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Barros L, Silva S, Cruz AC, da Silva E, Wanzeller AL, Carvalho V, Chiang J, Martins L. First Isolation and Molecular Characterization of Umatilla Virus (Sedoreoviridae, Orbivirus) in Brazil. Viruses 2024; 16:1050. [PMID: 39066213 PMCID: PMC11281679 DOI: 10.3390/v16071050] [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: 05/08/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
In this study, we provide a genomic description of the first isolation of the Umattila virus (UMAV) in Brazil. The virus was obtained from the blood of a bird (Turdus fumigatus) and isolated in a C6/36 cell culture. The viral genome contains ten segments, and its organization is characteristic of viruses of the genus Orbivirus (family Sedoreoviridae). The coding region of each segment was sequenced, demonstrating the nucleotide identity with UMAV. The phylogenetic inference results were in line with these findings and demonstrated the formation of two distinct monophyletic clades containing strains isolated around the world, where our isolate, belonging to the same clade as the prototype strain, was allocated to a different subclade, highlighting the genetic divergence between them. This work reports the first isolation of UMAV in Brazil, and due to the scarcity of information on this viral agent in the scientific literature, it is essential to carry out further studies to better understand its epidemiology, dispersion, and, in particular, its interactions with vertebrate hosts, vectors, and the environment.
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Affiliation(s)
| | | | | | | | | | | | - Jannifer Chiang
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, Pará, Brazil; (L.B.); (S.S.); (A.C.C.); (E.d.S.); (A.L.W.); (V.C.); (L.M.)
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Nurmukanova V, Matsvay A, Gordukova M, Shipulin G. Square the Circle: Diversity of Viral Pathogens Causing Neuro-Infectious Diseases. Viruses 2024; 16:787. [PMID: 38793668 PMCID: PMC11126052 DOI: 10.3390/v16050787] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Neuroinfections rank among the top ten leading causes of child mortality globally, even in high-income countries. The crucial determinants for successful treatment lie in the timing and swiftness of diagnosis. Although viruses constitute the majority of infectious neuropathologies, diagnosing and treating viral neuroinfections remains challenging. Despite technological advancements, the etiology of the disease remains undetermined in over half of cases. The identification of the pathogen becomes more difficult when the infection is caused by atypical pathogens or multiple pathogens simultaneously. Furthermore, the modern surge in global passenger traffic has led to an increase in cases of infections caused by pathogens not endemic to local areas. This review aims to systematize and summarize information on neuroinvasive viral pathogens, encompassing their geographic distribution and transmission routes. Emphasis is placed on rare pathogens and cases involving atypical pathogens, aiming to offer a comprehensive and structured catalog of viral agents with neurovirulence potential.
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Affiliation(s)
- Varvara Nurmukanova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Maria Gordukova
- G. Speransky Children’s Hospital No. 9, 123317 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
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3
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Abstract
PURPOSE OF REVIEW Tick-borne encephalitis continues to be one of the most significant causes of viral encephalitis in Europe and Asia. This review will focus on recent developments in the epidemiology, pathogenesis and therapeutic approaches related to infection with tick-borne encephalitis virus. RECENT FINDINGS There is a growing consensus that tick-borne encephalitis viruses are increasing in geographical range, with countries previously free of disease reporting detection of both human cases and presence of virus within indigenous tick populations. The drivers for this are multifactorial but underpinned by human-mediated climate change. Recent developments in pathogenesis have focussed on the intracellular response to infection, particularly in different cell types within the central nervous system (CNS) that are revealing the array of cellular networks triggered by infection. This in turn highlights the need for small molecule therapeutics, such as nucleoside analogues, that can enter the CNS, and the intracellular environment, to inhibit virus replication following neuroinvasion. SUMMARY Based on continued epidemiological surveillance, tick-borne encephalitis viruses will increasingly affect human populations in Europe and Asia. Much of the research highlighted in this review demonstrates incremental advances in our understanding of these viruses. However, more is required if effective prevention and treatment of this devastating encephalitic viruses are to be realized.
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Affiliation(s)
- Nicholas Johnson
- Vector-Borne Diseases, Virology Department, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, UK
| | - Camille V Migné
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, Laboratoire de Santé Animale, Maison-Alfort, France
| | - Gaëlle Gonzalez
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR 1161 Virologie, Laboratoire de Santé Animale, Maison-Alfort, France
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4
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Perveen N, Muhammad K, Muzaffar SB, Zaheer T, Munawar N, Gajic B, Sparagano OA, Kishore U, Willingham AL. Host-pathogen interaction in arthropod vectors: Lessons from viral infections. Front Immunol 2023; 14:1061899. [PMID: 36817439 PMCID: PMC9929866 DOI: 10.3389/fimmu.2023.1061899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Haematophagous arthropods can harbor various pathogens including viruses, bacteria, protozoa, and nematodes. Insects possess an innate immune system comprising of both cellular and humoral components to fight against various infections. Haemocytes, the cellular components of haemolymph, are central to the insect immune system as their primary functions include phagocytosis, encapsulation, coagulation, detoxification, and storage and distribution of nutritive materials. Plasmatocytes and granulocytes are also involved in cellular defense responses. Blood-feeding arthropods, such as mosquitoes and ticks, can harbour a variety of viral pathogens that can cause infectious diseases in both human and animal hosts. Therefore, it is imperative to study the virus-vector-host relationships since arthropod vectors are important constituents of the ecosystem. Regardless of the complex immune response of these arthropod vectors, the viruses usually manage to survive and are transmitted to the eventual host. A multidisciplinary approach utilizing novel and strategic interventions is required to control ectoparasite infestations and block vector-borne transmission of viral pathogens to humans and animals. In this review, we discuss the arthropod immune response to viral infections with a primary focus on the innate immune responses of ticks and mosquitoes. We aim to summarize critically the vector immune system and their infection transmission strategies to mammalian hosts to foster debate that could help in developing new therapeutic strategies to protect human and animal hosts against arthropod-borne viral infections.
