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Li R, Sun K, Tuplin A, Harris M. A structural and functional analysis of opal stop codon translational readthrough during Chikungunya virus replication. J Gen Virol 2023; 104:10.1099/jgv.0.001909. [PMID: 37862073 PMCID: PMC7615711 DOI: 10.1099/jgv.0.001909] [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: 10/21/2023] Open
Abstract
Chikungunya virus (CHIKV) is an alphavirus, transmitted by Aedes species mosquitoes. The CHIKV single-stranded positive-sense RNA genome contains two open reading frames, coding for the non-structural (nsP) and structural proteins of the virus. The non-structural polyprotein precursor is proteolytically cleaved to generate nsP1-4. Intriguingly, most isolates of CHIKV (and other alphaviruses) possess an opal stop codon close to the 3' end of the nsP3 coding sequence and translational readthrough is necessary to produce full-length nsP3 and the nsP4 RNA polymerase. Here we investigate the role of this stop codon by replacing the arginine codon with each of the three stop codons in the context of both a subgenomic replicon and infectious CHIKV. Both opal and amber stop codons were tolerated in mammalian cells, but the ochre was not. In mosquito cells all three stop codons were tolerated. Using SHAPE analysis we interrogated the structure of a putative stem loop 3' of the stop codon and used mutagenesis to probe the importance of a short base-paired region at the base of this structure. Our data reveal that this stem is not required for stop codon translational readthrough, and we conclude that other factors must facilitate this process to permit productive CHIKV replication.
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Affiliation(s)
- Raymond Li
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | | | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
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2
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van Bree JW, Visser I, Duyvestyn JM, Aguilar-Bretones M, Marshall EM, van Hemert MJ, Pijlman GP, van Nierop GP, Kikkert M, Rockx BH, Miesen P, Fros JJ. Novel approaches for the rapid development of rationally designed arbovirus vaccines. One Health 2023; 16:100565. [PMID: 37363258 PMCID: PMC10288159 DOI: 10.1016/j.onehlt.2023.100565] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Vector-borne diseases, including those transmitted by mosquitoes, account for more than 17% of infectious diseases worldwide. This number is expected to rise with an increased spread of vector mosquitoes and viruses due to climate change and man-made alterations to ecosystems. Among the most common, medically relevant mosquito-borne infections are those caused by arthropod-borne viruses (arboviruses), especially members of the genera Flavivirus and Alphavirus. Arbovirus infections can cause severe disease in humans, livestock and wildlife. Severe consequences from infections include congenital malformations as well as arthritogenic, haemorrhagic or neuroinvasive disease. Inactivated or live-attenuated vaccines (LAVs) are available for a small number of arboviruses; however there are no licensed vaccines for the majority of these infections. Here we discuss recent developments in pan-arbovirus LAV approaches, from site-directed attenuation strategies targeting conserved determinants of virulence to universal strategies that utilize genome-wide re-coding of viral genomes. In addition to these approaches, we discuss novel strategies targeting mosquito saliva proteins that play an important role in virus transmission and pathogenesis in vertebrate hosts. For rapid pre-clinical evaluations of novel arbovirus vaccine candidates, representative in vitro and in vivo experimental systems are required to assess the desired specific immune responses. Here we discuss promising models to study attenuation of neuroinvasion, neurovirulence and virus transmission, as well as antibody induction and potential for cross-reactivity. Investigating broadly applicable vaccination strategies to target the direct interface of the vertebrate host, the mosquito vector and the viral pathogen is a prime example of a One Health strategy to tackle human and animal diseases.
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Affiliation(s)
- Joyce W.M. van Bree
- Laboratory of Virology, Wageningen University & Research, Wageningen, the Netherlands
| | - Imke Visser
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jo M. Duyvestyn
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Eleanor M. Marshall
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Martijn J. van Hemert
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Barry H.G. Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Jelke J. Fros
- Laboratory of Virology, Wageningen University & Research, Wageningen, the Netherlands
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3
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Nath A, Kumar S, Gurav YK, Gangopadhayya A, Ghuge O, Sreelakshmi PR, Jadhav A, Rajan LS, Yadav K, Shinde K, Shil P, Sudeep A, Lole KS. Genomic Characterization of Mosquito Isolates of Chikungunya Virus (Outbreak Strains 2022) Using Next-Generation Sequencing. Vector Borne Zoonotic Dis 2023. [PMID: 37184895 DOI: 10.1089/vbz.2022.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Background: A massive outbreak of dengue-like illness was reported from Pune district of Maharashtra, India during May-June 2022. Isolation and characterization of the etiological agent at genomic level for possible mutations that led to higher transmissibility is the topic of the study. Methods: Entomological investigations were carried out by ICMR-National Institute of Virology (Pune, India); Aedes aegypti mosquitoes were collected and processed for virus detection by molecular techniques. Positive mosquito pools were processed for virus isolation in cell culture. Sanger sequencing and whole-genome sequencing (WGS) using Oxford Nanopore Technology platform were used for genomic characterization. Results: Reverse transcriptase RT-PCR and qRT-PCR analysis detected chikungunya virus (CHIKV) in mosquito samples. Six CHIKV isolates were obtained. WGS revealed four nonsynonymous mutations in the structural polyprotein region, and five in the nonstructural polyprotein encoding region when compared with Yawat-2000 and Shivane-2016 strains. Sixty-four nucleotide changes in the nonstructural polyprotein region and 35 in the structural polyprotein region were detected. One isolate had an exclusive amino acid change, T1123I, in the nsP2 (protease) region. Conclusion: Abundant Ae. aegypti breeding and detection of CHIKV RNA in mosquitoes confirmed it as a chikungunya outbreak. Novel mutations detected in the epidemic strain warrants investigations to address their role in disease severity, transmission, and fitness.
