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Kutschera LS, Wolfinger MT. Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology. Virus Evol 2022; 8:veac051. [PMID: 35822110 PMCID: PMC9272599 DOI: 10.1093/ve/veac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/17/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the aetiological agent of tick-borne
encephalitis, an infectious disease of the central nervous system that is often associated
with severe sequelae in humans. While TBEV is typically classified into three subtypes,
recent evidence suggests a more varied range of TBEV subtypes and lineages that differ
substantially in the architecture of their 3ʹ untranslated region (3ʹUTR). Building on
comparative genomic approaches and thermodynamic modelling, we characterize the TBEV UTR
structureome diversity and propose a unified picture of pervasive non-coding RNA structure
conservation. Moreover, we provide an updated phylogeny of TBEV, building on more than 220
publicly available complete genomes, and investigate the molecular epidemiology and
phylodynamics with Nextstrain, a web-based visualization framework for real-time pathogen
evolution.
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Affiliation(s)
- Lena S Kutschera
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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Mayanja MN, Mwiine FN, Lutwama JJ, Ssekagiri A, Egesa M, Thomson EC, Kohl A. Mosquito-borne arboviruses in Uganda: history, transmission and burden. J Gen Virol 2021; 102. [PMID: 34609940 DOI: 10.1099/jgv.0.001680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mosquito-transmitted arboviruses constitute a large proportion of emerging infectious diseases that are both a public health problem and a threat to animal populations. Many such viruses were identified in East Africa, a region where they remain important and from where new arboviruses may emerge. We set out to describe and review the relevant mosquito-borne viruses that have been identified specifically in Uganda. We focused on the discovery, burden, mode of transmission, animal hosts and clinical manifestation of those previously involved in disease outbreaks. A search for mosquito-borne arboviruses detected in Uganda was conducted using search terms 'Arboviruses in Uganda' and 'Mosquitoes and Viruses in Uganda' in PubMed and Google Scholar in 2020. Twenty-four mosquito-borne viruses from different animal hosts, humans and mosquitoes were documented. The majority of these were from family Peribunyaviridae, followed by Flaviviridae, Togaviridae, Phenuiviridae and only one each from family Rhabdoviridae and Reoviridae. Sixteen (66.7%) of the viruses were associated with febrile illnesses. Ten (41.7%) of them were first described locally in Uganda. Six of these are a public threat as they have been previously associated with disease outbreaks either within or outside Uganda. Historically, there is a high burden and endemicity of arboviruses in Uganda. Given the many diverse mosquito species known in the country, there is also a likelihood of many undescribed mosquito-borne viruses. Next generation diagnostic platforms have great potential to identify new viruses. Indeed, four novel viruses, two of which were from humans (Ntwetwe and Nyangole viruses) and two from mosquitoes (Kibale and Mburo viruses) were identified in the last decade using next generation sequencing. Given the unbiased approach of detection of viruses by this technology, its use will undoubtedly be critically important in the characterization of mosquito viromes which in turn will inform other diagnostic efforts.
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Affiliation(s)
- Martin N Mayanja
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Frank N Mwiine
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alfred Ssekagiri
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses Egesa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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Mayanja MN, Mwiine FN, Lutwama JJ, Ssekagiri A, Egesa M, Thomson EC, Kohl A. Mosquito-borne arboviruses in Uganda: history, transmission and burden. J Gen Virol 2021; 102. [PMID: 34166178 DOI: 10.1099/jgv.0.001615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mosquito-transmitted arboviruses constitute a large proportion of emerging infectious diseases that are both a public health problem and a threat to animal populations. Many such viruses were identified in East Africa, a region where they remain important and from where new arboviruses may emerge. We set out to describe and review the relevant mosquito-borne viruses that have been identified specifically in Uganda. We focused on the discovery, burden, mode of transmission, animal hosts and clinical manifestation of those previously involved in disease outbreaks. A search for mosquito-borne arboviruses detected in Uganda was conducted using search terms 'Arboviruses in Uganda' and 'Mosquitoes and Viruses in Uganda' in PubMed and Google Scholar in 2020. Twenty-four mosquito-borne viruses from different animal hosts, humans and mosquitoes were documented. The majority of these were from family Peribunyaviridae, followed by Flaviviridae, Togaviridae, Phenuiviridae and only one each from family Rhabdoviridae and Reoviridae. Sixteen (66.7 %) of the viruses were associated with febrile illnesses. Ten (41.7 %) of them were first described locally in Uganda. Six of these are a public threat as they have been previously associated with disease outbreaks either within or outside Uganda. Historically, there is a high burden and endemicity of arboviruses in Uganda. Given the many diverse mosquito species known in the country, there is also a likelihood of many undescribed mosquito-borne viruses. New generation diagnostic platforms have great potential to identify new viruses. Indeed, four novel viruses, two of which were from humans (Ntwetwe and Nyangole viruses) and two from mosquitoes (Kibale and Mburo viruses) including the 2010 yellow fever virus (YFV) outbreak were identified in the last decade using next generation sequencing. Given the unbiased approach of detection of viruses by this technology, its use will undoubtedly be critically important in the characterization of mosquito viromes which in turn will inform other diagnostic efforts.
