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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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2
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Bakker JW, Pascoe EL, van de Water S, van Keulen L, de Vries A, Woudstra LC, Esser HJ, Pijlman GP, de Boer WF, Sprong H, Kortekaas J, Wichgers Schreur PJ, Koenraadt CJM. Infection of wild-caught wood mice (Apodemus sylvaticus) and yellow-necked mice (A. flavicollis) with tick-borne encephalitis virus. Sci Rep 2023; 13:21627. [PMID: 38062065 PMCID: PMC10703896 DOI: 10.1038/s41598-023-47697-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
The distribution of tick-borne encephalitis virus (TBEV) is expanding to Western European countries, including the Netherlands, but the contribution of different rodent species to the transmission of TBEV is poorly understood. We investigated whether two species of wild rodents native to the Netherlands, the wood mouse Apodemus sylvaticus and the yellow-necked mouse Apodemus flavicollis, differ in their relative susceptibility to experimental infection with TBEV. Wild-caught individuals were inoculated subcutaneously with the classical European subtype of TBEV (Neudoerfl) or with TBEV-NL, a genetically divergent TBEV strain from the Netherlands. Mice were euthanised and necropsied between 3 and 21 days post-inoculation. None of the mice showed clinical signs or died during the experimental period. Nevertheless, TBEV RNA was detected up to 21 days in the blood of both mouse species and TBEV was also isolated from the brain of some mice. Moreover, no differences in infection rates between virus strains and mouse species were found in blood, spleen, or liver samples. Our results suggest that the wood mouse and the yellow-necked mouse may equally contribute to the transmission cycle of TBEV in the Netherlands. Future experimental infection studies that include feeding ticks will help elucidate the relative importance of viraemic transmission in the epidemiology of TBEV.
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Affiliation(s)
- Julian W Bakker
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Emily L Pascoe
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Sandra van de Water
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Lucien van Keulen
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Ankje de Vries
- National Institute of Public Health and the Environment (RIVM), Utrecht, The Netherlands
| | - Lianne C Woudstra
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Helen J Esser
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Hein Sprong
- National Institute of Public Health and the Environment (RIVM), Utrecht, The Netherlands
| | - Jeroen Kortekaas
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands
- Boehringer Ingelheim Animal Health, Saint Priest, France
| | - Paul J Wichgers Schreur
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
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3
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Grunwald DJ, Stroschein SM, Grinstead S, Mollov D, Rioux RA, Rakotondrafara AM. Targeting the Highly Conserved 3' Untranslated Region of Iris Severe Mosaic Virus for Sensitive Monitoring of the Disease Prevalence in Iris Production. PLANT DISEASE 2023; 107:3763-3772. [PMID: 37386702 DOI: 10.1094/pdis-04-23-0631-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Iris severe mosaic virus (ISMV, Potyviridae) can threaten the sustainability of iris production and the marketability of the plants. Effective intervention and control strategies require rapid and early detection of viral infections. The wide range of viral symptoms, from asymptomatic to severe chlorosis of the leaves, renders diagnosis solely based on visual indicators ineffective. A nested PCR-based diagnostic assay was developed for the reliable detection of ISMV in iris leaves and in rhizomes. Considering the genetic variability of ISMV, two primer pairs were designed to detect the highly conserved 3' untranslated region (UTR) of the viral genomic RNA. The specificity of the primer pairs was confirmed against four other potyviruses. The sensitivity of detection was enhanced by one order of magnitude using diluted cDNA and a nested approach. Nested PCR facilitated detecting ISMV on field-grown samples beyond the capabilities of a currently available immunological test and in iris rhizome, which would facilitate ensuring clean stock is planted. This approach dramatically improves the detection threshold of ISMV on potentially low virus titer samples. The study provides a practical, accurate, and sensitive tool for the early detection of a deleterious virus that infects a popular ornamental and landscape plant.
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Affiliation(s)
- Derrick J Grunwald
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53705
| | | | - Sam Grinstead
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD 20705
| | - Dimitre Mollov
- Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Renée A Rioux
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53705
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4
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Chiffi G, Grandgirard D, Leib SL, Chrdle A, Růžek D. Tick-borne encephalitis: A comprehensive review of the epidemiology, virology, and clinical picture. Rev Med Virol 2023; 33:e2470. [PMID: 37392370 DOI: 10.1002/rmv.2470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/31/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Tick-borne encephalitis virus (TBEV) is a flavivirus commonly found in at least 27 European and Asian countries. It is an emerging public health problem, with steadily increasing case numbers over recent decades. Tick-borne encephalitis virus affects between 10,000 and 15,000 patients annually. Infection occurs through the bite of an infected tick and, much less commonly, through infected milk consumption or aerosols. The TBEV genome comprises a positive-sense single-stranded RNA molecule of ∼11 kilobases. The open reading frame is > 10,000 bases long, flanked by untranslated regions (UTR), and encodes a polyprotein that is co- and post-transcriptionally processed into three structural and seven non-structural proteins. Tick-borne encephalitis virus infection results in encephalitis, often with a characteristic biphasic disease course. After a short incubation time, the viraemic phase is characterised by non-specific influenza-like symptoms. After an asymptomatic period of 2-7 days, more than half of patients show progression to a neurological phase, usually characterised by central and, rarely, peripheral nervous system symptoms. Mortality is low-around 1% of confirmed cases, depending on the viral subtype. After acute tick-borne encephalitis (TBE), a minority of patients experience long-term neurological deficits. Additionally, 40%-50% of patients develop a post-encephalitic syndrome, which significantly impairs daily activities and quality of life. Although TBEV has been described for several decades, no specific treatment exists. Much remains unknown regarding the objective assessment of long-lasting sequelae. Additional research is needed to better understand, prevent, and treat TBE. In this review, we aim to provide a comprehensive overview of the epidemiology, virology, and clinical picture of TBE.
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Affiliation(s)
- Gabriele Chiffi
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Denis Grandgirard
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Aleš Chrdle
- Department of Infectious Diseases, Hospital Ceske Budejovice, Ceske Budejovice, Czech Republic
- Faculty of Health and Social Sciences, University of South Bohemia, Ceske Budejovice, Czech Republic
- Royal Liverpool University Hospital, Liverpool, UK
| | - Daniel Růžek
- Veterinary Research Institute, Emerging Viral Diseases, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
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5
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Wang K, Zou S, Chen H, Higazy D, Gao X, Zhang Y, Cao S, Cui M. Zika virus replication on endothelial cells and invasion into the central nervous system by inhibiting interferon β translation. Virology 2023; 582:23-34. [PMID: 36996689 DOI: 10.1016/j.virol.2023.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
The blood-brain barrier (BBB) is one of the tightest physical barriers to prevent pathogens from invading the central nervous system (CNS). However, the mechanism by which Zika virus (ZIKV) crossing the BBB remains unresolved. We found ZIKV induced high morbidity and mortality in newborn mice, accompanied by inflammatory injury on CNS. ZIKV was found to replicate primarily in the cortex and hippocampus in neonatal mouse brains. An in vitro model revealed that ZIKV had no impact on hBMECs permeability but led to endothelial activation, as shown by the enhancement of adhesion molecules expression and F-actin redistribution. ZIKV replication in hBMECs might be associated with the suppression of IFN-β translation via inhibiting RPS6 phosphorylation. On the other hand, ZIKV infection induced IFN-stimulated genes (ISGs), activated the mitogen-activated protein kinase (MAPK) signaling pathway, and promoted chemokine secretion. This study provides an understanding of virus replication and transmigration across the BBB during ZIKV infection.