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Affiliation(s)
- Nighat Perveen
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Sabir Bin Muzaffar
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Tean Zaheer
- Department of Parasitology, University of Agriculture, Faisalabad, Pakistan
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bojan Gajic
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Olivier Andre Sparagano
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Uday Kishore
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Arve Lee Willingham
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, United Arab Emirates
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Li Z, Li Z, Yang Z, Li L, Gao L, Xie J, Liao D, Gao X, Hu Z, Niu B, Yao P, Zeng W, Li H, Yang H. Isolation and characterization of two novel serotypes of Tibet orbivirus from Culicoides and sentinel cattle in Yunnan Province of China. Transbound Emerg Dis 2022; 69:3371-3387. [PMID: 36047657 DOI: 10.1111/tbed.14691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 02/04/2023]
Abstract
Tibet orbivirus (TIBOV), a new candidate of Orbivirus genus, was initially isolated from mosquitoes in Tibet in 2009 and subsequently from both Culicoides and mosquitoes in several provinces of China and Japan. Little is known about the origin, genetic diversity, dissemination and pathogenicity of TIBOV, although its potential threat to animal health has been acknowledged. In this study, two viruses, V290/YNSZ and V298/YNJH, were isolated from the Culicoides and sentinel cattle in Yunnan Province. Their genome sequences, cell tropism in mammalian and insect cell lines along with pathogenicity in suckling mice were determined. Genome phylogenetic analyses confirmed their classification as TIBOV species; however, OC1 proteins of the V290/YNSZ and V298/YNJH shared maximum sequence identities of 31.5% and 33.9% with other recognized TIBOV serotypes (TIBOV-1 to TIBOV-4) and formed two monophyletic branches in phylogenetic tree, indicating they represented two novel TIBOV serotypes which were tentatively designated as TIBOV-5 and TIBOV-6. The viruses replicated robustly in BHK, Vero and C6/36 cells and triggered overt clinical symptoms in suckling mice after intracerebral inoculation, causing mortality of 100% and 25%. Cross-sectional epidemiology analysis revealed silent circulation of TIBOV in Yunnan Province with overall prevalence of 16.4% (18/110) in cattle, 10.8% (13/120) in goats and 5.5% (6/110) in swine. The prevalence patterns of four investigated TIBOV serotypes (TIBOV-1, -2, -5 and 6) differed from each one another, with their positive rates ranging from 8.2% (9/110) for TIBOV-2 in cattle to 0.9% (1/110) for TIBOV-1 and TIBOV-5 in cattle and swine. Our findings provided new insights for diversity, pathogenicity and epidemiology of TIBOV and formed a basis for future studies addressing the geographical distribution and the zoonotic potential of TIBOV.
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Affiliation(s)
- Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Zhuoran Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Zhenxing Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Le Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Lin Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Jiarui Xie
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Defang Liao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Xiang Gao
- Animal Disease Control and Prevention Center of Jinghong County, Jinghong, China
| | - Zhongyan Hu
- Animal Disease Control and Prevention Center of Jinghong County, Jinghong, China
| | - Baosheng Niu
- Animal Disease Control and Prevention Center of Shizong County, Qujing, China
| | - Pingfen Yao
- Animal Disease Control and Prevention Center of Shizong County, Qujing, China
| | - Weikun Zeng
- School of Medicine, Kunming University, Kunming, China
| | - Huachun Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Heng Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China.,College of Agriculture and Life Sciences, Kunming University, Kunming, China
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Mock F, Viehweger A, Barth E, Marz M. VIDHOP, viral host prediction with deep learning. Bioinformatics 2021; 37:318-325. [PMID: 32777818 PMCID: PMC7454304 DOI: 10.1093/bioinformatics/btaa705] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/17/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Motivation Zoonosis, the natural transmission of infections from animals to humans, is a far-reaching global problem. The recent outbreaks of Zikavirus, Ebolavirus, and Coronavirus are examples of viral zoonosis, which occur more frequently due to globalization. In case of a virus outbreak, it is helpful to know which host organism was the original carrier of the virus to prevent further spreading of viral infection. Recent approaches aim to predict a viral host based on the viral genome, often in combination with the potential host genome and arbitrarily selected features. These methods are limited in the number of different hosts they can predict or the accuracy of the prediction. Results Here, we present a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. We tested our deep neural network (DNN) on three different virus species (influenza A virus, rabies lyssavirus, rotavirus A). We achieved for each virus species an AUC between 0.93 and 0.98, allowing highly accurate predictions while using only fractions (100-400 bp) of the viral genome sequences. We show that deep neural networks are suitable to predict the host of a virus, even with a limited amount of sequences and highly unbalanced available data. The trained DNNs are the core of our virus-host prediction tool VIDHOP (VIrus Deep learning HOst Prediction). VIDHOP also allows the user to train and use models for other viruses. Availability VIDHOP is freely available under https://github.com/flomock/vidhop Supplementary information Available at DOI 10.17605/OSF.IO/UXT7
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Affiliation(s)
- Florian Mock
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Jena 07743, Germany
| | - Adrian Viehweger
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Jena 07743, Germany
| | - Emanuel Barth
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Manja Marz
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Jena 07743, Germany.,RNA Bioinformatics/High Throughput Analysis, Leibnitz Institute for Age Research - Fritz Lipmann Institute (FLI), Jena 07743, Germany.,RNA Bioinformatics/High Throughput Analysis, German Center for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig 04103, Germany.,RNA Bioinformatics/High Throughput Analysis, European Virus Bioinformatics Center (EVBC), Jena 07743, Germany
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7
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Dedkov VG, Dolgova AS, Safonova MV, Samoilov AE, Belova OA, Kholodilov IS, Matsvay AD, Speranskaya AS, Khafizov K, Karganova GG. Isolation and characterization of Wad Medani virus obtained in the tuva Republic of Russia. Ticks Tick Borne Dis 2020; 12:101612. [PMID: 33291056 DOI: 10.1016/j.ttbdis.2020.101612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Wad Medani virus (WMV) belongs to the genus Orbivirus and is a poorly studied arbovirus with unclear medical significance. Presently, a limited number of WMV strains are characterized and available in NCBI GenBank, some isolated many years ago. A new WMV strain was isolated in 2012 from Dermacentor nuttalli ticks collected from sheep in the Tuva Republic, Russia, and sequenced using high-throughput methods. Complete coding sequences were obtained revealing signs of multiple intersegment reassortments. These point to a high variability potential in WMV that may lead to the formation of strains with novel properties. These new data on WMV can promote better understanding of: ecological features of its circulation; relationships within the genus Orbivirus; and the medical significance of the virus.