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Affiliation(s)
- Amol Nath
- ICMR-National Institute of Virology, Pune, India
| | - Surendra Kumar
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | - Yogesh K Gurav
- Department of Dengue, ICMR-National Institute of Virology, Pune, India
| | | | - Onkar Ghuge
- ICMR-National Institute of Virology, Pune, India
| | | | - Abhijeet Jadhav
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | - Lekshmi S Rajan
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | | | - Krishna Shinde
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | - Pratip Shil
- Department of Bioinformatics, ICMR-National Institute of Virology, Pune, India
| | - Anakkathil Sudeep
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
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Cottis S, Blisnick AA, Failloux AB, Vernick KD. Determinants of Chikungunya and O'nyong-Nyong Virus Specificity for Infection of Aedes and Anopheles Mosquito Vectors. Viruses 2023; 15:589. [PMID: 36992298 PMCID: PMC10051923 DOI: 10.3390/v15030589] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023] Open
Abstract
Mosquito-borne diseases caused by viruses and parasites are responsible for more than 700 million infections each year. Anopheles and Aedes are the two major vectors for, respectively, malaria and arboviruses. Anopheles mosquitoes are the primary vector of just one known arbovirus, the alphavirus o'nyong-nyong virus (ONNV), which is closely related to the chikungunya virus (CHIKV), vectored by Aedes mosquitoes. However, Anopheles harbor a complex natural virome of RNA viruses, and a number of pathogenic arboviruses have been isolated from Anopheles mosquitoes in nature. CHIKV and ONNV are in the same antigenic group, the Semliki Forest virus complex, are difficult to distinguish via immunodiagnostic assay, and symptomatically cause essentially the same human disease. The major difference between the arboviruses appears to be their differential use of mosquito vectors. The mechanisms governing this vector specificity are poorly understood. Here, we summarize intrinsic and extrinsic factors that could be associated with vector specificity by these viruses. We highlight the complexity and multifactorial aspect of vectorial specificity of the two alphaviruses, and evaluate the level of risk of vector shift by ONNV or CHIKV.
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Affiliation(s)
- Solène Cottis
- Genetics and Genomics of Insect Vectors Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris Cité, CNRS UMR2000, F-75015 Paris, France
- Graduate School of Life Sciences ED515, Sorbonne Université UPMC Paris VI, 75252 Paris, France
| | - Adrien A. Blisnick
- Arboviruses and Insect Vectors Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
| | - Anna-Bella Failloux
- Arboviruses and Insect Vectors Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
| | - Kenneth D. Vernick
- Genetics and Genomics of Insect Vectors Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris Cité, CNRS UMR2000, F-75015 Paris, France
- Graduate School of Life Sciences ED515, Sorbonne Université UPMC Paris VI, 75252 Paris, France
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5
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Basavappa MG, Ferretti M, Dittmar M, Stoute J, Sullivan MC, Whig K, Shen H, Liu KF, Schultz DC, Beiting DP, Lynch KW, Henao-Mejia J, Cherry S. The lncRNA ALPHA specifically targets chikungunya virus to control infection. Mol Cell 2022; 82:3729-3744.e10. [PMID: 36167073 PMCID: PMC10464526 DOI: 10.1016/j.molcel.2022.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/06/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022]
Abstract
Arthropod-borne viruses, including the alphavirus chikungunya virus (CHIKV), cause acute disease in millions of people and utilize potent mechanisms to antagonize and circumvent innate immune pathways including the type I interferon (IFN) pathway. In response, hosts have evolved antiviral counterdefense strategies that remain incompletely understood. Recent studies have found that long noncoding RNAs (lncRNAs) regulate classical innate immune pathways; how lncRNAs contribute to additional antiviral counterdefenses remains unclear. Using high-throughput genetic screening, we identified a cytoplasmic antiviral lncRNA that we named antiviral lncRNA prohibiting human alphaviruses (ALPHA), which is transcriptionally induced by alphaviruses and functions independently of IFN to inhibit the replication of CHIKV and its closest relative, O'nyong'nyong virus (ONNV), but not other viruses. Furthermore, we showed that ALPHA interacts with CHIKV genomic RNA and restrains viral RNA replication. Together, our findings reveal that ALPHA and potentially other lncRNAs can mediate non-canonical antiviral immune responses against specific viruses.
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Affiliation(s)
- Megha G Basavappa
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julian Stoute
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Megan C Sullivan
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kanupriya Whig
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Shen
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David C Schultz
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel P Beiting
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Zou M, Su C, Li T, Zhang J, Li D, Luan N, Ma D, Liu J, Sun Q, Peng X, Liu H. Genetic Characterization of Chikungunya Virus Among Febrile Dengue Fever–Like Patients in Xishuangbanna, Southwestern Part of China. Front Cell Infect Microbiol 2022; 12:914289. [PMID: 35832380 PMCID: PMC9271616 DOI: 10.3389/fcimb.2022.914289] [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: 04/06/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Co-infection of chikungunya virus (CHIKV) has been recently reported during dengue fever epidemics. However, the infection of CHIKV is often neglected due to its misdiagnosis as dengue virus (DENV) infection. In the summer of 2019 when dengue fever was epidemic, we collected 697 serum samples from febrile dengue fever–like patients in Xishuangbanna, southwestern part of China. DENV RNA was detectable in 99.42% of these patients. Notably, 88 patients (12.62%) showed the presence of CHIKV RNA, among which 86 patients were co-infected with DENV and CHIKV. We sequenced and analyzed the full genome of CHIKV virus in four out of 88 samples (two CHIKV infected and two co-infected). The results suggested that the four strains were all Asian genotype and had the highest homology (99.4%) with the SZ1239 strain (accession number MG664851) isolated in 2012 and possibly introduced from Indonesia. Further comparison with the conserved sequences in the whole genome of 47 strains of CHIKV showed that there were 13 and 15 amino acid mutants in structural proteins and non-structural proteins, respectively. The previously reported adaptive mutations of E2-W64R, E2-I211T, E2-K233E, E1-A98T, and E1-K211E occurred in the four strains of this study. In conclusion, this study reports a co-infection of CHIKV during the DENV epidemic in the city Xishuangbanna, 2019. Molecular epidemiology revealed that CHIKV identified in this study was indigenous and belongs to Asian lineage with lineage-specific mutations and some reported adaptive mutations, which is distinct from the recently reported CHIKV (East/Central/South African) in Ruili, the city next to Xishuangbanna.