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6
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Mao L, He Y, Wu Z, Wang X, Guo J, Zhang S, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Mao S, Wu Y, Zhang S, Huang J, Ou X, Gao Q, Sun D, Cheng A, Chen S. Stem-Loop I of the Tembusu Virus 3'-Untranslated Region Is Responsible for Viral Host-Specific Adaptation and the Pathogenicity of the Virus in Mice. Microbiol Spectr 2022; 10:e0244922. [PMID: 36214697 PMCID: PMC9602528 DOI: 10.1128/spectrum.02449-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/17/2022] [Indexed: 01/04/2023] Open
Abstract
Tembusu virus (TMUV), an avian mosquito-borne flavivirus, was first identified from Culex tritaeniorhynchus in 1955. To validate the effects of the 3'-untranslated region (3'UTR) in viral host-specific adaptation, we generated a set of chimeric viruses using CQW1 (duck strain) and MM 1775 (mosquito strain) as backbones with heterogeneous 3'UTRs. Compared with rMM 1775, rMM-CQ3'UTR (recombinant MM 1775 virus carrying the 3'UTR of CQW1) exhibited enhanced proliferation in vitro, with peak titers increasing by 5-fold in duck embryonic fibroblast (DEF) cells or 12-fold in baby hamster kidney (BHK-21) cells; however, the neurovirulence of rMM-CQ3'UTR was attenuated in 14-day-old Kunming mice via intracranial injection, with slower weight loss, lower mortality, and reduced viral loads. In contrast, rCQ-MM3'UTR showed similar growth kinetics in vitro and neurovirulence in mice compared with those of rCQW1. Then, the Stem-loop I (SLI) structure, which showed the highest variation within the 3'UTR between CQW1 and MM 1775, was further chosen for making chimeric viruses. The peak titers of rMM-CQ3'UTRSLI displayed a 15- or 4-fold increase in vitro, and the neurovirulence in mice was attenuated, compared with that of rMM 1775; rCQ-MM3'UTRSLI displayed comparable multiplication ability in vitro but was significantly attenuated in mice, in contrast with rCQW1. In conclusion, we demonstrated that the TMUV SLI structure of the 3'UTR was responsible for viral host-specific adaptation of the mosquito-derived strain in DEF and BHK-21 cells and regulated viral pathogenicity in 14-day-old mice, providing a new understanding of the functions of TMUV 3'UTR in viral host switching and the pathogenicity changes in mice. IMPORTANCE Mosquito-borne flaviviruses (MBFVs) constitute a large number of mosquito-transmitted viruses. The 3'-untranslated region (3'UTR) of MBFV has been suggested to be relevant to viral host-specific adaptation. However, the evolutionary strategies for host-specific fitness among MBFV are different, and the virulence-related structures within the 3'UTR are largely unknown. Here, using Tembusu virus (TMUV), an avian MBFV as models, we observed that the duck-derived SLI of the 3'UTR significantly enhanced the proliferation ability of mosquito-derived TMUV in baby hamster kidney (BHK-21) and duck embryonic fibroblast (DEF) cells, suggesting that the SLI structure was crucial for viral host-specific adaptation of mosquito-derived TMUVs in mammalian and avian cells. In addition, all SLI mutant viruses exhibited reduced viral pathogenicity in mice, indicating that SLI structure was a key factor for the pathogenicity in mice. This study provides a new insight into the functions of the MBFV 3'UTR in viral host switching and pathogenicity changes in mice.
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Affiliation(s)
- Li Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhen Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiaqi Guo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Senzhao Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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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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8
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Zakotnik S, Knap N, Bogovič P, Zorec TM, Poljak M, Strle F, Avšič-Županc T, Korva M. Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing. Viruses 2022; 14:v14061267. [PMID: 35746738 PMCID: PMC9231111 DOI: 10.3390/v14061267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/30/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
The clinical presentation of tick-borne encephalitis virus (TBEV) infection varies from asymptomatic to severe meningoencephalitis or meningoencephalomyelitis. The TBEV subtype has been suggested as one of the most important risk factors for disease severity, but TBEV genetic characterization is difficult. Infection is usually diagnosed in the post-viremic phase, and so relevant clinical samples of TBEV are extremely rare and, when present, are associated with low viral loads. To date, only two complete TBEV genomes sequenced directly from patient clinical samples are publicly available. The aim of this study was to develop novel protocols for the direct sequencing of the TBEV genome, enabling studies of viral genetic determinants that influence disease severity. We developed a novel oligonucleotide primer scheme for amplification of the complete TBEV genome. The primer set was tested on 21 clinical samples with various viral loads and collected over a 15-year period using the two most common sequencing platforms. The amplicon-based strategy was compared to direct shotgun sequencing. Using the novel primer set, we successfully obtained nearly complete TBEV genomes (>90% of genome) from all clinical samples, including those with extremely low viral loads. Comparison of consensus sequences of the TBEV genome generated using the novel amplicon-based strategy and shotgun sequencing showed no difference. We conclude that the novel primer set is a powerful tool for future studies on genetic determinants of TBEV that influence disease severity and will lead to a better understanding of TBE pathogenesis.
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Affiliation(s)
- Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Petra Bogovič
- Department of Infectious Diseases, Ljubljana University Medical Center, SI-1000 Ljubljana, Slovenia; (P.B.); (F.S.)
| | - Tomaž Mark Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Franc Strle
- Department of Infectious Diseases, Ljubljana University Medical Center, SI-1000 Ljubljana, Slovenia; (P.B.); (F.S.)
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
- Correspondence:
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9
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Ponomareva EP, Ternovoi VA, Mikryukova TP, Protopopova EV, Tupota NL, Loktev VB. Genetic Variability of Tick-Borne Encephalitis Virus Genome 5'-UTR from Northern Eurasia. Mol Biol 2021. [DOI: 10.1134/s002689332102028x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Zhang YN, Li N, Zhang QY, Liu J, Zhan SL, Gao L, Zeng XY, Yu F, Zhang HQ, Li XD, Deng CL, Shi PY, Yuan ZM, Yuan SP, Ye HQ, Zhang B. Rational design of West Nile virus vaccine through large replacement of 3' UTR with internal poly(A). EMBO Mol Med 2021; 13:e14108. [PMID: 34351689 PMCID: PMC8422072 DOI: 10.15252/emmm.202114108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022] Open
Abstract
The genus Flavivirus comprises numerous emerging and re-emerging arboviruses causing human illness. Vaccines are the best approach to prevent flavivirus diseases. But pathogen diversities are always one of the major hindrances for timely development of new vaccines when confronting unpredicted flavivirus outbreaks. We used West Nile virus (WNV) as a model to develop a new live-attenuated vaccine (LAV), WNV-poly(A), by replacing 5' portion (corresponding to SL and DB domains in WNV) of 3'-UTR with internal poly(A) tract. WNV-poly(A) not only propagated efficiently in Vero cells, but also was highly attenuated in mouse model. A single-dose vaccination elicited robust and long-lasting immune responses, conferring full protection against WNV challenge. Such "poly(A)" vaccine strategy may be promising for wide application in the development of flavivirus LAVs because of its general target regions in flaviviruses.
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Affiliation(s)
- Ya-Nan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Na Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Qiu-Yan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Jing Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Shun-Li Zhan
- Beijing Shunlei Biotechnology Co. Ltd., Beijing, China
| | - Lei Gao
- Beijing Shunlei Biotechnology Co. Ltd., Beijing, China
| | - Xiang-Yue Zeng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fang Yu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Hong-Qing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Dan Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Lin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, TX, USA
| | - Zhi-Ming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Han-Qing Ye
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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11
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Egyed L, Biksi I, Varga T, Zöldi V, Dán Á. Analysing the genomes of two tick-borne encephalitis viruses isolated in Hungary in 1952 and 2019. Ticks Tick Borne Dis 2021; 12:101806. [PMID: 34455141 DOI: 10.1016/j.ttbdis.2021.101806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/20/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022]
Abstract
The genomes of two Tick-borne encephalitis virus (TBEV) strains were fully sequenced and compared to those of known Hungarian strains. One was a laboratory strain (KEM-1) isolated in 1952, which had gone through hundreds of passages both on Vero cell cultures and in laboratory mice, while the other was a recent isolate (2019) from questing female ticks. The laboratory strain formed a monophyletic group with the already published 4 Hungarian strains on the evolutionary tree, located relatively close to Finnish (Kumlinge) and Russian (Absettarov) strains. This KEM-1 strain was phylogenetically distantly related both to the geographically close reference strain Neudörfl and the chronologically close Czech isolates from 1953. The 2019 isolate, KEM-195 was related to TBEV isolates from Southern Slovakia and Styria, and had the longest (328 nucleotides) deletion in its 3'-non-coding region among published sequences of strains of European subtype. Our results show that decades of laboratory passage have not altered the viral genome too much and that at least two distinct branches of TBEV strains circulate in Hungary.