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Affiliation(s)
- Vladimir G Dedkov
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint-Petersburg, Russia; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia.
| | - Anna S Dolgova
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint-Petersburg, Russia
| | - Marina V Safonova
- Anti-Plague Center, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Andrei E Samoilov
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint-Petersburg, Russia; Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Oxana A Belova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides FSBSI Chumakov FSC R&D IBP RAS, Moscow, Russia
| | - Ivan S Kholodilov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides FSBSI Chumakov FSC R&D IBP RAS, Moscow, Russia
| | - Alina D Matsvay
- FSBI "Center of Strategic Planning" of the Ministry of Health, Moscow, Russia; Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Anna S Speranskaya
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Kamil Khafizov
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia; Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Galina G Karganova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides FSBSI Chumakov FSC R&D IBP RAS, Moscow, Russia; Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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Wu D, Tan Q, Zhang H, Huang P, Zhou H, Zhang X, Sun J, Huang L, Liang G. Genomic and biological features of a novel orbivirus isolated from mosquitoes, in China. Virus Res 2020; 285:197990. [PMID: 32437817 DOI: 10.1016/j.virusres.2020.197990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/11/2020] [Accepted: 04/24/2020] [Indexed: 01/05/2023]
Abstract
A novel orbivirus had been identified as a member of the Orbivirus genus, which was isolated from pooled Culex fatigans mosquitoes in Guangdong of China, named as the Fengkai virus (FKOV). The cytopathic effects (CPEs) on both Aedes albopictus cells (C6/36) and mammalian cell lines (Vero and BHK-21) emerged in the cell cultures inoculated above virus in. Experimental confirmation as the Orbivirus genus was conducted by the Real-time PCR and based on Ion Torrent Next-Generation in sequencing. The Identities of VP1, VP2 and VP3 in amino acid sequences between the Tibet orbivirus (TIBOV) and this strain were 98.6%, 42.9%, and 99.9%, respectively, which indicated that this strain shares the same genus (VP1, Pol) and species (VP3, T2) with TIBOV but was greatly different in VP2 and VP5 (10.3%) of TIBOV. The VP2 and VP5 diversities of both TIBOV and FKOV strains suggested both serotypes are distinct with each other. As natural evolution and circulation, this strain might expand its host ranges and infect human beings as a potential and severe pathogen.
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Affiliation(s)
- De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Qiqi Tan
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ping Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; School of Public Health, Southern Medical University, China.
| | - Huiqiong Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Xin Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Jiufeng Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Institute of Public Health, Guangzhou, China
| | - Liming Huang
- School of Public Health, Southern Medical University, China
| | - Guodong Liang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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9
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Tomazatos A, Marschang RE, Maranda I, Baum H, Bialonski A, Spînu M, Lühken R, Schmidt-Chanasit J, Cadar D. Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes ( Natrix natrix). Viruses 2020; 12:v12020243. [PMID: 32098186 PMCID: PMC7077223 DOI: 10.3390/v12020243] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 01/22/2023] Open
Abstract
The discovery and characterization of novel arthropod-borne viruses provide valuable information on their genetic diversity, ecology, evolution and potential to threaten animal or public health. Arbovirus surveillance is not conducted regularly in Romania, being particularly very scarce in the remote and diverse areas like the Danube Delta. Here we describe the detection and genetic characterization of a novel orbivirus (Reoviridae: Orbivirus) designated as Letea virus, which was found in grass snakes (Natrix natrix) during a metagenomic and metatranscriptomic survey conducted between 2014 and 2017. This virus is the first orbivirus discovered in reptiles. Phylogenetic analyses placed Letea virus as a highly divergent species in the Culicoides-/sand fly-borne orbivirus clade. Gene reassortment and intragenic recombination were detected in the majority of the nine Letea virus strains obtained, implying that these mechanisms play important roles in the evolution and diversification of the virus. However, the screening of arthropods, including Culicoides biting midges collected within the same surveillance program, tested negative for Letea virus infection and could not confirm the arthropod vector of the virus. The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic associations warrant further screening of arthropods, as well as sustained surveillance efforts for elucidation of Letea virus natural cycle and possible implications for animal and human health.
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Affiliation(s)
- Alexandru Tomazatos
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
| | - Rachel E. Marschang
- Cell Culture Lab, Microbiology Department, Laboklin GmbH & Co. KG, 97688 Bad Kissingen, Germany;
| | - Iulia Maranda
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
| | - Heike Baum
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
| | - Alexandra Bialonski
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
| | - Marina Spînu
- Department of Clinical Sciences-Infectious Diseases, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania;
| | - Renke Lühken
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
- Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20148 Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
- Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20148 Hamburg, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany; (A.T.); (I.M.); (H.B.); (A.B.); (R.L.); (J.S.-C.)
