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Mandary MB, Masomian M, Poh CL. Impact of RNA Virus Evolution on Quasispecies Formation and Virulence. Int J Mol Sci 2019; 20:E4657. [PMID: 31546962 PMCID: PMC6770471 DOI: 10.3390/ijms20184657] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 12/19/2022] Open
Abstract
RNA viruses are known to replicate by low fidelity polymerases and have high mutation rates whereby the resulting virus population tends to exist as a distribution of mutants. In this review, we aim to explore how genetic events such as spontaneous mutations could alter the genomic organization of RNA viruses in such a way that they impact virus replications and plaque morphology. The phenomenon of quasispecies within a viral population is also discussed to reflect virulence and its implications for RNA viruses. An understanding of how such events occur will provide further evidence about whether there are molecular determinants for plaque morphology of RNA viruses or whether different plaque phenotypes arise due to the presence of quasispecies within a population. Ultimately this review gives an insight into whether the intrinsically high error rates due to the low fidelity of RNA polymerases is responsible for the variation in plaque morphology and diversity in virulence. This can be a useful tool in characterizing mechanisms that facilitate virus adaptation and evolution.
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Affiliation(s)
- Madiiha Bibi Mandary
- Center for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia
| | - Malihe Masomian
- Center for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia
| | - Chit Laa Poh
- Center for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia.
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2
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Simo Tchetgna H, Sem Ouilibona R, Nkili-Meyong AA, Caron M, Labouba I, Selekon B, Njouom R, Leroy EM, Nakoune E, Berthet N. Viral Exploration of Negative Acute Febrile Cases Observed during Chikungunya Outbreaks in Gabon. Intervirology 2019; 61:174-184. [PMID: 30625488 DOI: 10.1159/000495136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/28/2018] [Indexed: 11/19/2022] Open
Abstract
Non-malarial febrile illness outbreaks were documented in 2007 and 2010 in Gabon. After investigation, these outbreaks were attributed to the chikungunya and dengue viruses (CHIKV and DENV). However, for more than half of the samples analyzed, the causative agent was not identified. Given the geographical and ecological position of Gabon, where there is a great animal and microbial diversity, the circulation of other emerging viruses was suspected in these samples lacking aetiology. A total of 436 undiagnosed samples, collected between 2007 and 2013, and originating from 14 urban, suburban, and rural Gabonese locations were selected. These samples were used for viral isolation on newborn mice and VERO cells. In samples with signs of viral replication, cell supernatants and brain suspensions were used to extract nucleic acids and perform real-time RT-PCR targeting specific arboviruses, i.e., CHIKV, DENV, yellow fever, Rift Valley fever, and West Nile and Zika viruses. Virus isolation was conclusive for 43 samples either on newborn mice or by cell culture. Virus identification by RT-PCR led to the identification of CHIKV in 37 isolates. A total of 18 complete genomes and 19 partial sequences containing the E2 and E1 genes of CHIKV were sequenced using next-generation sequencing technology or the Sanger method. Phylogenetic analysis of the complete genomes showed that all the sequences belong to the East Central South Africa lineage. Furthermore, we identified 2 distinct clusters. The first cluster was made up of sequences from the western part of Gabon, whereas the second cluster was made up of sequences from the southern regions, reflecting the way CHIKV spread across the country following its initial introduction in 2007. Similar results were obtained when analyzing the CHIKV genes of the E2 and E1 structural proteins. Moreover, study of the mutations found in the E2 and E1 structural proteins revealed the presence of several mutations that facilitate the adaptation to the Aedes albopictus mosquito, such as E2 I211T and E1 A226V, in all the Gabonese CHIKV strains. Finally, sequencing of 6 additional viral isolates failed to lead to any conclusive identification.
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Affiliation(s)
| | | | | | - Melanie Caron
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Ingrid Labouba
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (IRD 224 - CNRS 5290 - UM1-UM2), Institut de Recherche pour le Développement, Montpellier, France
| | | | - Nicolas Berthet
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon, .,Cellule d'Intervention Biologique d'Urgence, Unité Environnement et risques infectieux, Institut Pasteur, Paris, France, .,Centre National de Recherche Scientifique (CNRS) UMR3569, Paris, France,
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3
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Saha A, Acharya BN, Priya R, Tripathi NK, Shrivastava A, Rao MK, Kesari P, Narwal M, Tomar S, Bhagyawant SS, Parida M, Dash PK. Development of nsP2 protease based cell free high throughput screening assay for evaluation of inhibitors against emerging Chikungunya virus. Sci Rep 2018; 8:10831. [PMID: 30018455 PMCID: PMC6050329 DOI: 10.1038/s41598-018-29024-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 06/20/2018] [Indexed: 01/17/2023] Open
Abstract
Chikungunya virus has emerged as one of the most important global arboviral threats over the last decade. Inspite of large scale morbidity, with long lasting polyarthralgia, so far no licensed vaccine or antiviral is available. CHIKV nsP2 protease is crucial for processing of viral nonstructural polypeptide precursor to release enzymes required for viral replication, thus making it a promising drug target. In this study, high cell density cultivation (HCDC) of Escherichia coli in batch process was carried out to produce rCHIKV nsP2pro in a cost-effective manner. The purified nsP2pro and fluorogenic peptide substrate have been adapted for fluorescence resonance energy transfer (FRET) based high throughput screening (HTS) assay with Z’ value and CV of 0.67 ± 0.054 and <10% respectively. We used this cell free HTS system to screen panel of metal ions and its conjugate which revealed zinc acetate as a potential candidate, which was further found to inhibit CHIKV in Vero cells. Scale-up process has not been previously reported for any of the arboviral nonstructural enzymes. The successful scale-up method for viral protease together with a HTS assay could lead to the development of industrial level large-scale screening platform for identification of protease inhibitors against emerging and re-emerging viruses.