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Affiliation(s)
- L Egyed
- Veterinary Medical Research Institute, ELKH, Hungária krt. 21, Budapest 1143, Hungary.
| | - I Biksi
- SCG Diagnosztika Ltd., Délegyháza, Hungary
| | - T Varga
- SCG Diagnosztika Ltd., Délegyháza, Hungary
| | - V Zöldi
- Department of Pest control, National Centre for Epidemiology, Budapest, Hungary
| | - Á Dán
- Danam.Vet. Molbiol, Kőszeg, Hungary
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12
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Diagne MM, Ndione MHD, Gaye A, Barry MA, Diallo D, Diallo A, Mwakibete LL, Diop M, Ndiaye EH, Ahyong V, Diouf B, Mhamadi M, Diagne CT, Danfakha F, Diop B, Faye O, Loucoubar C, Fall G, Tato CM, Sall AA, Weaver SC, Diallo M, Faye O. Yellow Fever Outbreak in Eastern Senegal, 2020-2021. Viruses 2021; 13:v13081475. [PMID: 34452343 PMCID: PMC8402698 DOI: 10.3390/v13081475] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/07/2023] Open
Abstract
Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees of impact on populations in perpetual renewal. We report an outbreak that occurred from October 2020 to February 2021 in eastern Senegal, notified and managed through the synergistic effort yellow fever national surveillance implemented by the Senegalese Ministry of Health in collaboration with the World Health Organization, the countrywide 4S network set up by the Ministry of Health, the Institut Pasteur de Dakar, and the surveillance of arboviruses and hemorrhagic fever viruses in human and vector populations implemented since mid 2020 in eastern Senegal. Virological analyses highlighted the implication of sylvatic mosquito species in virus transmission. Genomic analysis showed a close relationship between the circulating strain in eastern Senegal, 2020, and another one from the West African lineage previously detected and sequenced two years ago from an unvaccinated Dutch traveler who visited the Gambia and Senegal before developing signs after returning to Europe. Moreover, genome analysis identified a 6-nucleotide deletion in the variable domain of the 3′UTR with potential impact on the biology of the viral strain that merits further investigations. Integrated surveillance of yellow fever virus but also of other arboviruses of public health interest is crucial in an ecosystem such as eastern Senegal.
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Affiliation(s)
- Moussa Moïse Diagne
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
- Correspondence: ; Tel.: +221-77-405-9928
| | - Marie Henriette Dior Ndione
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Alioune Gaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Diawo Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Lusajo L. Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - El Hadji Ndiaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Babacar Diouf
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Moufid Mhamadi
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cheikh Tidiane Diagne
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Fodé Danfakha
- Kedougou Medical Region, Ministry of Health, Kedougou 26005, Senegal;
| | - Boly Diop
- Prevention Department, Ministry of Health, Dakar 220, Senegal;
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Mawlouth Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
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13
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The Pseudo-Circular Genomes of Flaviviruses: Structures, Mechanisms, and Functions of Circularization. Cells 2021; 10:cells10030642. [PMID: 33805761 PMCID: PMC7999817 DOI: 10.3390/cells10030642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 11/23/2022] Open
Abstract
The circularization of viral genomes fulfills various functions, from evading host defense mechanisms to promoting specific replication and translation patterns supporting viral proliferation. Here, we describe the genomic structures and associated host factors important for flaviviruses genome circularization and summarize their functional roles. Flaviviruses are relatively small, single-stranded, positive-sense RNA viruses with genomes of approximately 11 kb in length. These genomes contain motifs at their 5′ and 3′ ends, as well as in other regions, that are involved in circularization. These motifs are highly conserved throughout the Flavivirus genus and occur both in mature virions and within infected cells. We provide an overview of these sequence motifs and RNA structures involved in circularization, describe their linear and circularized structures, and discuss the proteins that interact with these circular structures and that promote and regulate their formation, aiming to clarify the key features of genome circularization and understand how these affect the flaviviruses life cycle.
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14
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Clark JJ, Gilray J, Orton RJ, Baird M, Wilkie G, Filipe ADS, Johnson N, McInnes CJ, Kohl A, Biek R. Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Negl Trop Dis 2020; 14:e0008133. [PMID: 32925939 PMCID: PMC7515184 DOI: 10.1371/journal.pntd.0008133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 09/24/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors. Tick-borne pathogens represent a major emerging threat to public health and in recent years have been expanding into new areas. LIV is a neglected virus endemic to the UK and Ireland (though it has been detected in Scandinavia and Russia) which is closely related to the major human pathogen TBEV, but predominantly causes disease in sheep and grouse. The recent detection of TBEV in the UK, which has also emerged elsewhere in Europe, requires more detailed understanding of the spread and sequence diversity of LIV. This could be important for diagnosis and vaccination, but also to improve our understanding of the evolution and emergence of these tick-borne viruses. Here we describe the sequencing of 22 LIV isolates which have been sampled from several host species across the past century. We have utilised this dataset to investigate the evolutionary pressures that LIV is subjected to and have explored the evolution of LIV using phylogenetic analysis. Crucially we were unable to estimate a reliable molecular clock rate for LIV and found that this problem also extends to a larger phylogeny of TBEV sequences. This work highlights a previously unknown caveat of tick-borne flavivirus evolutionary analysis which may be important for understanding the evolution of these important pathogens.
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Affiliation(s)
- Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Moredun Research Institute, Edinburgh, United Kingdom
- * E-mail: (JC); (RB)
| | - Janice Gilray
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Margaret Baird
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Gavin Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicholas Johnson
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- Faculty of Health and Medical Science, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine - University of Glasgow, Glasgow, United Kingdom
- * E-mail: (JC); (RB)
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15
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Liu Y, Zhang Y, Wang M, Cheng A, Yang Q, Wu Y, Jia R, Liu M, Zhu D, Chen S, Zhang S, Zhao X, Huang J, Mao S, Ou X, Gao Q, Wang Y, Xu Z, Chen Z, Zhu L, Luo Q, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. Structures and Functions of the 3' Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals. Front Cell Infect Microbiol 2020; 10:453. [PMID: 32974223 PMCID: PMC7481400 DOI: 10.3389/fcimb.2020.00453] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022] Open
Abstract
The 3′ untranslated region (3′ UTR) of positive-sense single-stranded RNA [ssRNA(+)] viruses is highly structured. Multiple elements in the region interact with other nucleotides and proteins of viral and cellular origin to regulate various aspects of the virus life cycle such as replication, translation, and the host-cell response. This review attempts to summarize the primary and higher order structures identified in the 3′UTR of ssRNA(+) viruses and their functional roles.
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Affiliation(s)
- Yuanzhi Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - XinXin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yin Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhiwen Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qihui Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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16
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Analysis of the Function of the Lymphocytic Choriomeningitis Virus S Segment Untranslated Region on Growth Capacity In Vitro and on Virulence In Vivo. Viruses 2020; 12:v12080896. [PMID: 32824338 PMCID: PMC7474432 DOI: 10.3390/v12080896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/18/2022] Open
Abstract
Lymphocytic choriomeningitis virus (LCMV) is a prototypic arenavirus. The function of untranslated regions (UTRs) of the LCMV genome has not been well studied except for the extreme 19 nucleotide residues of both the 5′ and 3′ termini. There are internal UTRs composed of 58 and 41 nucleotide residues in the 5′ and 3′ UTRs, respectively, in the LCMV S segment. Their functional roles have yet to be elucidated. In this study, reverse genetics and minigenome systems were established for LCMV strain WE and the function of these regions were analyzed. It was revealed that nucleotides 20–40 and 20–38 located downstream of the 19 nucleotides in the 5′ and 3′ termini, respectively, were involved in viral genome replication and transcription. Furthermore, it was revealed that the other internal UTRs (nucleotides 41–77 and 39–60 in the 5′ and 3′ termini, respectively) in the S segment were involved in virulence in vivo, even though these regions did not affect viral growth capacity in Vero cells. The introduction of LCMV with mutations in these regions attenuates the virus and may enable the production of LCMV vaccine candidates.