- Correspondence:
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10
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Safonova MV, Gmyl AP, Lukashev AN, Speranskaya AS, Neverov AD, Fedonin GG, Pimkina EV, Matsvay AD, Khafizov KF, Karganova GG, Kozlovskaya LI, Valdokhina AV, Bulanenko VP, Dedkov VG. Genetic diversity of Kemerovo virus and phylogenetic relationships within the Great Island virus genetic group. Ticks Tick Borne Dis 2019; 11:101333. [PMID: 31787560 DOI: 10.1016/j.ttbdis.2019.101333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 11/27/2022]
Abstract
Kemerovo virus (KEMV) is a member of the Great Island virus genetic group, belonging to the tick-borne arboviruses of the genus Orbivirus within the family Reoviridae. Nine strains of KEMV, which were isolated from various locations in Russia, were sequenced by high-throughput sequencing to study their intraspecific diversity and the interspecific relationships of viruses within the Great Island genetic group. For the first time, multiple reassortment within KEMV was reliably demonstrated. Different types of independently emerged alternative reading frames in segment 9 and heterogeneity of the viral population in one of the KEMV strains were found. The hypothesis of the role of an alternative open reading frame (ORF) in segment 9 in KEMV cellular tropism was not confirmed in this study.
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Affiliation(s)
- Marina V Safonova
- Plague Control Center, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia.
| | - Anatoly P Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna S Speranskaya
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Alexey D Neverov
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Gennady G Fedonin
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Ekaterina V Pimkina
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Alina D Matsvay
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Kamil F Khafizov
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Galina G Karganova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russia
| | - Lubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna V Valdokhina
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Victoria P Bulanenko
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Vladimir G Dedkov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia; Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint-Petersburg, Russia
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11
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Maia LMS, Pinto AZDL, Carvalho MSD, Melo FLD, Ribeiro BM, Slhessarenko RD. Novel Viruses in Mosquitoes from Brazilian Pantanal. Viruses 2019; 11:v11100957. [PMID: 31627274 PMCID: PMC6832572 DOI: 10.3390/v11100957] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/24/2019] [Accepted: 10/03/2019] [Indexed: 01/25/2023] Open
Abstract
Viruses are ubiquitous and diverse microorganisms arising as a result of interactions within their vertebrate and invertebrate hosts. Here we report the presence of different viruses in the salivary glands of 1657 mosquitoes classified over 28 culicinae species from the North region of the Brazilian Pantanal wetland through metagenomics, viral isolation, and RT-PCR. In total, 12 viruses were found, eight putative novel viruses with relatively low similarity with pre-existing species of viruses within their families, named Pirizal iflavirus, Furrundu phlebovirus, Pixé phlebovirus, Guampa vesiculovirus, Chacororé flavivirus, Rasqueado orbivirus, Uru chuvirus, and Bororo circovirus. We also found the already described Lobeira dielmorhabdovirus, Sabethes flavivirus, Araticum partitivirus, and Murici totivirus. Therefore, these findings underscore the vast diversity of culicinae and novel viruses yet to be explored in Pantanal, the largest wetland on the planet.
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Affiliation(s)
- Laura Marina Siqueira Maia
- Programa de Pós-Graduação em Ciências da Sáude, Laboratório de Virologia, Universidade Federal de Mato Grosso (UFMT), 78060-900 Cuiabá, Mato Grosso, Brazil.
| | - Andressa Zelenski de Lara Pinto
- Programa de Pós-Graduação em Ciências da Sáude, Laboratório de Virologia, Universidade Federal de Mato Grosso (UFMT), 78060-900 Cuiabá, Mato Grosso, Brazil.
| | - Michellen Santos de Carvalho
- Programa de Pós-Graduação em Ciências da Sáude, Laboratório de Virologia, Universidade Federal de Mato Grosso (UFMT), 78060-900 Cuiabá, Mato Grosso, Brazil.
| | - Fernando Lucas de Melo
- Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil.
| | - Bergmann Morais Ribeiro
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil.
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Sáude, Laboratório de Virologia, Universidade Federal de Mato Grosso (UFMT), 78060-900 Cuiabá, Mato Grosso, Brazil.
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12
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Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ. Exploiting the Legacy of the Arbovirus Hunters. Viruses 2019; 11:E471. [PMID: 31126128 PMCID: PMC6563318 DOI: 10.3390/v11050471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Steve G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Naomi L Forrester
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Jean Paul Gonzalez
- Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS 66502, USA.
| | | | - Sergey Alkhovsky
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia.
| | - Sai Kit Lam
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, Perth, Western Australia 6102, Australia.
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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13
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Ulrich K, Wehner S, Bekaert M, Di Paola N, Dilcher M, Muir KF, Taggart JB, Matejusova I, Weidmann M. Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades. J Gen Virol 2018; 99:1567-1581. [PMID: 30358526 DOI: 10.1099/jgv.0.001155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV), the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982 to 2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59 % of the IPNV isolates belonged to the persistent type and 32 % to the low-virulent type, and only one highly pathogenic strain (1.79 %) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Under-representation of CpG dinucleotides in the IPNV genome to minimize detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes, together with the assumption of adaptation and immune escape, indicates that IPNV is evolving with the host.
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Affiliation(s)
- Kristina Ulrich
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Michaël Bekaert
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Nicholas Di Paola
- 3Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Meik Dilcher
- 4Canterbury Health Laboratories, Christchurch, New-Zealand
| | | | - John B Taggart
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Manfred Weidmann
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
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14
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Dedkov VG, Simonova EG, Beshlebova OV, Safonova MV, Stukolova OA, Verigina EV, Savinov GV, Karaseva IP, Blinova EA, Granitov VM, Arsenjeva IV, Shipulin GA. The burden of tick-borne diseases in the Altai region of Russia. Ticks Tick Borne Dis 2017. [PMID: 28648773 DOI: 10.1016/j.ttbdis.2017.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This article presents the results of a comprehensive survey of the burden of tick-borne infectious diseases (TBIDs) in the Altai region of Russia. Official data for TBID incidence were analyzed and 201 samples from patients with suspected TBID were studied. Furthermore, questing ticks and ticks recovered from humans were examined to estimate prevalence of TBID-causative agents. The Altai region was determined to have a heightened risk for TBIDs in Russia. The most epidemiologically significant tick-borne illness in this area is spotted fever group rickettsiosis, while nationally in Russia, the leading TBID is Lyme borreliosis. The prevalence of mixed infection was 12.4% among the studied cases. Additionally, the prevalence of poorly studied pathogens - Kemerovo virus (KEMV) and Rickettsia tarasevichiae - in ticks from the Altai region was determined.
