviral therapies.
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Kolliopoulou A, Santos D, Taning CNT, Wynant N, Vanden Broeck J, Smagghe G, Swevers L. PIWI pathway against viruses in insects. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1555. [PMID: 31183996 DOI: 10.1002/wrna.1555] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are an animal-specific class of small non-coding RNAs that are generated via a biogenesis pathway distinct from small interfering RNAs (siRNAs) and microRNAs (miRNAs). There are variations in piRNA biogenesis that depend on several factors, such as the cell type (germline or soma), the organism, and the purpose for which they are being produced, such as transposon-targeting, viral-targeting, or gene-derived piRNAs. Interestingly, the genes involved in the PIWI/piRNA pathway are more rapidly evolving compared with other RNA interference (RNAi) genes. In this review, the role of the piRNA pathway in the antiviral response is reviewed based on recent findings in insect models such as Drosophila, mosquitoes, midges and the silkworm, Bombyx mori. We extensively discuss the special features that characterize host-virus piRNA responses with respect to the proteins and the genes involved, the viral piRNAs' sequence characteristics, the target strand orientation biases as well as the viral piRNA target hotspots across the viral genomes. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Dulce Santos
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Clauvis Nji Tizi Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Niels Wynant
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
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Aedes aegypti microRNA, miR-2944b-5p interacts with 3'UTR of chikungunya virus and cellular target vps-13 to regulate viral replication. PLoS Negl Trop Dis 2019; 13:e0007429. [PMID: 31166953 PMCID: PMC6576790 DOI: 10.1371/journal.pntd.0007429] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 06/17/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
Background RNA interference is among the most important mechanisms that serve to restrict virus replication within mosquitoes, where microRNAs (miRNAs) are important in regulating viral replication and cellular functions. These miRNAs function by binding to complementary sequences mostly in the untranslated regions of the target. Chikungunya virus (CHIKV) genome consists of two open reading frames flanked by 5′ and 3′ untranslated regions on the two sides. A recent study from our laboratory has shown that Aedes miRNAs are regulated during CHIKV infection. The present study was undertaken to further understand the role of these miRNAs in CHIKV replication. Methods/Findings We observe that miR-2944b-5p binds to the 3′ untranslated region of CHIKV and the binding is abated when the binding sites are abolished. Loss-of-function studies of miR-2944b-5p using antagomirs, both in vitro and in vivo, reveal an increase in CHIKV viral replication, thereby directly implying a role of miR-2944b-5p in CHIKV replication. We further showed that the mitochondrial membrane potential of the mosquito cells is maintained by this miRNA during CHIKV replication, and cellular factor vps-13 plays a contributing role. Conclusions Our study has opened new avenues to understand vector-virus interactions and provides novel insights into CHIKV replication in Aedes aegypti. Furthermore, our study has shown miR-2944b-5p to be playing role, where one of its target vps-13 also contributes, in maintaining mitochondrial membrane potential in Aedes aegypti. Aedes aegypti mosquito transmits pathogenic viruses like chikungunya virus (CHIKV). Inside the vector, the virus replicates in a way so that it is able to survive within the mosquito without causing damage to it. However, once in the mammalian host, it becomes pathogenic and induces death to the infected cells. Amongst several mosquito specific factors that allows or rejects the virus survival, microRNAs play a decisive role. In several studies, miRNAs have shown to be playing role in controlling virus replication either by binding to viral genome or to suppress the expression of any host factor. In the present study, we identified an Aedes miRNA, miR-2944b-5p, which binds to 3'UTR of CHIKV and regulates the replication of the virus in the mosquito. Analysis of the mode of action of this regulation revealed that miR-2944b-5p played a role in maintaining mitochondrial membrane potential during CHIKV replication by targeting cellular factor vps-13.