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17
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Different Degrees of 5'-to-3' DAR Interactions Modulate Zika Virus Genome Cyclization and Host-Specific Replication. J Virol 2020; 94:JVI.01602-19. [PMID: 31826997 PMCID: PMC7022364 DOI: 10.1128/jvi.01602-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/06/2019] [Indexed: 01/06/2023] Open
Abstract
Mosquito-borne flaviviruses, which include many important human pathogens, such as West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV), have caused numerous emerging epidemics in recent years. Details of the viral genome functions necessary for effective viral replication in mosquito and vertebrate hosts remain obscure. Here, using ZIKV as a model, we found that the conserved "downstream of AUG region" (DAR), which is known to be an essential element for genome cyclization, is involved in viral replication in a host-specific manner. Mutational analysis of the DAR element showed that a single-nucleotide mismatch between the 5' DAR and the 3' DAR had little effect on ZIKV replication in mammalian cells but dramatically impaired viral propagation in mosquito cells. The revertant viruses passaged in mosquito cells generated compensatory mutations restoring the base pairing of the DAR, further confirming the importance of the complementarity of the DAR in mosquito cells. We demonstrate that a single-nucleotide mutation in the DAR is sufficient to destroy long-range RNA interaction of the ZIKV genome and affects de novo RNA synthesis at 28°C instead of 37°C, resulting in the different replication efficiencies of the mutant viruses in mosquito and mammalian cells. Our results reveal a novel function of the circular form of the flavivirus genome in host-specific viral replication, providing new ideas to further explore the functions of the viral genome during host adaptation.IMPORTANCE Flaviviruses naturally cycle between the mosquito vector and vertebrate hosts. The disparate hosts provide selective pressures that drive virus genome evolution to maintain efficient replication during host alteration. Host adaptation may occur at different stages of the viral life cycle, since host-specific viral protein processing and virion conformations have been reported in the individual hosts. However, the viral determinants and the underlying mechanisms associated with host-specific functions remain obscure. In this study, using Zika virus, we found that the DAR-mediated genome cyclization regulates viral replication differently and is under different selection pressures in mammalian and mosquito cells. A more constrained complementarity of the DAR is required in mosquito cells than in mammalian cells. Since the DAR element is stably maintained among mosquito-borne flaviviruses, our findings could provide new information for understanding the role of flavivirus genome cyclization in viral adaptation and RNA evolution in the two hosts.
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Velay A, Paz M, Cesbron M, Gantner P, Solis M, Soulier E, Argemi X, Martinot M, Hansmann Y, Fafi-Kremer S. Tick-borne encephalitis virus: molecular determinants of neuropathogenesis of an emerging pathogen. Crit Rev Microbiol 2019; 45:472-493. [PMID: 31267816 DOI: 10.1080/1040841x.2019.1629872] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tick-borne encephalitis virus (TBEV) is a zoonotic agent causing severe encephalitis. The transmission cycle involves the virus, the Ixodes tick vector, and a vertebrate reservoir, such as small mammals (rodents, or shrews). Humans are accidentally involved in this transmission cycle. Tick-borne encephalitis (TBE) has been a growing public health problem in Europe and Asia over the past 30 years. The mechanisms involved in the development of TBE are very complex and likely multifactorial, involving both host and viral factors. The purpose of this review is to provide an overview of the current literature on TBE neuropathogenesis in the human host and to demonstrate the emergence of common themes in the molecular pathogenesis of TBE in humans. We discuss and review data on experimental study models and on both viral (molecular genetics of TBEV) and host (immune response, and genetic background) factors involved in TBE neuropathogenesis in the context of human infection.
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Affiliation(s)
- Aurélie Velay
- Virology Laboratory, University Hospital of Strasbourg , Strasbourg , France.,INSERM, IRM UMR_S 1109 , Strasbourg , France
| | - Magali Paz
- Virology Laboratory, University Hospital of Strasbourg , Strasbourg , France
| | - Marlène Cesbron
- Virology Laboratory, University Hospital of Strasbourg , Strasbourg , France
| | - Pierre Gantner
- Virology Laboratory, University Hospital of Strasbourg , Strasbourg , France.,INSERM, IRM UMR_S 1109 , Strasbourg , France
| | - Morgane Solis
- Virology Laboratory, University Hospital of Strasbourg , Strasbourg , France.,INSERM, IRM UMR_S 1109 , Strasbourg , France
| | | | - Xavier Argemi
- Service des maladies infectieuses et tropicales, Hôpitaux Universitaires de Strasbourg , Strasbourg , France
| | - Martin Martinot
- Service de Médecine Interne et de Rhumatologie, Hôpitaux Civils de Colmar , Colmar , France
| | - Yves Hansmann
- Service des maladies infectieuses et tropicales, Hôpitaux Universitaires de Strasbourg , Strasbourg , France
| | - Samira Fafi-Kremer
- Virology Laboratory, University Hospital of Strasbourg , Strasbourg , France.,INSERM, IRM UMR_S 1109 , Strasbourg , France
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19
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Ignatieva EV, Yurchenko AA, Voevoda MI, Yudin NS. Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population. BMC Med Genomics 2019; 12:61. [PMID: 31122248 PMCID: PMC6533173 DOI: 10.1186/s12920-019-0503-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Tick-borne encephalitis (TBE) is a viral infectious disease caused by tick-borne encephalitis virus (TBEV). TBEV infection is responsible for a variety of clinical manifestations ranging from mild fever to severe neurological illness. Genetic factors involved in the host response to TBEV that may potentially play a role in the severity of the disease are still poorly understood. In this study, using whole-exome sequencing, we aimed to identify genetic variants and genes associated with severe forms of TBE as well as biological pathways through which the identified variants may influence the severity of the disease. Results Whole-exome sequencing data analysis was performed on 22 Russian patients with severe forms of TBE and 17 Russian individuals from the control group. We identified 2407 candidate genes harboring rare, potentially pathogenic variants in exomes of patients with TBE and not containing any rare, potentially pathogenic variants in exomes of individuals from the control group. According to DAVID tool, this set of 2407 genes was enriched with genes involved in extracellular matrix proteoglycans pathway and genes encoding proteins located at the cell periphery. A total of 154 genes/proteins from these functional groups have been shown to be involved in protein-protein interactions (PPIs) with the known candidate genes/proteins extracted from TBEVHostDB database. By ranking these genes according to the number of rare harmful minor alleles, we identified two genes (MSR1 and LMO7), harboring five minor alleles, and three genes (FLNA, PALLD, PKD1) harboring four minor alleles. When considering genes harboring genetic variants associated with severe forms of TBE at the suggestive P-value < 0.01, 46 genes containing harmful variants were identified. Out of these 46 genes, eight (MAP4, WDFY4, ACTRT2, KLHL25, MAP2K3, MBD1, OR10J1, and OR2T34) were additionally found among genes containing rare pathogenic variants identified in patients with TBE; and five genes (WDFY4,ALK, MAP4, BNIPL, EPPK1) were found to encode proteins that are involved in PPIs with proteins encoded by genes from TBEVHostDB. Three genes out of five (MAP4, EPPK1, ALK) were found to encode proteins located at cell periphery. Conclusions Whole-exome sequencing followed by systems biology approach enabled to identify eight candidate genes (MAP4, WDFY4, ACTRT2, KLHL25, MAP2K3, MBD1, OR10J1, and OR2T34) that can potentially determine predisposition to severe forms of TBE. Analyses of the genetic risk factors for severe forms of TBE revealed a significant enrichment with genes controlling extracellular matrix proteoglycans pathway as well as genes encoding components of cell periphery. Electronic supplementary material The online version of this article (10.1186/s12920-019-0503-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena V Ignatieva
- Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Andrey A Yurchenko
- Laboratory of Infectious Disease Genomics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Mikhail I Voevoda
- Novosibirsk State University, Novosibirsk, 630090, Russia.,Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630004, Russia
| | - Nikolay S Yudin
- Laboratory of Infectious Disease Genomics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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20
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Ternovoi VA, Gladysheva AV, Ponomareva EP, Mikryukova TP, Protopopova EV, Shvalov AN, Konovalova SN, Chausov EV, Loktev VB. Variability in the 3' untranslated regions of the genomes of the different tick-borne encephalitis virus subtypes. Virus Genes 2019; 55:448-457. [PMID: 31111398 DOI: 10.1007/s11262-019-01672-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/14/2019] [Indexed: 12/21/2022]
Abstract
Tick-borne encephalitis viruses (TBEVs) are usually divided into three major subtypes: European (TBEV-Eu), Siberian (TBEV-Sib) and Far Eastern (TBEV-FE). The TBEV-Eu strains have the longest genomes, and TBEV-FE strains have the smallest genomes. Changes in the variable region of the untranslated region (V3' UTR) play a major role in determining the viral genome length. Analyses of the 3' UTRs of the different subtypes of TBEV have revealed significant changes in the secondary structures of the V3' UTR of TBEV. More complex secondary structures of the V3' UTR regions are typical for TBEV-Eu. The Siberian strain Tomsk-PT122 was isolated from birds and has an unusual 3' UTR. Several short fragment (24-26 nucleotides) insertions derived from the viral E (2) and NS4a (1) genes have been found in the V3' UTR of Tomsk-PT122. Additionally, the length of the V3' UTR increases from 21 to 37 nucleotides during passages of the C11-13 strain of TBEV-Sib into PEK, 293 and Neuro-2a cells. The elongation of the V3' UTRs of Tomsk-PT122 and C11-13 is the first direct evidence of an intragenomic 3' UTR modification (insertion) for TBEV. Thus, the obtained results suggest that changing the length of the V3' UTR in the genome is typical for different TBEV subtypes and can play an essential role in effective TBEV replication in different host cells.