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Affiliation(s)
- Meng Zou
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Chunyan Su
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Tingting Li
- Joint Laboratory for Prevention and Control of Cross-border Transmission Disease, People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, China
| | - Jing Zhang
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Daiying Li
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Ning Luan
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Dehong Ma
- Joint Laboratory for Prevention and Control of Cross-border Transmission Disease, People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, China
| | - Jiansheng Liu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Hongqi Liu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
- *Correspondence: Hongqi Liu,
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7
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Tanaka A, Suzuki Y. Genome-Wide Approaches to Unravel the Host Factors Involved in Chikungunya Virus Replication. Front Microbiol 2022; 13:866271. [PMID: 35401487 PMCID: PMC8988064 DOI: 10.3389/fmicb.2022.866271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/26/2022] [Indexed: 01/05/2023] Open
Abstract
Chikungunya virus (CHIKV), the causative agent of Chikungunya fever (CHIKVF) that is often characterized by fever, headache, rash, and arthralgia, is transmitted to humans by Aedes mosquito bites. Although the mortality rate associated with CHIKV infection is not very high, CHIKVF has been confirmed in more than 40 countries, not only in tropical but also in temperate areas. Therefore, CHIKV is a growing major threat to the public health of the world. However, a specific drug is not available for CHIKV infection. As demonstrated by many studies, the processes completing the replication of CHIKV are assisted by many host factors, whereas it has become clear that the host cell possesses some factors limiting the virus replication. This evidence will provide us with an important clue for the development of pharmacological treatment against CHIKVF. In this review, we briefly summarize cellular molecules participating in the CHIKV infection, particularly focusing on introducing recent genome-wide screen studies that enabled illuminating the virus-host interactions.
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Affiliation(s)
- Atsushi Tanaka
- Division of Research Animal Laboratory and Translational Medicine, Research and Development Center, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
- *Correspondence: Atsushi Tanaka,
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
- Youichi Suzuki,
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8
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Chaudhary S, Jain J, Kumar R, Shrinet J, Weaver SC, Auguste AJ, Sunil S. Chikungunya virus molecular evolution in India since its re-emergence in 2005. Virus Evol 2021; 7:veab074. [PMID: 34754512 PMCID: PMC8570154 DOI: 10.1093/ve/veab074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is among the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of fifty clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analysed them along with 753 genomes available on the Virus Pathogen Database and Analysis Resource sampled over fifteen years (2005-20) from a range of locations across the globe and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.
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Affiliation(s)
| | - Jaspreet Jain
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Abstract
Alphaviruses are positive-strand RNA viruses, typically transmitted by mosquitoes between vertebrate hosts. They encode four essential replication proteins, the non-structural proteins nsP1-4, which possess the enzymatic activities of RNA capping, RNA helicase, site-specific protease, ADP-ribosyl removal and RNA polymerase. Alphaviruses have been key models in the study of membrane-associated RNA replication, which is a conserved feature among the positive-strand RNA viruses of animals and plants. We review new structural and functional information on the nsPs and their interaction with host proteins and membranes, as well as with viral RNA sequences. The dodecameric ring structure of nsP1 is likely to be one of the evolutionary innovations that facilitated the success of the progenitors of current positive-strand RNA viruses.
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Affiliation(s)
- Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia.
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10
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Abstract
Alphaviruses have positive-strand RNA genomes containing two open reading frames (ORFs). The first ORF encodes the nonstructural (ns) polyproteins P123 and P1234 that act as precursors for the subunits of the viral RNA replicase (nsP1 to nsP4). Processing of P1234 leads to the formation of a negative-strand replicase consisting of nsP4 (RNA polymerase) and P123 components. Subsequent processing of P123 results in a positive-strand replicase. The second ORF encoding the structural proteins is expressed via the synthesis of a subgenomic RNA. Alphavirus replicase is capable of using template RNAs that contain essential cis-active sequences. Here, we demonstrate that the replicases of nine alphaviruses, expressed in the form of separate P123 and nsP4 components, are active. Their activity depends on the abundance of nsP4. The match of nsP4 to its template strongly influences efficient subgenomic RNA synthesis. nsP4 of Barmah Forest virus (BFV) formed a functional replicase only with matching P123, while nsP4s of other alphaviruses were compatible also with several heterologous P123s. The P123 components of Venezuelan equine encephalitis virus and Sindbis virus (SINV) required matching nsP4s, while P123 of other viruses could form active replicases with different nsP4s. Chimeras of Semliki Forest virus, harboring the nsP4 of chikungunya virus, Ross River virus, BFV, or SINV were viable. In contrast, chimeras of SINV, harboring an nsP4 from different alphaviruses, exhibited a temperature-sensitive phenotype. These findings highlight the possibility for formation of new alphaviruses via recombination events and provide a novel approach for the development of attenuated chimeric viruses for vaccination strategies. IMPORTANCE A key element of every virus with an RNA genome is the RNA replicase. Understanding the principles of RNA replicase formation and functioning is therefore crucial for understanding and responding to the emergence of new viruses. Reconstruction of the replicases of nine alphaviruses from nsP4 and P123 polyproteins revealed that the nsP4 of the majority of alphaviruses, including the mosquito-specific Eilat virus, could form a functional replicase with P123 originating from a different virus, and the corresponding chimeric viruses were replication-competent. nsP4 also had an evident role in determining the template RNA preference and the efficiency of RNA synthesis. The revealed broad picture of the compatibility of the replicase components of alphaviruses is important for understanding the formation and functioning of the alphavirus RNA replicase and highlights the possibilities for recombination between different alphavirus species.