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Rückert C, Prasad AN, Garcia-Luna SM, Robison A, Grubaugh ND, Weger-Lucarelli J, Ebel GD. Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infection. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 109:13-23. [PMID: 30959110 PMCID: PMC6516063 DOI: 10.1016/j.ibmb.2019.04.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 05/31/2023]
Abstract
RNA interference is a crucial antiviral mechanism in arthropods, including in mosquito vectors of arthropod-borne viruses (arboviruses). Although the exogenous small interfering RNA (siRNA) pathway constitutes an efficient antiviral response in mosquitoes, virus-derived P-element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) have been implicated in the response to alpha-, bunya- and flaviviruses in Aedes spp. mosquitoes. Culex mosquitoes transmit several medically important viruses including West Nile virus (WNV), but are considerably less well studied than Aedes mosquitoes and little is known about antiviral RNA interference in Culex mosquitoes. Therefore, we sequenced small RNA (sRNA) libraries from different Culex cell lines and tissues infected with WNV. The clear majority of virus-derived sRNA reads were 21 nt siRNAs in all cell lines and tissues tested, with no evidence for a role of WNV-derived piRNAs. Additionally, we aligned sRNA reads from Culex quinquefasciatus Hsu cells to the insect-specific rhabdovirus, Merida virus, which persistently replicates in these cells. We found that a significant proportion of the sRNA response to Merida virus consisted of piRNAs. Since viral DNA forms have been implicated in siRNA and piRNA responses of Aedes spp. mosquitoes, we also tested for viral DNA forms in WNV infected Culex cells. We detected viral DNA in Culex tarsalis cells infected with WNV and, to a lesser amount, WNV and Merida virus-derived DNA in Culex quinquefasciatus Hsu cells. In conclusion, Hsu cells generated Merida virus-derived piRNAs, but our data suggests that the major sRNA response of Culex cells and mosquitoes to WNV infection is the exogenous siRNA response. It is also evident that sRNA responses differ significantly between specific virus-mosquito combinations. Future work using additional Culex-borne viruses may further elucidate how virus-derived piRNAs are generated in Culex cells and what role they may play in controlling replication of different viruses.
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Affiliation(s)
- Claudia Rückert
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Abhishek N Prasad
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Selene M Garcia-Luna
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Alexis Robison
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Nathan D Grubaugh
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Yale School of Public Health, Department of Epidemiology of Microbial Diseases, Laboratory of Epidemiology of Public Health, New Haven, CT, USA
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Zárate S, Hernández-Perez F, Taboada B, Martínez NE, Alcaráz-Estrada SL, Del Moral O, Yocupicio-Monroy M. Complete genome of DENV2 isolated from mosquitoes in Mexico. INFECTION GENETICS AND EVOLUTION 2019; 71:98-107. [PMID: 30905775 DOI: 10.1016/j.meegid.2019.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/13/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Dengue virus is the most prevalent arbovirus in Mexico, and although the diversity of this virus has been studied, the vast majority of sequences have been derived from viruses isolated from the human host. In this work, we aimed to sequence and to analyze DENVs derived from wild mosquitoes captured in Acapulco Guerrero, Mexico. We succeeded in determining three full genome sequences of such viruses and were able to compare them with other reported sequences from human and mosquito-derived DENVs. We found 15 nonsynonymous and 88 synonymous substitutions that were present more frequently in mosquito viruses than what would be expected by chance, although the limited number of genomes reported so far puts a constraint on the conclusions that can be derived from these analyses. Also, given the high depth of coverage attained in one of the genomes a variant analysis was carried out, finding 68 polymorphic sites in this genome. Interestingly, six of them corresponded to SNV that were detected as potentially differential between mosquitoes and humans, indicating that a that at least some positions may be maintained as polymorphic, which may facilitate host transmission.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México.
| | | | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, México
| | | | | | - Oscar Del Moral
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, México
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44
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Ciota AT. The role of co-infection and swarm dynamics in arbovirus transmission. Virus Res 2019; 265:88-93. [PMID: 30879977 DOI: 10.1016/j.virusres.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Arthropod-borne viruses (arboviruses) are transmitted by hematophagous insects, primarily mosquitoes. The geographic range and prevalence of mosquito-borne viruses and their vectors has dramatically increased over the last 50 years. As a result, the most medically important arboviurses now co-exist in many regions, resulting in an increased frequency of co-infections in hosts and vectors. In addition to concurrent infections with human pathogens, mosquito-only viruses and/or enzootic viruses not associated with human disease are ubiquitous in mosquito populations. Moreover, mosquito-borne viruses are largely RNA viruses that exist within individual hosts as a diverse and dynamic swarm of closely related genotypes. Interactions among co-infecting viruses and genotypes can have profound effects on virulence, fitness and evolution. Here, we review our understanding of how these complex interactions influence transmission of mosquito-borne viruses, focusing on the often-neglected virus interactions in the mosquito vector, and identify gaps in our knowledge that should guide future studies.