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Affiliation(s)
- Vladimir A Ternovoi
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Anastasia V Gladysheva
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Eugenia P Ponomareva
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Tamara P Mikryukova
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Elena V Protopopova
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Alexander N Shvalov
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Svetlana N Konovalova
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Eugene V Chausov
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia
| | - Valery B Loktev
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, 630559, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia.
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21
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Maeki T, Tajima S, Ikeda M, Kato F, Taniguchi S, Nakayama E, Takasaki T, Lim CK, Saijo M. Analysis of cross-reactivity between flaviviruses with sera of patients with Japanese encephalitis showed the importance of neutralization tests for the diagnosis of Japanese encephalitis. J Infect Chemother 2019; 25:786-790. [PMID: 31105002 DOI: 10.1016/j.jiac.2019.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/23/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022]
Abstract
Japanese encephalitis (JE) is one of the most important viral encephalitis in Asia. JE is caused by the Japanese encephalitis virus (JEV), which belongs to the genus Flavivirus, family Flaviviridae. The diagnosis of JE is usually based on serological assays, and it has been reported that cross-reactivity between flaviviruses has complicated the interpretations of results from serological assays. Therefore, analysis of the cross-reactivity is an important subject for serological diagnosis of JE and other diseases caused by flaviviruses. In the present study, the cross-reactivity of the sera of patients with JE to other flaviviruses was analyzed using enzyme-linked immunosorbent assay (ELISA) and neutralization tests. Sixteen serum samples were collected from patients with JE and were tested for: i) IgM antibody against West Nile virus (WNV), dengue virus (DENV), zika virus (ZIKV), and tick-borne encephalitis virus (TBEV) using IgM-ELISA, ii) IgG antibody against DENV and TBEV using IgG-ELISA, and iii) neutralization tests with DENV 1-4, ZIKV, TBEV, and WNV. Out of the 16 samples tested using ELISA, 11 and 14 samples were positive for IgM and IgG, respectively, against at least one of the other flaviviruses. In neutralization tests, neutralizing potency against DENV, ZIKV, or TBEV was not detected in any samples. Although 13 samples showed neutralizing potency against WNV, their neutralizing antibody titers were equal to or less than one-eighth of those against JEV. These results show that neutralization tests are more specific than ELISA, indicating the importance of the neutralization tests in the diagnosis of JE.
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Affiliation(s)
- Takahiro Maeki
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan.
| | - Shigeru Tajima
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Makiko Ikeda
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Fumihiro Kato
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Satoshi Taniguchi
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Eri Nakayama
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, 1-3-1 Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan
| | - Chang-Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
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Abstract
Tick-borne encephalitis virus (TBEV), a member of the genus Flavivirus within the family Flaviviridae, causes fatal encephalitis with severe sequelae in humans. TBEV is
prevalent over a wide area of the Eurasian continent including Europe, Russia, Far-Eastern Asia, and Japan. While it was previously thought that TBEV was not endemic in Japan, the first
confirmed case of serologically diagnosed TBE was reported in 1993 in the southern area of Hokkaido Prefecture, Japan. In addition, TBEV has been isolated from dogs, wild rodents and ticks
in the area. Our epizootiological survey indicated that endemic foci of TBEV were maintained in Hokkaido and other areas of Honshu. TBEV can be divided into three subtypes based on
phylogenetic analyses. The Japanese isolates were classified as the Far Eastern subtype, which causes severe neural disorders with a higher mortality rate up to 30%. However, how viral
replication and pathogenicity contribute to the neurological manifestations remains unclear. Recent studies have revealed distinctive mechanisms of TBEV pathogenicity and viral genetic
factors associated with virulence. This review discusses the recent findings regarding the epidemiology and pathogenesis of TBEV.
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Affiliation(s)
- Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
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23
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Kellman EM, Offerdahl DK, Melik W, Bloom ME. Viral Determinants of Virulence in Tick-Borne Flaviviruses. Viruses 2018; 10:v10060329. [PMID: 29914165 PMCID: PMC6024809 DOI: 10.3390/v10060329] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/27/2022] Open
Abstract
Tick-borne flaviviruses have a global distribution and cause significant human disease, including encephalitis and hemorrhagic fever, and often result in neurologic sequelae. There are two distinct properties that determine the neuropathogenesis of a virus. The ability to invade the central nervous system (CNS) is referred to as the neuroinvasiveness of the agent, while the ability to infect and damage cells within the CNS is referred to as its neurovirulence. Examination of laboratory variants, cDNA clones, natural isolates with varying pathogenicity, and virally encoded immune evasion strategies have contributed extensively to our understanding of these properties. Here we will review the major viral determinants of virulence that contribute to pathogenesis and influence both neuroinvasiveness and neurovirulence properties of tick-borne flaviviruses, focusing particularly on the envelope protein (E), nonstructural protein 5 (NS5), and the 3′ untranslated region (UTR).
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Affiliation(s)
- Eliza M Kellman
- Laboratory of Virology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA.
| | - Danielle K Offerdahl
- Laboratory of Virology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA.
| | - Wessam Melik
- School of Medical Sciences, Orebro University, SE-703 62 Örebro, Sweden.
| | - Marshall E Bloom
- Laboratory of Virology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA.
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24
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Barrows NJ, Campos RK, Liao KC, Prasanth KR, Soto-Acosta R, Yeh SC, Schott-Lerner G, Pompon J, Sessions OM, Bradrick SS, Garcia-Blanco MA. Biochemistry and Molecular Biology of Flaviviruses. Chem Rev 2018; 118:4448-4482. [PMID: 29652486 DOI: 10.1021/acs.chemrev.7b00719] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA-protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes. In this review, we examine the molecular biology of flaviviruses touching on the structure and function of viral components and how these interact with host factors. The latter are functionally divided into pro-viral and antiviral factors, both of which, not surprisingly, include many RNA binding proteins. In the interface between the virus and the hosts we highlight the role of a noncoding RNA produced by flaviviruses to impair antiviral host immune responses. Throughout the review, we highlight areas of intense investigation, or a need for it, and potential targets and tools to consider in the important battle against pathogenic flaviviruses.