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Alphavirus Virulence Determinants. Pathogens 2021; 10:pathogens10080981. [PMID: 34451445 PMCID: PMC8401390 DOI: 10.3390/pathogens10080981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 11/17/2022] Open
Abstract
Alphaviruses are important pathogens that continue to cause outbreaks of disease in humans and animals worldwide. Diseases caused by alphavirus infections include acute symptoms of fever, rash, and nausea as well as chronic arthritis and severe-to-fatal conditions including myocarditis and encephalitis. Despite their prevalence and the significant public health threat they pose, there are currently no effective antiviral treatments or vaccines against alphaviruses. Various genetic determinants of alphavirus virulence, including genomic RNA elements and specific protein residues and domains, have been described by researchers to play key roles in the development of disease, the immune response to infection, and virus transmissibility. Here, we focus on the determinants that are currently described in the literature. Understanding how these molecular determinants shape viral infections can lead to new strategies for the development of therapies and vaccines to combat these viruses.
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12
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LaPointe AT, Sokoloski KJ. De-Coding the Contributions of the Viral RNAs to Alphaviral Pathogenesis. Pathogens 2021; 10:pathogens10060771. [PMID: 34205345 PMCID: PMC8233893 DOI: 10.3390/pathogens10060771] [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: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Alphaviruses are positive-sense RNA arboviruses that are capable of causing severe disease in otherwise healthy individuals. There are many aspects of viral infection that determine pathogenesis and major efforts regarding the identification and characterization of virulence determinants have largely focused on the roles of the nonstructural and structural proteins. Nonetheless, the viral RNAs of the alphaviruses themselves play important roles in regard to virulence and pathogenesis. In particular, many sequences and secondary structures within the viral RNAs play an important part in the development of disease and may be considered important determinants of virulence. In this review article, we summarize the known RNA-based virulence traits and host:RNA interactions that influence alphaviral pathogenesis for each of the viral RNA species produced during infection. Overall, the viral RNAs produced during infection are important contributors to alphaviral pathogenesis and more research is needed to fully understand how each RNA species impacts the host response to infection as well as the development of disease.
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Affiliation(s)
- Autumn T. LaPointe
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KT 40202, USA;
| | - Kevin J. Sokoloski
- Center for Predictive Medicine and Emerging Infectious Diseases, University of Louisville, Louisville, KT 40202, USA
- Correspondence:
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Abdullah N, Ahemad N, Aliazis K, Khairat JE, Lee TC, Abdul Ahmad SA, Adnan NAA, Macha NO, Hassan SS. The Putative Roles and Functions of Indel, Repetition and Duplication Events in Alphavirus Non-Structural Protein 3 Hypervariable Domain (nsP3 HVD) in Evolution, Viability and Re-Emergence. Viruses 2021; 13:v13061021. [PMID: 34071712 PMCID: PMC8228767 DOI: 10.3390/v13061021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/23/2022] Open
Abstract
Alphavirus non-structural proteins 1–4 (nsP1, nsP2, nsP3, and nsP4) are known to be crucial for alphavirus RNA replication and translation. To date, nsP3 has been demonstrated to mediate many virus–host protein–protein interactions in several fundamental alphavirus mechanisms, particularly during the early stages of replication. However, the molecular pathways and proteins networks underlying these mechanisms remain poorly described. This is due to the low genetic sequence homology of the nsP3 protein among the alphavirus species, especially at its 3′ C-terminal domain, the hypervariable domain (HVD). Moreover, the nsP3 HVD is almost or completely intrinsically disordered and has a poor ability to form secondary structures. Evolution in the nsP3 HVD region allows the alphavirus to adapt to vertebrate and insect hosts. This review focuses on the putative roles and functions of indel, repetition, and duplication events that have occurred in the alphavirus nsP3 HVD, including characterization of the differences and their implications for specificity in the context of virus–host interactions in fundamental alphavirus mechanisms, which have thus directly facilitated the evolution, adaptation, viability, and re-emergence of these viruses.
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Affiliation(s)
- Nurshariza Abdullah
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia;
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
| | - Konstantinos Aliazis
- Institute of Immunology and Immunotherapy, Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Jasmine Elanie Khairat
- Institute of Biological Sciences, Faculty of Science, University Malaya, Kuala Lumpur 50603, Malaysia;
| | - Thong Chuan Lee
- Faculty of Industrial Sciences & Technology, University Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan 26300, Pahang, Malaysia;
| | - Siti Aisyah Abdul Ahmad
- Immunogenetic Unit, Allergy and Immunology Research Center, Institute for Medical Research, Ministry of Health Malaysia, Shah Alam 40170, Selangor, Malaysia;
| | - Nur Amelia Azreen Adnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nur Omar Macha
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
- Correspondence: ; Tel.: +60-3-5514-6340
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Chikungunya Virus Strains from Each Genetic Clade Bind Sulfated Glycosaminoglycans as Attachment Factors. J Virol 2020; 94:JVI.01500-20. [PMID: 32999033 PMCID: PMC7925169 DOI: 10.1128/jvi.01500-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