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Affiliation(s)
- V G Dedkov
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia; Research Institute of Occupational Health, Moscow, Russia.
| | - E G Simonova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia; I.M. Sechenov First Moscow Medical University, Moscow, Russia
| | | | - M V Safonova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - O A Stukolova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - E V Verigina
- I.M. Sechenov First Moscow Medical University, Moscow, Russia
| | - G V Savinov
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - I P Karaseva
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - E A Blinova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | | | | | - G A Shipulin
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
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15
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Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV. Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 2017; 25:3597-3605. [PMID: 28396019 DOI: 10.1016/j.bmc.2017.03.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023]
Abstract
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.
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Affiliation(s)
- Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Vavilov Str. 32, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia.
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Evgeny S Belyaev
- Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38/2, Moscow 119334, Russia
| | - Yury I Kostyukevich
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia
| | - Vladimir G Dedkov
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia.
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16
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Occurrence and genetic variability of Kemerovo virus in Ixodes ticks from different regions of Western Siberia, Russia and Kazakhstan. INFECTION GENETICS AND EVOLUTION 2017; 47:56-63. [DOI: 10.1016/j.meegid.2016.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
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17
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Engelbrecht A, Matthee S, du Toit N, Matthee CA. Limited dispersal in an ectoparasitic mite,Laelaps giganteus, contributes to significant phylogeographic congruence with the rodent host,Rhabdomys. Mol Ecol 2016; 25:1006-21. [DOI: 10.1111/mec.13523] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 12/09/2015] [Accepted: 12/20/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Adriaan Engelbrecht
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Nina du Toit
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Conrad A. Matthee
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
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18
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Dilcher M, Faye O, Faye O, Weber F, Koch A, Sadegh C, Weidmann M, Sall AA. Zahedan rhabdovirus, a novel virus detected in ticks from Iran. Virol J 2015; 12:183. [PMID: 26542354 PMCID: PMC4635997 DOI: 10.1186/s12985-015-0410-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/26/2015] [Indexed: 12/18/2022] Open
Abstract
Background Rhabdoviridae infect a wide range of vertebrates, invertebrates and plants. Their transmission can occur via various arthropod vectors. In recent years, a number of novel rhabdoviruses have been identified from various animal species, but so far only few tick-transmitted rhabdoviruses have been described. Methods We isolated a novel rhabdovirus, provisionally named Zahedan rhabdovirus (ZARV), from Hyalomma anatolicum anatolicum ticks collected in Iran. The full-length genome was determined using 454 next-generation sequencing and the phylogenetic relationship to other rhabdoviruses was analyzed. Inoculation experiments in mammalian Vero cells and mice were conducted and a specific PCR assay was developed. Results The complete genome of ZARV has a size of 11,230 nucleotides (nt) with the typical genomic organization of Rhabdoviridae. Phylogenetic analysis confirms that ZARV is closely related to Moussa virus (MOUV) from West Africa and Long Island tick rhabdovirus (LITRV) from the U.S., all forming a new monophyletic clade, provisionally designated Zamolirhabdovirus, within the Dimarhabdovirus supergroup. The glycoprotein (G) contains 12 conserved cysteins which are specific for animal rhabdoviruses infecting fish and mammals. In addition, ZARV is able to infect mammalian Vero cells and is lethal for mice when inoculated intracerebrally or subcutaneously. The developed PCR assay can be used to specifically detect ZARV. Conclusion The novel tick-transmitted rhabdovirus ZARV is closely related to MOUV and LITRV. All three viruses seem to form a new monophyletic clade. ZARV might be pathogenic for mammals, since it can infect Vero cells, is lethal for mice and its glycoprotein contains 12 conserved cysteins only found in animal rhabdoviruses. The mammalian host of ZARV remains to be identified.
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Affiliation(s)
- Meik Dilcher
- Department of Virology, Univerity Medical Center Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany.
| | - Oumar Faye
- Institute Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal.
| | - Ousmane Faye
- Institute Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal.
| | - Franziska Weber
- Department of Virology, Univerity Medical Center Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany.
| | - Andrea Koch
- Department of Virology, Univerity Medical Center Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany.
| | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK.
| | - Amadou Alpha Sall
- Institute Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal.
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19
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Ejiri H, Lim CK, Isawa H, Kuwata R, Kobayashi D, Yamaguchi Y, Takayama-Ito M, Kinoshita H, Kakiuchi S, Horiya M, Kotaki A, Takasaki T, Maeda K, Hayashi T, Sasaki T, Kobayashi M, Saijo M, Sawabe K. Genetic and biological characterization of Muko virus, a new distinct member of the species Great Island virus (genus Orbivirus, family Reoviridae), isolated from ixodid ticks in Japan. Arch Virol 2015; 160:2965-77. [PMID: 26350980 DOI: 10.1007/s00705-015-2588-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 08/26/2015] [Indexed: 12/27/2022]
Abstract
Among the tick-borne orbiviruses (genus Orbivirus, family Reoviridae), 36 serotypes are currently classified within a single virus species, Great Island virus. In this study, we report the first characterization of a tick-borne orbivirus isolated from the tick Ixodes turdus in Japan, which we identified as a new member of the species Great Island virus. The virus isolate, designated Muko virus (MUV), replicated and induced cytopathic effects in BHK-21, Vero E6, and CCL-141 cells and caused high mortality in suckling mice after intracerebral inoculation. Full genome sequence analysis showed that MUV shared the greatest phylogenetic similarity with Tribeč virus in terms of the amino acid sequences of all viral proteins except for outer capsid protein 1 (OC1; VP4 of MUV). Analysis of genome segment 9 in MUV detected an uninterrupted open reading frame that overlaps with VP6 (Hel), which putatively encodes a molecular and functional equivalent of NS4 from Great Island virus. Our study provides new insights into the geographic distribution, genetic diversity, and evolutionary history of the members of the species Great Island virus.