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Affiliation(s)
- Nicholas J Barrows
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Rafael K Campos
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Kuo-Chieh Liao
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Ruben Soto-Acosta
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Shih-Chia Yeh
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Geraldine Schott-Lerner
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Julien Pompon
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore.,MIVEGEC, IRD, CNRS, Université de Montpellier , Montpellier 34090 , France
| | - October M Sessions
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
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25
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Ignatieva EV, Igoshin AV, Yudin NS. A database of human genes and a gene network involved in response to tick-borne encephalitis virus infection. BMC Evol Biol 2017; 17:259. [PMID: 29297316 PMCID: PMC5751789 DOI: 10.1186/s12862-017-1107-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Tick-borne encephalitis is caused by the neurotropic, positive-sense RNA virus, tick-borne encephalitis virus (TBEV). TBEV infection can lead to a variety of clinical manifestations ranging from slight fever to severe neurological illness. Very little is known about genetic factors predisposing to severe forms of disease caused by TBEV. The aims of the study were to compile a catalog of human genes involved in response to TBEV infection and to rank genes from the catalog based on the number of neighbors in the network of pairwise interactions involving these genes and TBEV RNA or proteins. RESULTS Based on manual review and curation of scientific publications a catalog comprising 140 human genes involved in response to TBEV infection was developed. To provide access to data on all genes, the TBEVhostDB web resource ( http://icg.nsc.ru/TBEVHostDB/ ) was created. We reconstructed a network formed by pairwise interactions between TBEV virion itself, viral RNA and viral proteins and 140 genes/proteins from TBEVHostDB. Genes were ranked according to the number of interactions in the network. Two genes/proteins (CCR5 and IFNAR1) that had maximal number of interactions were revealed. It was found that the subnetworks formed by CCR5 and IFNAR1 and their neighbors were a fragments of two key pathways functioning during the course of tick-borne encephalitis: (1) the attenuation of interferon-I signaling pathway by the TBEV NS5 protein that targeted peptidase D; (2) proinflammation and tissue damage pathway triggered by chemokine receptor CCR5 interacting with CD4, CCL3, CCL4, CCL2. Among nine genes associated with severe forms of TBEV infection, three genes/proteins (CCR5, IL10, ARID1B) were found to have protein-protein interactions within the network, and two genes/proteins (IFNL3 and the IL10, that was just mentioned) were up- or down-regulated in response to TBEV infection. Based on this finding, potential mechanisms for participation of CCR5, IL10, ARID1B, and IFNL3 in the host response to TBEV infection were suggested. CONCLUSIONS A database comprising 140 human genes involved in response to TBEV infection was compiled and the TBEVHostDB web resource, providing access to all genes was created. This is the first effort of integrating and unifying data on genetic factors that may predispose to severe forms of diseases caused by TBEV. The TBEVHostDB could potentially be used for assessment of risk factors for severe forms of tick-borne encephalitis and for the design of personalized pharmacological strategies for the treatment of TBEV infection.
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Affiliation(s)
- Elena V Ignatieva
- Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Center for Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Alexander V Igoshin
- Laboratory of Infectious Disease Genomics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nikolay S Yudin
- Laboratory of Infectious Disease Genomics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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26
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Yoshii K, Song JY, Park SB, Yang J, Schmitt HJ. Tick-borne encephalitis in Japan, Republic of Korea and China. Emerg Microbes Infect 2017; 6:e82. [PMID: 28928417 PMCID: PMC5625319 DOI: 10.1038/emi.2017.69] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/29/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022]
Abstract
Tick-borne encephalitis virus (TBEV) causes mild or moderate febrile illness in humans that may progress to encephalitis, leading to severe long-term complications and sometimes death. TBEV is prevalent in the Eurasian continent and has been isolated in China, Japan and Republic of Korea (ROK). The TBEV isolates from Japan are of the Far-Eastern subtype; in ROK, the isolates are of the Western subtype; and all TBEV isolates in China are of the Far-Eastern subtype, except one strain that was identified most recently as the Siberian subtype. TBE is endemic to the northeast, northwest and southeast of China; only two confirmed TBE cases have been reported in Japan to date; and no TBE case has been confirmed in ROK. For TBE patients in China, the onset of disease is acute with no biphasic course for disease presentation. The clinical spectrum of disease phenotypes may be wider than currently understood, since serological evidence suggests the presence of TBEV infections in healthy people, indicating that asymptomatic or unspecific manifestations of TBEV infection may exist. The current treatment for TBE is supportive care. In China, vaccines against TBEV have been developed and are available with demonstrated immunogenicity and safety, although efficacy data are lacking. No vaccines are available in ROK or Japan.
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Affiliation(s)
- Kentaro Yoshii
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University Guro Hospital, Gurodongro 148, Gurogu, Seoul 08308, Republic of Korea
| | - Seong-Beom Park
- Pfizer Pharmaceuticals Korea Ltd, Seoul 100-771, Republic of Korea
| | - Junfeng Yang
- Pfizer Investment Co., Ltd. The Fifth Square, Tower B, 9/F, No. 3-7, Chaoyangmen North Avenue, Dongcheng District, Beijing 100010, China
| | - Heinz-Josef Schmitt
- Scientific Affairs, Pfizer Vaccines Europe, 23-25 Avenue du Dr Lannelongue, Paris 75014, France
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The 5' and 3' Untranslated Regions of the Flaviviral Genome. Viruses 2017; 9:v9060137. [PMID: 28587300 PMCID: PMC5490814 DOI: 10.3390/v9060137] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/16/2017] [Accepted: 05/29/2017] [Indexed: 01/30/2023] Open
Abstract
Flaviviruses are enveloped arthropod-borne viruses with a single-stranded, positive-sense RNA genome that can cause serious illness in humans and animals. The 11 kb 5′ capped RNA genome consists of a single open reading frame (ORF), and is flanked by 5′ and 3′ untranslated regions (UTR). The ORF is a polyprotein that is processed into three structural and seven non-structural proteins. The UTRs have been shown to be important for viral replication and immune modulation. Both of these regions consist of elements that are essential for genome cyclization, resulting in initiation of RNA synthesis. Genome mutation studies have been employed to investigate each component of the essential elements to show the necessity of each component and its role in viral RNA replication and growth. Furthermore, the highly structured 3′UTR is responsible for the generation of subgenomic flavivirus RNA (sfRNA) that helps the virus evade host immune response, thereby affecting viral pathogenesis. In addition, changes within the 3′UTR have been shown to affect transmissibility between vector and host, which can influence the development of vaccines.
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Eyer L, Zouharová D, Širmarová J, Fojtíková M, Štefánik M, Haviernik J, Nencka R, de Clercq E, Růžek D. Antiviral activity of the adenosine analogue BCX4430 against West Nile virus and tick-borne flaviviruses. Antiviral Res 2017; 142:63-67. [DOI: 10.1016/j.antiviral.2017.03.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/10/2017] [Accepted: 03/18/2017] [Indexed: 01/20/2023]
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Asghar N, Pettersson JHO, Dinnetz P, Andreassen Å, Johansson M. Deep sequencing analysis of tick-borne encephalitis virus from questing ticks at natural foci reveals similarities between quasispecies pools of the virus. J Gen Virol 2017; 98:413-421. [PMID: 28073402 PMCID: PMC5797951 DOI: 10.1099/jgv.0.000704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10 000 to 15 000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV persistence in nature. This adaptation is facilitated by the error-prone nature of the virus’s RNA-dependent RNA polymerase, which generates genetically distinct virus variants called quasispecies. TBEV shows a focal geographical distribution pattern where each focus represents a TBEV hotspot. Here, we sequenced and characterized two TBEV genomes, JP-296 and JP-554, from questing Ixodes ricinus ticks at a TBEV focus in central Sweden. Phylogenetic analysis showed geographical clustering among the newly sequenced strains and three previously sequenced Scandinavian strains, Toro-2003, Saringe-2009 and Mandal-2009, which originated from the same ancestor. Among these five Scandinavian TBEV strains, only Mandal-2009 showed a large deletion within the 3′ non-coding region (NCR), similar to the highly virulent TBEV strain Hypr. Deep sequencing of JP-296, JP-554 and Mandal-2009 revealed significantly high quasispecies diversity for JP-296 and JP-554, with intact 3′NCRs, compared to the low diversity in Mandal-2009, with a truncated 3′NCR. Single-nucleotide polymorphism analysis showed that 40 % of the single-nucleotide polymorphisms were common between quasispecies populations of JP-296 and JP-554, indicating a putative mechanism for how TBEV persists and is maintained within its natural foci.