Alphavirus infections are a global health threat, contributing to outbreaks of disease in many parts of the world. Recent epidemics caused by CHIKV, an arthritogenic alphavirus, resulted in more than 8.5 million cases as the virus has spread into new geographic regions, including the Western Hemisphere. CHIKV causes disease in the majority of people infected, leading to severe and debilitating arthritis. Despite the severity of CHIKV disease, there are no licensed therapeutics. Since attachment factors and receptors are determinants of viral tropism and pathogenesis, understanding these virus-host interactions can enhance our knowledge of CHIKV infection. We analyzed over 670 glycans and identified GAGs as the main glycan bound by CHIKV. We defined specific GAG components required for CHIKV binding and assessed strain-specific differences in GAG binding capacity. These studies provide insight about cell surface molecules that CHIKV binds, which could facilitate the development of antiviral therapeutics targeting the CHIKV attachment step. Chikungunya virus (CHIKV) is an arthritogenic alphavirus that causes debilitating musculoskeletal disease. CHIKV displays broad cell, tissue, and species tropism, which may correlate with the attachment factors and entry receptors used by the virus. Cell surface glycosaminoglycans (GAGs) have been identified as CHIKV attachment factors. However, the specific types of GAGs and potentially other glycans to which CHIKV binds and whether there are strain-specific differences in GAG binding are not fully understood. To identify the types of glycans bound by CHIKV, we conducted glycan microarray analyses and discovered that CHIKV preferentially binds GAGs. Microarray results also indicate that sulfate groups on GAGs are essential for CHIKV binding and that CHIKV binds most strongly to longer GAG chains of heparin and heparan sulfate. To determine whether GAG binding capacity varies among CHIKV strains, a representative strain from each genetic clade was tested. While all strains directly bound to heparin and chondroitin sulfate in enzyme-linked immunosorbent assays (ELISAs) and depended on heparan sulfate for efficient cell binding and infection, we observed some variation by strain. Enzymatic removal of cell surface GAGs and genetic ablation that diminishes GAG expression reduced CHIKV binding and infectivity of all strains. Collectively, these data demonstrate that GAGs are the preferred glycan bound by CHIKV, enhance our understanding of the specific GAG moieties required for CHIKV binding, define strain differences in GAG engagement, and provide further evidence for a critical function of GAGs in CHIKV cell attachment and infection. IMPORTANCE Alphavirus infections are a global health threat, contributing to outbreaks of disease in many parts of the world. Recent epidemics caused by CHIKV, an arthritogenic alphavirus, resulted in more than 8.5 million cases as the virus has spread into new geographic regions, including the Western Hemisphere. CHIKV causes disease in the majority of people infected, leading to severe and debilitating arthritis. Despite the severity of CHIKV disease, there are no licensed therapeutics. Since attachment factors and receptors are determinants of viral tropism and pathogenesis, understanding these virus-host interactions can enhance our knowledge of CHIKV infection. We analyzed over 670 glycans and identified GAGs as the main glycan bound by CHIKV. We defined specific GAG components required for CHIKV binding and assessed strain-specific differences in GAG binding capacity. These studies provide insight about cell surface molecules that CHIKV binds, which could facilitate the development of antiviral therapeutics targeting the CHIKV attachment step.
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Madden EA, Plante KS, Morrison CR, Kutchko KM, Sanders W, Long KM, Taft-Benz S, Cruz Cisneros MC, White AM, Sarkar S, Reynolds G, Vincent HA, Laederach A, Moorman NJ, Heise MT. Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus. J Virol 2020; 94:e00701-20. [PMID: 32999019 PMCID: PMC7925192 DOI: 10.1128/jvi.00701-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3'UTR variants. A duplication in the 3'UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3'UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis.IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes febrile illness and debilitating arthralgia in humans. CHIKV causes explosive outbreaks but there are no approved therapies to treat or prevent CHIKV infection. The CHIKV genome contains functional RNA secondary structures that are essential for proper virus replication. Since RNA secondary structures have only been defined for a small portion of the CHIKV genome, we used a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA. We identified 23 highly specific structured regions of the genome, and confirmed the functional importance of one structure using mutagenesis. Furthermore, we defined the RNA secondary structure of three CHIKV 3'UTR variants that differ in their ability to replicate in mosquito cells. Our study highlights the complexity of the CHIKV genome and describes new systems for designing compensatory mutations to test the functional relevance of viral RNA secondary structures.
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Affiliation(s)
- Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth S Plante
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Clayton R Morrison
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrina M Kutchko
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristin M Long
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon Taft-Benz
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Sanjay Sarkar
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Grace Reynolds
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather A Vincent
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alain Laederach
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathanial J Moorman
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
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16
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Suzuki Y, Tanaka A, Maeda Y, Emi A, Fujioka Y, Sakaguchi S, Vasudevan SG, Kobayashi T, Lim CK, Takasaki T, Wu H, Nakano T. Construction and characterization of an infectious clone generated from Chikungunya virus SL11131 strain. Virology 2020; 552:52-62. [PMID: 33059320 DOI: 10.1016/j.virol.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/08/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes Chikungunya fever in humans. In this study, we generated two DNA-based CHIKV infectious clones derived from an Indian Ocean Lineage SL11131 strain and a prototype Ross strain. When the replication capabilities of the infectious CHIKV in various cell lines were evaluated, the SL11131 strain was found to replicate more efficiently than the Ross strain in Aedes albopictus C6/36 cells, whereas SL11131 underwent limited replication in a BHK-21-derivative cell line named BHK-DRV. Infection experiments using chimeric CHIKV between SL11131 and Ross revealed that these different replication activities of SL11131 in C6/36 and BHK-DRV cells were determined by structural and nonstructural genes, respectively. Therefore, the infectious clones created in this study will be a useful tool for investigating the virological features of a recent epidemic strain of CHIKV and benefit the development of effective prevention and treatment of CHIKV infection.