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Affiliation(s)
- Martin N Mayanja
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Frank N Mwiine
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alfred Ssekagiri
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses Egesa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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Sharif N, Sarkar MK, Ferdous RN, Ahmed SN, Billah MB, Talukder AA, Zhang M, Dey SK. Molecular Epidemiology, Evolution and Reemergence of Chikungunya Virus in South Asia. Front Microbiol 2021; 12:689979. [PMID: 34163459 PMCID: PMC8215147 DOI: 10.3389/fmicb.2021.689979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 11/23/2022] Open
Abstract
Chikungunya virus (CHIKV) is a vector (mosquito)-transmitted alphavirus (family Togaviridae). CHIKV can cause fever and febrile illness associated with severe arthralgia and rash. Genotypic and phylogenetic analysis are important to understand the spread of CHIKV during epidemics and the diversity of circulating strains for the prediction of effective control measures. Molecular epidemiologic analysis of CHIKV is necessary to understand the complex interaction of vectors, hosts and environment that influences the genotypic evolution of epidemic strains. In this study, different works published during 1950s to 2020 concerning CHIKV evolution, epidemiology, vectors, phylogeny, and clinical outcomes were analyzed. Outbreaks of CHIKV have been reported from Bangladesh, Bhutan, India, Pakistan, Sri Lanka, Nepal, and Maldives in South Asia during 2007–2020. Three lineages- Asian, East/Central/South African (ECSA), and Indian Ocean Lineage (IOL) are circulating in South Asia. Lineage, ECSA and IOL became predominant over Asian lineage in South Asian countries during 2011–2020 epidemics. Further, the mutant E1-A226V is circulating in abundance with Aedes albopictus in India, Bangladesh, Nepal, and Bhutan. CHIKV is underestimated as clinical symptoms of CHIKV infection merges with the symptoms of dengue fever in South Asia. Failure to inhibit vector mediated transmission and predict epidemics of CHIKV increase the risk of larger global epidemics in future. To understand geographical spread of CHIKV, most of the studies focused on CHIKV outbreak, biology, pathogenesis, infection, transmission, and treatment. This updated study will reveal the collective epidemiology, evolution and phylogenies of CHIKV, supporting the necessity to investigate the circulating strains and vectors in South Asia.
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Affiliation(s)
- Nadim Sharif
- Department of Microbiology, Jahangirnagar University, Savar, Bangladesh
| | | | - Rabeya Nahar Ferdous
- Department of Microbiology, Bangladesh University of Health Sciences, Dhaka, Bangladesh
| | | | - Md Baki Billah
- Department of Zoology, Jahangirnagar University, Savar, Bangladesh
| | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Savar, Bangladesh
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, United States
| | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Savar, Bangladesh
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Proteomic Discovery of VEEV E2-Host Partner Interactions Identifies GRP78 Inhibitor HA15 as a Potential Therapeutic for Alphavirus Infections. Pathogens 2021; 10:pathogens10030283. [PMID: 33801554 PMCID: PMC8000471 DOI: 10.3390/pathogens10030283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022] Open
Abstract
Alphaviruses are a genus of the Togaviridae family and are widely distributed across the globe. Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV), cause encephalitis and neurological sequelae while chikungunya virus (CHIKV) and Sindbis virus (SINV) cause arthralgia. There are currently no approved therapeutics or vaccines available for alphaviruses. In order to identify novel therapeutics, a V5 epitope tag was inserted into the N-terminus of the VEEV E2 glycoprotein and used to identify host-viral protein interactions. Host proteins involved in protein folding, metabolism/ATP production, translation, cytoskeleton, complement, vesicle transport and ubiquitination were identified as VEEV E2 interactors. Multiple inhibitors targeting these host proteins were tested to determine their effect on VEEV replication. The compound HA15, a GRP78 inhibitor, was found to be an effective inhibitor of VEEV, EEEV, CHIKV, and SINV. VEEV E2 interaction with GRP78 was confirmed through coimmunoprecipitation and colocalization experiments. Mechanism of action studies found that HA15 does not affect viral RNA replication but instead affects late stages of the viral life cycle, which is consistent with GRP78 promoting viral assembly or viral protein trafficking.
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