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Affiliation(s)
- Alexander T Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA; Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA.
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45
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Marklewitz M, Junglen S. Evolutionary and ecological insights into the emergence of arthropod-borne viruses. Acta Trop 2019; 190:52-58. [PMID: 30339799 DOI: 10.1016/j.actatropica.2018.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/19/2018] [Accepted: 10/12/2018] [Indexed: 02/05/2023]
Abstract
The emergence of arthropod-borne viruses (arboviruses) is of global concern as they can rapidly spread across countries and to new continents as the recent examples of chikungunya virus and Zika virus have demonstrated. Whereas the global movement patterns of emerging arboviruses are comparatively well studied, there is little knowledge on initial emergence processes that enable sylvatic (enzootic) viruses to leave their natural amplification cycle and infect humans or livestock, often also involving infection of anthropophilic vector species. Emerging arboviruses almost exclusively originate in highly biodiverse ecosystems of tropical countries. Changes in host population diversity and density can affect pathogen transmission patterns and are likely to influence arbovirus emergence processes. This review focuses on concepts from disease ecology, explaining the interplay between biodiversity and pathogen emergence.
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Affiliation(s)
- Marco Marklewitz
- Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany; German Center for Infection Research (DZIF), Germany
| | - Sandra Junglen
- Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany; German Center for Infection Research (DZIF), Germany.
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46
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Worwa G, Hutton AA, Brault AC, Reisen WK. Comparative fitness of West Nile virus isolated during California epidemics. PLoS Negl Trop Dis 2019; 13:e0007135. [PMID: 30716113 PMCID: PMC6375641 DOI: 10.1371/journal.pntd.0007135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 02/14/2019] [Accepted: 01/07/2019] [Indexed: 11/30/2022] Open
Abstract
West Nile virus (WNV) has been circulating in California since its first detection in 2003, causing repeated outbreaks affecting public, wildlife and veterinary health. Epidemics of WNV are difficult to predict due to the multitude of factors influencing transmission dynamics among avian and mosquito hosts. Typically, high levels of WNV amplification are required for outbreaks to occur, and therefore associated viral strains may exhibit enhanced virulence and mortality in competent bird species resulting in increased mosquito infection prevalence. In our previous study, most WNV isolates made from California during 2007-08 showed increased fitness when competed in House Finches (HOFI, Haemorhous mexicanus) and Culex tarsalis Coquillett mosquitoes against COAV997-5nt, a genetically marked recombinant virus derived from a 2003 California strain. Herein, we evaluated the competitive fitness of WNV strains isolated during California epidemics in 2004, 2005, 2007, 2011 and 2012 against COAV997-5nt. These outbreak isolates did not produce elevated mortality in HOFIs, but replicated more efficiently than did COAV997-5nt based on quantification of WNV RNA copies in sera, thereby demonstrating increased competitive fitness. Oral co-infections in Cx. tarsalis resulted in similar virus-specific infection and transmission rates, indicating that outbreak isolates did not have a fitness advantage over COAV997-5nt. Collectively, WNV isolates from outbreaks demonstrated relatively greater avian, but not vector, replicative fitness compared to COAV997-5nt, similar to previously characterized non-outbreak isolates of WNV. Our results indicated that ecological rather than viral factors may facilitate WNV amplification to outbreak levels, but monitoring viral phenotypes through competitive fitness studies may provide insight into altered replication and transmission potential among emerging WNV strains.