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Affiliation(s)
- Naveed Asghar
- School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden.,School of Medical Sciences, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - John H-O Pettersson
- Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway.,Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Patrik Dinnetz
- School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Åshild Andreassen
- Department of Virology, Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Magnus Johansson
- School of Medical Sciences, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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The role of the poly(A) tract in the replication and virulence of tick-borne encephalitis virus. Sci Rep 2016; 6:39265. [PMID: 27982069 PMCID: PMC5159820 DOI: 10.1038/srep39265] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/21/2016] [Indexed: 12/11/2022] Open
Abstract
The tick-borne encephalitis virus (TBEV) is a flavivirus transmitted to humans, usually via tick bites. The virus causes tick-borne encephalitis (TBE) in humans, and symptoms range from mild flu-like symptoms to severe and long-lasting sequelae, including permanent brain damage. It has been suggested that within the population of viruses transmitted to the mammalian host, quasispecies with neurotropic properties might become dominant in the host resulting in neurological symptoms. We previously demonstrated the existence of TBEV variants with variable poly(A) tracts within a single blood-fed tick. To characterize the role of the poly(A) tract in TBEV replication and virulence, we generated infectious clones of Torö-2003 with the wild-type (A)3C(A)6 sequence (Torö-6A) or with a modified (A)3C(A)38 sequence (Torö-38A). Torö-38A replicated poorly compared to Torö-6A in cell culture, but Torö-38A was more virulent than Torö-6A in a mouse model of TBE. Next-generation sequencing of TBEV genomes after passaging in cell culture and/or mouse brain revealed mutations in specific genomic regions and the presence of quasispecies that might contribute to the observed differences in virulence. These data suggest a role for quasispecies development within the poly(A) tract as a virulence determinant for TBEV in mice.
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MicroRNA-based control of tick-borne flavivirus neuropathogenesis: Challenges and perspectives. Antiviral Res 2016; 127:57-67. [PMID: 26794396 DOI: 10.1016/j.antiviral.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/10/2015] [Accepted: 01/13/2016] [Indexed: 01/01/2023]
Abstract
In recent years, microRNA-targeting has become an effective strategy for selective control of tissue-tropism and pathogenicity of both DNA and RNA viruses. Previously, we reported the successful application of this strategy to control the neurovirulent phenotype of a model chimeric tick-borne encephalitis/dengue type 4 virus (TBEV/DEN4), containing the structural protein genes of a highly virulent TBEV in the genetic backbone of non-neuroinvasive DEN4 virus. In the present study, we investigated the suitability of this approach for the attenuation of the more neurovirulent chimeric virus (TBEV/LGTV), which is based on the genetic backbone of the naturally attenuated member of the TBEV serocomplex, a Langat virus (LGTV). Unlike the TBEV/DEN4, the TBEV/LGTV virus retained the ability of its parental viruses to spread from the peripheral site of inoculation to the CNS. We evaluated ten potential sites in the 3'NCR of the TBEV/LGTV genome for placement of microRNA (miRNA) targets and found that the TBEV/LGTV genome is more restrictive for such genetic manipulations compared to TBEV/DEN4. In addition, unlike TBEV/DEN4 virus, the introduction of multiple miRNA targets into either the 3'NCR or ORF of the TBEV/LGTV genome had only a modest effect on virus attenuation in the developing CNS of highly permissive newborn mice. However, simultaneous miRNA-targeting in the ORF and 3'NCR had synergistic effect on control and silencing of virus replication in the brain and completely abolished the virus neurotropism. Furthermore, neuroinvasiveness of miRNA-targeted TBEV/LGTV viruses in very sensitive immunodeficient SCID mice was significantly limited. Immunocompetent animals immunized with such viruses were completely protected against challenge with the neurovirulent LGTV parent. These findings support the rationale of the miRNA-targeting approach to develop live attenuated virus vaccines against various neurotropic viruses.
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32
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Wu JQH. Virulence determinants of New World alphaviruses and broad-acting therapeutic strategies. Future Virol 2015. [DOI: 10.2217/fvl.15.8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
ABSTRACT New World alphaviruses of eastern equine encephalitis virus (EEEV), western equine encephalitis virus (WEEV) and Venezuelan equine encephalitis virus (VEEV) are endemic in North and South America, and infect humans and equine through mosquitoes. In addition, these viruses are highly infectious when aerosolized, making them potential biowarfare and bioterrorism agents. Currently, no approved vaccines or drugs are available for prevention and treatment. Extensive studies have been carried out to understand molecular mechanisms of virulence among New World alphaviruses. This review will focus on virus-encoded, interferon antagonizing proteins which play major role in determination of virulence of New World alphaviruses. Understanding of molecular mechanism of these proteins will shed light on development of broad-acting antivirals against New World alphaviruses.
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Sakai M, Muto M, Hirano M, Kariwa H, Yoshii K. Virulence of tick-borne encephalitis virus is associated with intact conformational viral RNA structures in the variable region of the 3'-UTR. Virus Res 2015; 203:36-40. [PMID: 25801453 DOI: 10.1016/j.virusres.2015.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 02/07/2023]
Abstract
Tick-borne encephalitis virus (TBEV) is maintained between ticks and mammals in nature and causes severe neurological disease in human. However, the mechanism of viral pathogenicity is unknown. Previously, we showed that the deletion in the variable region of the 3'-untranslated region (UTR) is involved in the pathogenicity of the strains from the Far-Eastern subtype of TBEV. To investigate the detailed function of the variable region, we constructed recombinant TBEV with partial deletions in the region. In a mouse model, the partial deletions drastically increased the virulence of the virus, with no effect on virus multiplication in mouse brain. Furthermore, the mutations did not affect the production of subgenomic flavivirus RNA from the 3'-UTR, and the induction of interferon (IFN) and IFN-stimulated genes. These data suggested that the conformational structure of the variable region is associated with the pathogenicity of the Far-Eastern subtype of TBEV. These findings provide a foundation for further research to identify the pathogenic mechanisms of TBEV.
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Affiliation(s)
- Mizuki Sakai
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Memi Muto
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Minato Hirano
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Hiroaki Kariwa
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan.
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Brinton MA, Basu M. Functions of the 3' and 5' genome RNA regions of members of the genus Flavivirus. Virus Res 2015; 206:108-19. [PMID: 25683510 DOI: 10.1016/j.virusres.2015.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/04/2015] [Indexed: 11/26/2022]
Abstract
The positive sense genomes of members of the genus Flavivirus in the family Flaviviridae are ∼ 11 kb in length and have a 5' type I cap but no 3' poly-A. The 3' and 5' terminal regions contain short conserved sequences that are proposed to be repeated remnants of an ancient sequence. However, the functions of most of these conserved sequences have not yet been determined. The terminal regions of the genome also contain multiple conserved RNA structures. Functional data for many of these structures have been obtained. Three sets of complementary 3' and 5' terminal region sequences, some of which are located in conserved RNA structures, interact to form a panhandle structure that is required for initiation of minus strand RNA synthesis with the 5' terminal structure functioning as the promoter. How the switch from the terminal RNA structure base pairing to the long distance RNA-RNA interaction is triggered and regulated is not well understood but evidence suggests involvement of a cell protein binding to three sites on the 3' terminal RNA structures and a cis-acting metastable 3' RNA element in the 3' terminal RNA structure. Cell proteins may also be involved in facilitating exponential replication of nascent genomic RNA within replication vesicles at later times of the infection cycle. Other conserved RNA structures and/or sequences in the 3' and 5' terminal regions have been proposed to regulate genome translation. Additional functions of the 3' and 5' terminal sequences have also been reported.