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Affiliation(s)
- Hiroko Ejiri
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Chang-Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Yukie Yamaguchi
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Mutsuyo Takayama-Ito
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Hitomi Kinoshita
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Satsuki Kakiuchi
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Madoka Horiya
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Akira Kotaki
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Tomohiko Takasaki
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Toshihiko Hayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Toshinori Sasaki
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Mutsuo Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuiku-ku, Tokyo, 162-8640, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
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20
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Genetic characterization of the tick-borne orbiviruses. Viruses 2015; 7:2185-209. [PMID: 25928203 PMCID: PMC4452902 DOI: 10.3390/v7052185] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/18/2015] [Accepted: 04/21/2015] [Indexed: 12/24/2022] Open
Abstract
The International Committee for Taxonomy of Viruses (ICTV) recognizes four species of tick-borne orbiviruses (TBOs): Chenuda virus, Chobar Gorge virus, Wad Medani virus and Great Island virus (genus Orbivirus, family Reoviridae). Nucleotide (nt) and amino acid (aa) sequence comparisons provide a basis for orbivirus detection and classification, however full genome sequence data were only available for the Great Island virus species. We report representative genome-sequences for the three other TBO species (virus isolates: Chenuda virus (CNUV); Chobar Gorge virus (CGV) and Wad Medani virus (WMV)). Phylogenetic comparisons show that TBOs cluster separately from insect-borne orbiviruses (IBOs). CNUV, CGV, WMV and GIV share low level aa/nt identities with other orbiviruses, in ‘conserved’ Pol, T2 and T13 proteins/genes, identifying them as four distinct virus-species. The TBO genome segment encoding cell attachment, outer capsid protein 1 (OC1), is approximately half the size of the equivalent segment from insect-borne orbiviruses, helping to explain why tick-borne orbiviruses have a ~1 kb smaller genome.
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21
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Karlberg H, Sharifi-Mood B, Mousavi-Jazi M, Dilcher M, Lindegren G, Mardani M, Bereskly S, Weidmann M, Mirazimi A. Molecular and serological findings in suspected patients with Crimean-Congo hemorrhagic fever virus in Iran. J Med Virol 2015; 87:686-93. [PMID: 25649667 DOI: 10.1002/jmv.24106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2014] [Indexed: 11/05/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is an arthropod-borne disease of humans associated with a severe clinical picture, including hemorrhagic syndrome and a high mortality rate. CCHF virus is widely distributed throughout large areas of the world. To characterize the serological status in CCHF patients, paired clinical samples were collected from suspected CCHF patients and analyzed by microbiological and other laboratory analyses with the aim of: determining the presence of neutralizing antibodies against CCHF virus; investigating the cross-reactivity of these neutralizing antibodies against virus isolated from the same outbreak and against other available laboratory strain; and studying the relationship between the isolated virus with other virus by whole genome sequencing. Patients at Boo-Ali Hospital, Zahedan, Iran, with clinical symptoms ranging from mild to severe hemorrhagic fever were included in the study. Two serum samples were taken from each patient, the first as soon as the patient matched the criteria for CCHF notification and the second when the patient was discharged from hospital (2 weeks later). Commercial and in-house assays revealed a positive IgM signal in acute serum samples from six patients. A novel finding was that CCHF patients develop neutralizing antibodies soon after infection. Interestingly these antibodies were able to neutralize other CCHF virus strains too. The complete sequence of the Zahedan 2007 isolate, including the hitherto unknown first L-segment sequence, was identified using an original clinical sample from one patient with confirmed CCHF infection.
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Affiliation(s)
- Helen Karlberg
- Public Health Agency of Sweden, Stockholm, Sweden; Karolinska Institute, Stockholm, Sweden
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22
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Acrani GO, Tilston-Lunel NL, Spiegel M, Weidmann M, Dilcher M, Andrade da Silva DE, Nunes MRT, Elliott RM. Establishment of a minigenome system for Oropouche virus reveals the S genome segment to be significantly longer than reported previously. J Gen Virol 2014; 96:513-523. [PMID: 25491420 DOI: 10.1099/jgv.0.000005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oropouche virus (OROV) is a medically important orthobunyavirus, which causes frequent outbreaks of a febrile illness in the northern parts of Brazil. However, despite being the cause of an estimated half a million human infections since its first isolation in Trinidad in 1955, details of the molecular biology of this tripartite, negative-sense RNA virus remain limited. We have determined the complete nucleotide sequence of the Brazilian prototype strain of OROV, BeAn 19991, and found a number of differences compared with sequences in the database. Most notable were that the S segment contained an additional 204 nt at the 3' end and that there was a critical nucleotide mismatch at position 9 within the base-paired terminal panhandle structure of each genome segment. In addition, we obtained the complete sequence of the Trinidadian prototype strain TRVL-9760 that showed similar characteristics to the BeAn 19991 strain. By using a T7 RNA polymerase-driven minigenome system, we demonstrated that cDNA clones of the BeAn 19991 L and S segments expressed functional proteins, and also that the newly determined terminal untranslated sequences acted as functional promoters in the minigenome assay. By co-transfecting a cDNA to the viral glycoproteins, virus-like particles were generated that packaged a minigenome and were capable of infecting naive cells.