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Affiliation(s)
- Gabriella Worwa
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Andra A. Hutton
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Aaron C. Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - William K. Reisen
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Abstract
Flaviviruses include a diverse group of medically important viruses that cycle between mosquitoes and humans. During this natural process of switching hosts, each species imposes different selective forces on the viral population. Using dengue virus (DENV) as model, we found that paralogous RNA structures originating from duplications in the viral 3' untranslated region (UTR) are under different selective pressures in the two hosts. These RNA structures, known as dumbbells (DB1 and DB2), were originally proposed to be enhancers of viral replication. Analysis of viruses obtained from infected mosquitoes showed selection of mutations that mapped in DB2. Recombinant viruses carrying the identified variations confirmed that these mutations greatly increase viral replication in mosquito cells, with low or no impact in human cells. Use of viruses lacking each of the DB structures revealed opposite viral phenotypes. While deletion of DB1 reduced viral replication about 10-fold, viruses lacking DB2 displayed a great increase of fitness in mosquitoes, confirming a functional diversification of these similar RNA elements. Mechanistic analysis indicated that DB1 and DB2 differentially modulate viral genome cyclization and RNA replication. We found that a pseudoknot formed within DB2 competes with long-range RNA-RNA interactions that are necessary for minus-strand RNA synthesis. Our results support a model in which a functional diversification of duplicated RNA elements in the viral 3' UTR is driven by host-specific requirements. This study provides new ideas for understanding molecular aspects of the evolution of RNA viruses that naturally jump between different species.IMPORTANCE Flaviviruses constitute the most relevant group of arthropod-transmitted viruses, including important human pathogens such as the dengue, Zika, yellow fever, and West Nile viruses. The natural alternation of these viruses between vertebrate and invertebrate hosts shapes the viral genome population, which leads to selection of different viral variants with potential implications for epidemiological fitness and pathogenesis. However, the selective forces and mechanisms acting on the viral RNA during host adaptation are still largely unknown. Here, we found that two almost identical tandem RNA structures present at the viral 3' untranslated region are under different selective pressures in the two hosts. Mechanistic studies indicated that the two RNA elements, known as dumbbells, contain sequences that overlap essential RNA cyclization elements involved in viral RNA synthesis. The data support a model in which the duplicated RNA structures differentially evolved to accommodate distinct functions for viral replication in the two hosts.
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48
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Nucleic Acid Sensing in Invertebrate Antiviral Immunity. NUCLEIC ACID SENSING AND IMMUNITY - PART B 2019; 345:287-360. [DOI: 10.1016/bs.ircmb.2018.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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49
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Donald CL, Varjak M, Aguiar ERGR, Marques JT, Sreenu VB, Schnettler E, Kohl A. Antiviral RNA Interference Activity in Cells of the Predatory Mosquito, Toxorhynchites amboinensis. Viruses 2018; 10:v10120694. [PMID: 30563205 PMCID: PMC6316411 DOI: 10.3390/v10120694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/19/2018] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Arthropod vectors control the replication of arboviruses through their innate antiviral immune responses. In particular, the RNA interference (RNAi) pathways are of notable significance for the control of viral infections. Although much has been done to understand the role of RNAi in vector populations, little is known about its importance in non-vector mosquito species. In this study, we investigated the presence of an RNAi response in Toxorhynchites amboinensis, which is a non-blood feeding species proposed as a biological control agent against pest mosquitoes. Using a derived cell line (TRA-171), we demonstrate that these mosquitoes possess a functional RNAi response that is active against a mosquito-borne alphavirus, Semliki Forest virus. As observed in vector mosquito species, small RNAs are produced that target viral sequences. The size and characteristics of these small RNAs indicate that both the siRNA and piRNA pathways are induced in response to infection. Taken together, this data suggests that Tx. amboinensis are able to control viral infections in a similar way to natural arbovirus vector mosquito species. Understanding their ability to manage arboviral infections will be advantageous when assessing these and similar species as biological control agents.
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Affiliation(s)
- Claire L Donald
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK.
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK.
| | - Eric Roberto Guimarães Rocha Aguiar
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 6627-Pampulha-Belo Horizonte-MG, CEP 31270-901, Brazil.
| | - João T Marques
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 6627-Pampulha-Belo Horizonte-MG, CEP 31270-901, Brazil.
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK.
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK.
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK.
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50
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Cholleti H, Berg M, Hayer J, Blomström AL. Vector-borne viruses and their detection by viral metagenomics. Infect Ecol Epidemiol 2018. [DOI: 10.1080/20008686.2018.1553465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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