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Affiliation(s)
- Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, USA.
| | - Mausumi Basu
- Department of Biology, Georgia State University, Atlanta, GA, USA
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35
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Formanová P, Černý J, Bolfíková BČ, Valdés JJ, Kozlova I, Dzhioev Y, Růžek D. Full genome sequences and molecular characterization of tick-borne encephalitis virus strains isolated from human patients. Ticks Tick Borne Dis 2014; 6:38-46. [PMID: 25311899 DOI: 10.1016/j.ttbdis.2014.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 12/30/2022]
Abstract
Tick-borne encephalitis virus (TBEV) causes tick-borne encephalitis (TBE), one of the most important human neuroinfections across Eurasia. Up to date, only three full genome sequences of human European TBEV isolates are available, mostly due to difficulties with isolation of the virus from human patients. Here we present full genome characterization of an additional five low-passage TBEV strains isolated from human patients with severe forms of TBE. These strains were isolated in 1953 within Central Bohemia in the former Czechoslovakia, and belong to the historically oldest human TBEV isolates in Europe. We demonstrate here that all analyzed isolates are distantly phylogenetically related, indicating that the emergence of TBE in Central Europe was not caused by one predominant strain, but rather a pool of distantly related TBEV strains. Nucleotide identity between individual sequenced TBEV strains ranged from 97.5% to 99.6% and all strains shared large deletions in the 3' non-coding region, which has been recently suggested to be an important determinant of virulence. The number of unique amino acid substitutions varied from 3 to 9 in individual isolates, but no characteristic amino acid substitution typical exclusively for all human TBEV isolates was identified when compared to the isolates from ticks. We did, however, correlate that the exploration of the TBEV envelope glycoprotein by specific antibodies were in close proximity to these unique amino acid substitutions. Taken together, we report here the largest number of patient-derived European TBEV full genome sequences to date and provide a platform for further studies on evolution of TBEV since the first emergence of human TBE in Europe.
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Affiliation(s)
- Petra Formanová
- Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; Faculty of Science, Masaryk University, Kotlářská 267/2, CZ-61137 Brno, Czech Republic
| | - Jiří Černý
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, CZ-37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 126, CZ-16521 Prague, Czech Republic
| | - James J Valdés
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Irina Kozlova
- Institute of Biomedical Technology, Irkutsk State Medical University of Russian Ministry of Health, Krasnogo Vosstanija 1, Irkutsk 664003, Russia; FSSFE Scientific Centre of Family Health and Human Reproduction Problems, Siberian Branch of the Russian Academy of Medical Sciences, Timirjazeva Street 16, 664003 Irkutsk, Russia
| | - Yuri Dzhioev
- Institute of Biomedical Technology, Irkutsk State Medical University of Russian Ministry of Health, Krasnogo Vosstanija 1, Irkutsk 664003, Russia; FSSFE Scientific Centre of Family Health and Human Reproduction Problems, Siberian Branch of the Russian Academy of Medical Sciences, Timirjazeva Street 16, 664003 Irkutsk, Russia
| | - Daniel Růžek
- Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; Faculty of Science, Masaryk University, Kotlářská 267/2, CZ-61137 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, CZ-37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
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36
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Asghar N, Lindblom P, Melik W, Lindqvist R, Haglund M, Forsberg P, Överby AK, Andreassen Å, Lindgren PE, Johansson M. Tick-borne encephalitis virus sequenced directly from questing and blood-feeding ticks reveals quasispecies variance. PLoS One 2014; 9:e103264. [PMID: 25058476 PMCID: PMC4110009 DOI: 10.1371/journal.pone.0103264] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/25/2014] [Indexed: 01/10/2023] Open
Abstract
The increased distribution of the tick-borne encephalitis virus (TBEV) in Scandinavia highlights the importance of characterizing novel sequences within the natural foci. In this study, two TBEV strains: the Norwegian Mandal 2009 (questing nymphs pool) and the Swedish Saringe 2009 (blood-fed nymph) were sequenced and phylogenetically characterized. Interestingly, the sequence of Mandal 2009 revealed the shorter form of the TBEV genome, similar to the highly virulent Hypr strain, within the 3′ non-coding region (3′NCR). A different genomic structure was found in the 3′NCR of Saringe 2009, as in-depth analysis demonstrated TBEV variants with different lengths within the poly(A) tract. This shows that TBEV quasispecies exists in nature and indicates a putative shift in the quasispecies pool when the virus switches between invertebrate and vertebrate environments. This prompted us to further sequence and analyze the 3′NCRs of additional Scandinavian TBEV strains and control strains, Hypr and Neudoerfl. Toro 2003 and Habo 2011 contained mainly a short (A)3C(A)6 poly(A) tract. A similar pattern was observed for the human TBEV isolates 1993/783 and 1991/4944; however, one clone of 1991/4944 contained an (A)3C(A)11 poly(A) sequence, demonstrating that quasispecies with longer poly(A) could be present in human isolates. Neudoerfl has previously been reported to contain a poly(A) region, but to our surprise the re-sequenced genome contained two major quasispecies variants, both lacking the poly(A) tract. We speculate that the observed differences are important factors for the understanding of virulence, spread, and control of the TBEV.
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Affiliation(s)
- Naveed Asghar
- School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Pontus Lindblom
- Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Wessam Melik
- School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
| | - Mats Haglund
- Department of Infectious Diseases, County Hospital, Kalmar, Sweden
| | - Pia Forsberg
- Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Clinic of Infectious Diseases, Linköping University Hospital, Linköping, Sweden
| | - Anna K. Överby
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
| | - Åshild Andreassen
- Division of Infectious Disease Control, Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Per-Eric Lindgren
- Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Medical Services, Department of Microbiology, County Hospital Ryhov, Jönköping, Sweden
| | - Magnus Johansson
- School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden
- School of Medicine, Örebro University, Örebro, Sweden
- iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- * E-mail:
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Tun MMN, Aoki K, Senba M, Buerano CC, Shirai K, Suzuki R, Morita K, Hayasaka D. Protective role of TNF-α, IL-10 and IL-2 in mice infected with the Oshima strain of Tick-borne encephalitis virus. Sci Rep 2014; 4:5344. [PMID: 24938868 PMCID: PMC4061546 DOI: 10.1038/srep05344] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/29/2014] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) causes acute central nervous system disease. Here, we investigated the roles of the TNF-α, IL-10 and other cytokines in appropriate KO mice following infection with Oshima and Sofjin strains of TBEV. Following infection with the Oshima strain, mortality rates were significantly increased in TNF-α KO and IL-10 KO mice compared with wild type (WT) mice. These results suggested that TNF-α and IL-10 play protective roles against fatal infection due to Oshima strain infection. However, viral loads and proinflammatory cytokine levels in the brain of TNF-α KO andIL-10 KO mice were not significantly different compared with those of WT mice. On the other hand, all WT, TNF-α KO and IL-10 KO mice died following infection with Sofjin strain. Interestingly, Sofjin-infected mice did not exhibit an up-regulated mRNA level of IL-2 in the spleen in all groups of mice, whereas Oshima-infected mice showed significantly increased level of IL-2 compared with mock-infected mice. From these results, we suggest that TNF-α, IL-10 and IL-2 are key factors for disease remission from fatal encephalitis due to infection with Oshima strain of TBEV.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine, Leading Graduate School Program, Nagasaki University, 852-8523, Nagasaki, Japan
| | - Kotaro Aoki
- Department of Virology, Institute of Tropical Medicine, Leading Graduate School Program, Nagasaki University, 852-8523, Nagasaki, Japan
| | - Masachika Senba
- Department of Pathology, Institute of Tropical Medicine, Leading Graduate School Program, Nagasaki University, 852-8523, Nagasaki, Japan
| | - Corazon C Buerano
- Department of Virology, Institute of Tropical Medicine, Leading Graduate School Program, Nagasaki University, 852-8523, Nagasaki, Japan
| | - Kenji Shirai
- Clinical Research Center, National Hospital Organization Sagamihara Hospital, Sakuradai 18-1, Sagamihara, Kanagawa 228-8522, Japan
| | - Ryuji Suzuki
- Clinical Research Center, National Hospital Organization Sagamihara Hospital, Sakuradai 18-1, Sagamihara, Kanagawa 228-8522, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Leading Graduate School Program, Nagasaki University, 852-8523, Nagasaki, Japan
| | - Daisuke Hayasaka
- Department of Virology, Institute of Tropical Medicine, Leading Graduate School Program, Nagasaki University, 852-8523, Nagasaki, Japan
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