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Affiliation(s)
- Youichi Suzuki
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan.
| | - Atsushi Tanaka
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Resilience Research Unit, Kyoto University, Kyoto, Japan
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akino Emi
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | | | - Takeshi Kobayashi
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Chang-Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hong Wu
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
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Cunha MS, Costa PAG, Correa IA, de Souza MRM, Calil PT, da Silva GPD, Costa SM, Fonseca VWP, da Costa LJ. Chikungunya Virus: An Emergent Arbovirus to the South American Continent and a Continuous Threat to the World. Front Microbiol 2020; 11:1297. [PMID: 32670231 PMCID: PMC7332961 DOI: 10.3389/fmicb.2020.01297] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/20/2020] [Indexed: 01/23/2023] Open
Abstract
Chikungunya virus (CHIKV) is an arthropod-borne virus (arbovirus) of epidemic concern, transmitted by Aedes ssp. mosquitoes, and is the etiologic agent of a febrile and incapacitating arthritogenic illness responsible for millions of human cases worldwide. After major outbreaks starting in 2004, CHIKV spread to subtropical areas and western hemisphere coming from sub-Saharan Africa, South East Asia, and the Indian subcontinent. Even though CHIKV disease is self-limiting and non-lethal, more than 30% of the infected individuals will develop chronic disease with persistent severe joint pain, tenosynovitis, and incapacitating polyarthralgia that can last for months to years, negatively impacting an individual’s quality of life and socioeconomic productivity. The lack of specific drugs or licensed vaccines to treat or prevent CHIKV disease associated with the global presence of the mosquito vector in tropical and temperate areas, representing a possibility for CHIKV to continually spread to different territories, make this virus an agent of public health burden. In South America, where Dengue virus is endemic and Zika virus was recently introduced, the impact of the expansion of CHIKV infections, and co-infection with other arboviruses, still needs to be estimated. In Brazil, the recent spread of the East/Central/South Africa (ECSA) and Asian genotypes of CHIKV was accompanied by a high morbidity rate and acute cases of abnormal disease presentation and severe neuropathies, which is an atypical outcome for this infection. In this review, we will discuss what is currently known about CHIKV epidemics, clinical manifestations of the human disease, the basic concepts and recent findings in the mechanisms underlying virus-host interaction, and CHIKV-induced chronic disease for both in vitro and in vivo models of infection. We aim to stimulate scientific debate on how the characterization of replication, host-cell interactions, and the pathogenic potential of the new epidemic viral strains can contribute as potential developments in the virology field and shed light on strategies for disease control.
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Affiliation(s)
- Marcela S Cunha
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro A G Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isadora Alonso Correa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos R M de Souza
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro Teles Calil
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo P Duarte da Silva
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Mesquita Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinícius Wakoff P Fonseca
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana J da Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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18
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Jain J, Kaur N, Haller SL, Kumar A, Rossi SL, Narayanan V, Kumar D, Gaind R, Weaver SC, Auguste AJ, Sunil S. Chikungunya Outbreaks in India: A Prospective Study Comparing Neutralization and Sequelae during Two Outbreaks in 2010 and 2016. Am J Trop Med Hyg 2020; 102:857-868. [PMID: 32067624 DOI: 10.4269/ajtmh.19-0481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chikungunya fever (CHIKF) is a major public health concern and is caused by chikungunya virus (CHIKV). In 2005, the virus was reintroduced into India, resulting in massive outbreaks in several parts of the country. During 2010 and 2016 outbreaks, we recruited 588 patients from a tertiary care hospital in New Delhi, India, during the acute phase of CHIKF; collected their blood and clinical data; and determined their arthralgic status 12 weeks post-onset of fever. We evaluated IgM/IgG CHIKV-binding antibodies and their neutralizing capacity, sequenced complete genomes of 21 CHIKV strains, and correlated mutations with patient sequelae status. We also performed infections in murine models using representative strains from each outbreak to evaluate differences in pathogenesis. Our screening and analysis revealed that patients of the 2016 outbreak developed earlier IgM and neutralizing antibody responses that were negatively correlated with sequelae, compared with 2010 patients. Mutations that correlated with human disease progression were also correlated with enhanced murine virulence and pathogenesis. Overall, our study suggests that the development of early neutralizing antibodies and sequence variation in clinical isolates are predictors of human sequelae.
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Affiliation(s)
- Jaspreet Jain
- Vector Borne Disease Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Navjot Kaur
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sherry L Haller
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, Centre for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas
| | - Ankit Kumar
- Vector Borne Disease Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shannan L Rossi
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, Centre for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas
| | - Vimal Narayanan
- Vector Borne Disease Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dilip Kumar
- Department of Medicine, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Rajni Gaind
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, Centre for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas
| | - Albert J Auguste
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, Centre for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas
| | - Sujatha Sunil
- Vector Borne Disease Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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19
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Suramin Inhibits Chikungunya Virus Replication by Interacting with Virions and Blocking the Early Steps of Infection. Viruses 2020; 12:v12030314. [PMID: 32191995 PMCID: PMC7150963 DOI: 10.3390/v12030314] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that can cause a debilitating disease that is primarily characterized by persistent joint pain. CHIKV has been emerging globally, while neither a vaccine nor antiviral medication is available. The anti-parasitic drug suramin was previously shown to inhibit CHIKV replication. In this study we aimed to obtain more detailed insight into its mechanism of action. We found that suramin interacts with virions and can inhibit virus binding to cells. It also appeared to inhibit post-attachment steps of the infection process, likely by preventing conformational changes of the envelope glycoproteins required for fusion and the progression of infection. Suramin-resistant CHIKV strains were selected and genotyping and reverse genetics experiments indicated that mutations in E2 were responsible for resistance. The substitutions N5R and H18Q were reverse engineered in the E2 glycoprotein in order to understand their role in resistance. The binding of suramin-resistant viruses with these two E2 mutations was inhibited by suramin like that of wild-type virus, but they appeared to be able to overcome the post-attachment inhibitory effect of suramin. Conversely, a virus with a G82R mutation in E2 (implicated in attenuation of vaccine strain 181/25), which renders it dependent on the interaction with heparan sulfate for entry, was more sensitive to suramin than wild-type virus. Using molecular modelling studies, we predicted the potential suramin binding sites on the mature spikes of the chikungunya virion. We conclude that suramin interferes with CHIKV entry by interacting with the E2 envelope protein, which inhibits attachment and also interferes with conformational changes required for fusion.