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Affiliation(s)
- Gustavo Olszanski Acrani
- Department of Cell and Molecular Biology, University of Sao Paulo School of Medicine, 3900, Av. Bandeirantes, Ribeirão Preto, SP 14049-900, Brazil.,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Natasha L Tilston-Lunel
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, Scotland, UK.,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Martin Spiegel
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Manfred Weidmann
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | | | - Marcio R T Nunes
- Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Richard M Elliott
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
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23
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Drinkwater B, Charleston MA. Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem. BMC Bioinformatics 2014; 15 Suppl 16:S14. [PMID: 25521705 PMCID: PMC4290644 DOI: 10.1186/1471-2105-15-s16-s14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heavily on heuristics to solve all but the most trivial cases. One notable approach utilises a metaheuristic to search only a subset of the exponential number of fixed node orderings possible for the phylogenetic histories in question. This is of particular interest as it is the only known heuristic that guarantees biologically feasible solutions. This has enabled research to focus on larger coevolutionary systems, such as coevolutionary associations between figs and their pollinator wasps, including over 200 taxa. Although able to converge on solutions for problem instances of this size, a reduction from the current cubic running time is required to handle larger systems, such as Wolbachia and their insect hosts. RESULTS Rather than solving this underlying problem optimally this work presents a greedy algorithm called TreeCollapse, which uses common topological patterns to recover an approximation of the coevolutionary history where the internal node ordering is fixed. This approach offers a significant speed-up compared to previous methods, running in linear time. This algorithm has been applied to over 100 well-known coevolutionary systems converging on Pareto optimal solutions in over 68% of test cases, even where in some cases the Pareto optimal solution has not previously been recoverable. Further, while TreeCollapse applies a local search technique, it can guarantee solutions are biologically feasible, making this the fastest method that can provide such a guarantee. CONCLUSION As a result, we argue that the newly proposed algorithm is a valuable addition to the field of coevolutionary research. Not only does it offer a significantly faster method to estimate the cost of cophylogeny mappings but by using this approach, in conjunction with existing heuristics, it can assist in recovering a larger subset of the Pareto front than has previously been possible.
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Affiliation(s)
- Benjamin Drinkwater
- School of Information Technologies, 1 Cleveland St, 2006 University of Sydney, Australia Full list of author information is available at the end of the article
| | - Michael A Charleston
- School of Information Technologies, 1 Cleveland St, 2006 University of Sydney, Australia Full list of author information is available at the end of the article
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24
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Dedkov VG, Dubina DA, Yurchenko OA, Bekova MV, Valdokhina AV, Shipulin GA. Characterization of Two Strains of Tribeč Virus Isolated in Ukraine. Vector Borne Zoonotic Dis 2014; 14:808-16. [DOI: 10.1089/vbz.2014.1683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vladimir G. Dedkov
- Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Rights and Human Welfare, Moscow, Russia
| | - Dmitriy A. Dubina
- I.I. Mechnikov, Ukrainian Anti-Plague Research Institute of the Ministry of Health of Ukraine, Odessa, Ukraine
| | - Oksana A. Yurchenko
- I.I. Mechnikov, Ukrainian Anti-Plague Research Institute of the Ministry of Health of Ukraine, Odessa, Ukraine
| | - Marina V. Bekova
- Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Rights and Human Welfare, Moscow, Russia
| | - Anna V. Valdokhina
- Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Rights and Human Welfare, Moscow, Russia
| | - German A. Shipulin
- Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Rights and Human Welfare, Moscow, Russia
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25
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Dedkov V, Markelov M, Gridneva K, Bekova M, Gmyl A, Kozlovskaya L, Karganova G, Romanova L, Pogodina V, Yakimenko V, Shipulin G. Prevalence of Kemerovo virus in ixodid ticks from the Russian Federation. Ticks Tick Borne Dis 2014; 5:651-5. [DOI: 10.1016/j.ttbdis.2014.04.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 04/14/2014] [Accepted: 04/24/2014] [Indexed: 11/29/2022]
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26
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First detection of Kemerovo virus in Ixodes pavlovskyi and Ixodes persulcatus ticks collected in Novosibirsk region, Russia. Ticks Tick Borne Dis 2014; 5:494-6. [DOI: 10.1016/j.ttbdis.2014.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/18/2014] [Accepted: 03/13/2014] [Indexed: 11/22/2022]
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27
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Silva SP, Dilcher M, Weber F, Hufert FT, Weidmann M, Cardoso JF, Carvalho VL, Chiang JO, Martins LC, Lima CPS, Da Silva DEA, Vianez-Júnior JLSG, Popov VL, Travassos da Rosa APA, Tesh RB, Vasconcelos PFC, Nunes MRT. Genetic and biological characterization of selected Changuinola viruses (Reoviridae, Orbivirus) from Brazil. J Gen Virol 2014; 95:2251-2259. [PMID: 24986085 DOI: 10.1099/vir.0.064691-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The genus Orbivirus of the family Reoviridae comprises 22 virus species including the Changuinola virus (CGLV) serogroup. The complete genome sequences of 13 CGLV serotypes isolated between 1961 and 1988 from distinct geographical areas of the Brazilian Amazon region were obtained. All viral sequences were obtained from single-passaged CGLV strains grown in Vero cells. CGLVs are the only orbiviruses known to be transmitted by phlebotomine sandflies. Ultrastructure and molecular analysis by electron microscopy and gel electrophoresis, respectively, revealed viral particles with typical orbivirus size and morphology, as well as the presence of a segmented genome with 10 segments. Full-length nucleotide sequencing of each of the ten RNA segments of the 13 CGLV serotypes provided basic information regarding the genome organization, encoded proteins and genetic traits. Segment 2 (encoding VP2) of the CGLV is uncommonly larger in comparison to those found in other orbiviruses and shows varying sizes even among different CGLV serotypes. Phylogenetic analysis support previous serological findings, which indicate that CGLV constitutes a separate serogroup within the genus Orbivirus. In addition, six out of 13 analysed CGLV serotypes showed reassortment of their genome segments.