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Affiliation(s)
- Amrita Saha
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Badri Narayan Acharya
- Synthetic Chemistry Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Raj Priya
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Nagesh K Tripathi
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ambuj Shrivastava
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - M Kameswara Rao
- Pharmacology & Toxicology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Pooja Kesari
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Manju Narwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | | | - Manmohan Parida
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Paban Kumar Dash
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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4
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Morley VJ, Noval MG, Chen R, Weaver SC, Vignuzzi M, Stapleford KA, Turner PE. Chikungunya virus evolution following a large 3'UTR deletion results in host-specific molecular changes in protein-coding regions. Virus Evol 2018; 4:vey012. [PMID: 29942653 PMCID: PMC6007266 DOI: 10.1093/ve/vey012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 3′untranslated region (UTR) in alphavirus genomes functions in virus replication and plays a role in determining virus host range. However, the molecular evolution of virus UTRs is understudied compared to the evolution of protein-coding regions. Chikungunya virus (CHIKV) has the longest 3′UTR among the alphaviruses (500–700 nt), and 3′UTR length and sequence structure vary substantially among different CHIKV lineages. Previous studies showed that genomic deletions and insertions are key drivers of CHIKV 3′UTR evolution. Inspired by hypothesized deletion events in the evolutionary history of CHIKV, we used experimental evolution to examine CHIKV adaptation in response to a large 3′UTR deletion. We engineered a CHIKV mutant with a 258 nt deletion in the 3′UTR (ΔDR1/2). This deletion reduced viral replication on mosquito cells, but did not reduce replication on mammalian cells. To examine how selective pressures from vertebrate and invertebrate hosts shape CHIKV evolution after a deletion in the 3′UTR, we passaged ΔDR1/2 virus populations strictly on primate cells, strictly on mosquito cells, or with alternating primate/mosquito cell passages. We found that virus populations passaged on a single host cell line increased in fitness relative to the ancestral deletion mutant on their selected host, and viruses that were alternately passaged improved on both hosts. Surprisingly, whole genome sequencing revealed few changes in the 3′UTR of passaged populations. Rather, virus populations evolved improved fitness through mutations in protein coding regions that were associated with specific hosts.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511-8934, USA
| | | | - Rubing Chen
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | | | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511-8934, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
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Sukkaew A, Thanagith M, Thongsakulprasert T, Mutso M, Mahalingam S, Smith DR, Ubol S. Heterogeneity of clinical isolates of chikungunya virus and its impact on the responses of primary human fibroblast-like synoviocytes. J Gen Virol 2018. [PMID: 29517478 DOI: 10.1099/jgv.0.001039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Low-passage clinical isolates of chikungunya virus (CHIKV) were found to be a mixture of large- and small-plaque viruses, with small-plaque viruses being the predominant species. To investigate the contribution of plaque variants to the pathology of the joint, primary human fibroblast-like synoviocytes (HFLS) were used. Large- and small-plaque viruses were purified from two clinical isolates, CHIKV-031C and CHIKV-033C, and were designated CHIKV-031L and CHIKV-031S and CHIKV-033L and CHIKV-033S, respectively. The replication efficiencies of these viruses in HFLSs were compared and it was found that CHIKV-031S and CHIKV-033S replicated with the highest efficiency, while the parental clinical isolates had the lowest efficiency. Interestingly, the cytopathic effects (CPE) induced by these viruses correlated with neither the efficiency of replication nor the plaque size. The small-plaque viruses and the clinical isolates induced cell death rapidly, while large-plaque viruses induced slow CPE in which only 50 % of the cells in infected cultures were rounded up and detached on day 5 of infection. The production of proinflammatory cytokines and chemokines from infected HFLSs was evaluated. The results showed that the large-plaque viruses and the clinical isolates, but not small-plaque variants, were potent inducers of IL-6, IL-8 and MCP-1, and were able to migrate monocytes/macrophages efficiently. Sequencing data revealed a number of differences in amino acid sequences between the small- and large-plaque viruses. The results suggest that it is common for clinical isolates of CHIKV to be heterogeneous, while the variants may have distinct roles in the pathology of the joint.
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Affiliation(s)
- Apamas Sukkaew
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Rd., Ratchatewi, Bangkok 10400, Thailand
| | | | | | - Margit Mutso
- Institute for Glycomics, Griffith University, Southport, Gold Coast, QLD, Australia
| | - Suresh Mahalingam
- Institute for Glycomics, Griffith University, Southport, Gold Coast, QLD, Australia
| | - Duncan R Smith
- Center for Emerging and Neglected Infectious Diseases, Mahidol University, Salaya Campus, Nakornpathom, Thailand.,Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, Thailand
| | - Sukathida Ubol
- Center for Emerging and Neglected Infectious Diseases, Mahidol University, Salaya Campus, Nakornpathom, Thailand.,Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Rd., Ratchatewi, Bangkok 10400, Thailand
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