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20
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Maljkovic Berry I, Eyase F, Pollett S, Konongoi SL, Joyce MG, Figueroa K, Ofula V, Koka H, Koskei E, Nyunja A, Mancuso JD, Jarman RG, Sang R. Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak. Am J Trop Med Hyg 2020; 100:1249-1257. [PMID: 30860010 PMCID: PMC6493958 DOI: 10.4269/ajtmh.18-0980] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In 2016, a chikungunya virus (CHIKV) outbreak was reported in Mandera, Kenya. This was the first major CHIKV outbreak in the country since the global reemergence of this virus in Kenya in 2004. We collected samples and sequenced viral genomes from this outbreak. All Kenyan genomes contained two mutations, E1:K211E and E2:V264A, recently reported to have an association with increased infectivity, dissemination, and transmission in the Aedes aegypti vector. Phylogeographic inference of temporal and spatial virus relationships showed that this variant emerged within the East, Central, and South African lineage between 2005 and 2008, most probably in India. It was also in India where the first large outbreak caused by this virus appeared, in New Delhi, 2010. More importantly, our results also showed that this variant is no longer contained to India. We found it present in several major outbreaks, including the 2016 outbreaks in Pakistan and Kenya, and the 2017 outbreak in Bangladesh. Thus, this variant may have a capability of driving large CHIKV outbreaks in different regions of the world. Our results point to the importance of continued genomic-based surveillance and prompt urgent vector competence studies to assess the level of vector susceptibility and virus transmission, and the impact this might have on this variant's epidemic potential and global spread.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Fredrick Eyase
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Samson Limbaso Konongoi
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.,United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Michael Gordon Joyce
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland.,Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Katherine Figueroa
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Victor Ofula
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Helen Koka
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Edith Koskei
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Albert Nyunja
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - James D Mancuso
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Rosemary Sang
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
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21
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Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977-2014. J Virol 2020; 94:JVI.01234-19. [PMID: 31666378 PMCID: PMC6955267 DOI: 10.1128/jvi.01234-19] [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: 08/06/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design. Ross River virus (RRV), an alphavirus of the Togaviridae family, is the most medically significant mosquito-borne virus of Australia. Past RRV phylogenetic and evolutionary analyses have been based on partial genome analyses only. Three geographically distinct RRV lineages, the Eastern, the Western, and the supposedly extinct North-Eastern lineage, were classified previously. We sought to expand on past phylogenies through robust genome-scale phylogeny to better understand RRV genetic diversity and evolutionary dynamics. We analyzed 106 RRV complete coding sequences, which included 13 genomes available on NCBI and 94 novel sequences derived for this study, sampled throughout Western Australia (1977–2014) and during the substantial Pacific Islands RRV epidemic (1979–1980). Our final data set comprised isolates sampled over 59 years (1959–2018) from a range of locations. Four distinct genotypes were defined, with the newly described genotype 4 (G4) found to be the contemporary lineage circulating in Western Australia. The prior geographical classification of RRV lineages was not supported by our findings, with evidence of geographical and temporal cocirculation of distinct genetic groups. Bayesian Markov chain Monte Carlo (MCMC) analysis revealed that RRV lineages diverged from a common ancestor approximately 94 years ago, with distinct lineages emerging roughly every 10 years over the past 50 years in periodic bursts of genetic diversity. Our study has enabled a more robust analysis of RRV evolutionary history and resolved greater genetic diversity that had been previously defined by partial E2 gene analysis. IMPORTANCE Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.
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Yang Y, Xu Z, Zheng H, Song J, Wu Y, Tong Z, Yuan J, Wong G, Liu WJ, Bi Y, Liu Y, Gao GF. Genetic and Phylogenetic Characterization of a Chikungunya Virus Imported into Shenzhen, China. Virol Sin 2019; 35:115-119. [PMID: 31637634 DOI: 10.1007/s12250-019-00166-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/23/2019] [Indexed: 10/25/2022] Open
Affiliation(s)
- Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhixiang Xu
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Haixia Zheng
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Jingdong Song
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Ying Wu
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhou Tong
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Gary Wong
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.,Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Quebec, G1V 0A6, Canada
| | - William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Yuhai Bi
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China. .,University of Chinese Academy of Sciences Medical School, Chinese Academy of Sciences, Beijing, 101408, China.
| | - George F Gao
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, Shenzhen, 518112, China. .,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China. .,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China. .,University of Chinese Academy of Sciences Medical School, Chinese Academy of Sciences, Beijing, 101408, China.
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Carpentier KS, Davenport BJ, Haist KC, McCarthy MK, May NA, Robison A, Ruckert C, Ebel GD, Morrison TE. Discrete viral E2 lysine residues and scavenger receptor MARCO are required for clearance of circulating alphaviruses. eLife 2019; 8:e49163. [PMID: 31596239 PMCID: PMC6839921 DOI: 10.7554/elife.49163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
The magnitude and duration of vertebrate viremia is a critical determinant of arbovirus transmission, geographic spread, and disease severity. We find that multiple alphaviruses, including chikungunya (CHIKV), Ross River (RRV), and o'nyong 'nyong (ONNV) viruses, are cleared from the circulation of mice by liver Kupffer cells, impeding viral dissemination. Clearance from the circulation was independent of natural antibodies or complement factor C3, and instead relied on scavenger receptor SR-A6 (MARCO). Remarkably, lysine to arginine substitutions at distinct residues within the E2 glycoproteins of CHIKV and ONNV (E2 K200R) as well as RRV (E2 K251R) allowed for escape from clearance and enhanced viremia and dissemination. Mutational analysis revealed that viral clearance from the circulation is strictly dependent on the presence of lysine at these positions. These findings reveal a previously unrecognized innate immune pathway that controls alphavirus viremia and dissemination in vertebrate hosts, ultimately influencing disease severity and likely transmission efficiency.
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Affiliation(s)
- Kathryn S Carpentier
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraUnited States
| | - Bennett J Davenport
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraUnited States
| | - Kelsey C Haist
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraUnited States
| | - Mary K McCarthy
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraUnited States
| | - Nicholas A May
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraUnited States
| | - Alexis Robison
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsUnited States
| | - Claudia Ruckert
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsUnited States
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsUnited States
| | - Thomas E Morrison
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraUnited States
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Kendra JA, Advani VM, Chen B, Briggs JW, Zhu J, Bress HJ, Pathy SM, Dinman JD. Functional and structural characterization of the chikungunya virus translational recoding signals. J Biol Chem 2018; 293:17536-17545. [PMID: 30242123 DOI: 10.1074/jbc.ra118.005606] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/18/2018] [Indexed: 12/26/2022] Open
Abstract
Climate change and human globalization have spurred the rapid spread of mosquito-borne diseases to naïve populations. One such emerging virus of public health concern is chikungunya virus (CHIKV), a member of the Togaviridae family, genus Alphavirus CHIKV pathogenesis is predominately characterized by acute febrile symptoms and severe arthralgia, which can persist in the host long after viral clearance. CHIKV has also been implicated in cases of acute encephalomyelitis, and its vertical transmission has been reported. Currently, no FDA-approved treatments exist for this virus. Recoding elements help expand the coding capacity in many viruses and therefore represent potential therapeutic targets in antiviral treatments. Here, we report the molecular and structural characterization of two CHIKV translational recoding signals: a termination codon read-through (TCR) element located between the nonstructural protein 3 and 4 genes and a programmed -1 ribosomal frameshift (-1 PRF) signal located toward the 3' end of the CHIKV 6K gene. Using Dual-Luciferase and immunoblot assays in HEK293T and U87MG mammalian cell lines, we validated and genetically characterized efficient TCR and -1 PRF. Analyses of RNA chemical modification data with selective 2'-hydroxyl acylation and primer extension (SHAPE) assays revealed that CHIKV -1 PRF is stimulated by a tightly structured, triple-stem hairpin element, consistent with previous observations in alphaviruses, and that the TCR signal is composed of a single large multibulged hairpin element. These findings illuminate the roles of RNA structure in translational recoding and provide critical information relevant for design of live-attenuated vaccines against CHIKV and related viruses.
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Affiliation(s)
- Joseph A Kendra
- From the Department of Cell Biology and Molecular Genetics and
| | - Vivek M Advani
- From the Department of Cell Biology and Molecular Genetics and.,First-Year Innovation and Research Experience Program, University of Maryland, College Park, Maryland 20742
| | - Bin Chen
- From the Department of Cell Biology and Molecular Genetics and
| | - Joseph W Briggs
- From the Department of Cell Biology and Molecular Genetics and
| | - Jinyi Zhu
- First-Year Innovation and Research Experience Program, University of Maryland, College Park, Maryland 20742
| | - Hannah J Bress
- First-Year Innovation and Research Experience Program, University of Maryland, College Park, Maryland 20742
| | - Sushrut M Pathy
- First-Year Innovation and Research Experience Program, University of Maryland, College Park, Maryland 20742
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25
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White SK, Mavian C, Salemi M, Morris JG, Elbadry MA, Okech BA, Lednicky JA, Dunford JC. A new "American" subgroup of African-lineage Chikungunya virus detected in and isolated from mosquitoes collected in Haiti, 2016. PLoS One 2018; 13:e0196857. [PMID: 29746539 PMCID: PMC5944945 DOI: 10.1371/journal.pone.0196857] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/20/2018] [Indexed: 01/06/2023] Open
Abstract
As part of on-going arboviral surveillance activity in a semi-rural region in Haiti, Chikungunya virus (CHIKV)-positive mosquito pools were identified in 2014 (the peak of the Caribbean Asian-clade epidemic), and again in 2016 by RT-PCR. In 2014, CHIKV was only identified in Aedes aegypti (11 positive pools/124 screened). In contrast, in sampling in 2016, CHIKV was not identified in Ae. aegypti, but, rather, in (a) a female Aedes albopictus pool, and (b) a female Culex quinquefasciatus pool. Genomic sequence analyses indicated that the CHIKV viruses in the 2016 mosquito pools were from the East-Central-South African (ECSA) lineage, rather than the Asian lineage. In phylogenetic studies, these ECSA lineage strains form a new ECSA subgroup (subgroup IIa) together with Brazilian ECSA lineage strains from an isolated human outbreak in 2014, and a mosquito pool in 2016. Additional analyses date the most recent common ancestor of the ECSA IIa subgroup around May 2007, and the 2016 Haitian CHIKV genomes around December 2015. Known CHIKV mutations associated with improved Ae. albopictus vector competence were not identified. Isolation of this newly identified lineage from Ae. albopictus is of concern, as this vector has a broader geographic range than Ae. aegypti, especially in temperate areas of North America, and stresses the importance for continued vector surveillance.
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Affiliation(s)
- Sarah Keller White
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - John Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Maha A. Elbadry
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - Bernard A. Okech
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - John A. Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - James C. Dunford
- US Navy and Marine Corps Public Health Center, Portsmouth, Virginia, United States of America
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The Enigmatic Alphavirus Non-Structural Protein 3 (nsP3) Revealing Its Secrets at Last. Viruses 2018; 10:v10030105. [PMID: 29495654 PMCID: PMC5869498 DOI: 10.3390/v10030105] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/21/2022] Open
Abstract
Alphaviruses encode 4 non-structural proteins (nsPs), most of which have well-understood functions in capping and membrane association (nsP1), polyprotein processing and RNA helicase activity (nsP2) and as RNA-dependent RNA polymerase (nsP4). The function of nsP3 has been more difficult to pin down and it has long been referred to as the more enigmatic of the nsPs. The protein comprises three domains, an N-terminal macro domain, a central zinc-binding domain and a C-terminal hypervariable domain (HVD). In this article, we review old and new literature about the functions of the three domains. Much progress in recent years has contributed to a picture of nsP3, particularly through its HVD as a hub for interactions with host cell molecules, with multiple effects on the biology of the host cell at early points in infection. These and many future discoveries will provide targets for anti-viral therapies as well as strategies for modification of vectors for vaccine and oncolytic interventions.
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