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Affiliation(s)
- Sandro P Silva
- Center for Technological Innovation of Evandro Chagas Institute, Ministry of Health, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Meik Dilcher
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, D-37075 Göttingen, Germany
| | - Franziska Weber
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, D-37075 Göttingen, Germany
| | - Frank T Hufert
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, D-37075 Göttingen, Germany
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Jedson F Cardoso
- Center for Technological Innovation of Evandro Chagas Institute, Ministry of Health, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Valéria L Carvalho
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Jannifer O Chiang
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Lívia C Martins
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Clayton P S Lima
- Center for Technological Innovation of Evandro Chagas Institute, Ministry of Health, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Daisy E A Da Silva
- Center for Technological Innovation of Evandro Chagas Institute, Ministry of Health, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - João L S G Vianez-Júnior
- Center for Technological Innovation of Evandro Chagas Institute, Ministry of Health, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Vsevolod L Popov
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Amélia P A Travassos da Rosa
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert B Tesh
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Pedro F C Vasconcelos
- Departamento de Patologia, Universidade do Estado do Pará, Belém, Brazil.,Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
| | - Márcio R T Nunes
- Center for Technological Innovation of Evandro Chagas Institute, Ministry of Health, BR 316, Km 07, s/n CEP 67.030-000, Ananindeua, Brazil
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28
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Cho TA, Mckendall RR. Clinical approach to the syndromes of viral encephalitis, myelitis, and meningitis. HANDBOOK OF CLINICAL NEUROLOGY 2014; 123:89-121. [PMID: 25015482 DOI: 10.1016/b978-0-444-53488-0.00004-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tracey A Cho
- Department of Neurology, Harvard Medical School and Neuro-ID Program, Massachusetts General Hospital, Boston, MA, USA
| | - Robert R Mckendall
- Departments of Neurology and Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, USA.
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29
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Cooper E, Anbalagan S, Klumper P, Scherba G, Simonson RR, Hause BM. Mobuck virus genome sequence and phylogenetic analysis: identification of a novel Orbivirus isolated from a white-tailed deer in Missouri, USA. J Gen Virol 2014; 95:110-116. [DOI: 10.1099/vir.0.058800-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The genus Orbivirus includes a diverse group of segmented dsRNA viruses that are transmitted via arthropods, have a global distribution and affect a wide range of hosts. A novel orbivirus was co-isolated with epizootic haemorrhagic disease virus (EHDV) from a white-tailed deer (Odocoileus virginianus) exhibiting clinical signs characteristic of EHDV. Using antiserum generated against EHDV, a pure isolate of the novel non-cytopathic orbivirus was obtained in Aedes albopictus cell culture. Genomic sequencing and phylogenetic analysis of predicted ORFs showed that eight of the ten ORFs were most homologous to Peruvian horse sickness virus (PHSV), with amino acid identities of 44.3–73.7 %. The remaining two ORFs, VP3 and VP5, were most similar to Middle Point orbivirus (35.9 %) and Yunnan orbivirus (59.8 %), respectively. Taxonomic classification of orbiviruses is largely based on homology of the major subcore structural protein VP2(T2), encoded by segment 2 for mobuck virus. With only 69.1 % amino acid identity to PHSV, we propose mobuck virus as the prototype of a new species of Orbivirus.
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Affiliation(s)
- Elyse Cooper
- Newport Laboratories, 1520 Prairie Drive, Worthington, MN 56187, USA
| | | | - Patricia Klumper
- Newport Laboratories, 1520 Prairie Drive, Worthington, MN 56187, USA
| | - Gail Scherba
- Department of Pathobiology and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61801, USA
| | - Randy R. Simonson
- Newport Laboratories, 1520 Prairie Drive, Worthington, MN 56187, USA
| | - Ben M. Hause
- Newport Laboratories, 1520 Prairie Drive, Worthington, MN 56187, USA
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30
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Changuinola Virus Serogroup, New Genomes within the Genus Orbivirus (Family Reoviridae) Isolated in the Brazilian Amazon Region. GENOME ANNOUNCEMENTS 2013; 1:1/6/e00940-13. [PMID: 24285662 PMCID: PMC3869324 DOI: 10.1128/genomea.00940-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the first complete genome sequence of a Changuinola virus (CGLV) serotype Irituia virus (BE AN 28873) isolated from a wild rodent (Oryzomys goeldi) in the municipality of Ipixuna, State of Pará, northern Brazil. All genome segments showed similarity with those belonging to members of the genus Orbivirus, family Reoviridae.
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31
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Toit ND, van Vuuren BJ, Matthee S, Matthee CA. Biogeography and host-related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts. Mol Ecol 2013; 22:5185-204. [DOI: 10.1111/mec.12459] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/12/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Nina du Toit
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Bettine J. van Vuuren
- Centre for Invasion Biology; Department of Zoology; University of Johannesburg; PO Box 524 Auckland Park South Africa
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Conrad A. Matthee
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
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32
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Dilcher M, Sall AA, Hufert FT, Weidmann M. Clarifying Bunyamwera virus riddles of the past. Virus Genes 2013; 47:160-3. [PMID: 23686694 DOI: 10.1007/s11262-013-0918-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 05/06/2013] [Indexed: 11/30/2022]
Abstract
Pyrosequencing data and phylogenetic analysis for the full genome of Ilesha virus, Ngari virus and Calovo virus are described clarifying their much discussed relationship within the species Bunyamwera virus of the genus Orthobunyavirus of the Bunyaviridae.
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Affiliation(s)
- Meik Dilcher
- Department of Virology, University Medical Center Goettingen, Kreuzbergring 57, 37075 Goettingen, Germany
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33
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Dilcher M, Sall AA, Hufert FT, Weidmann M. Full-length genome sequence of Ntaya virus. Virus Genes 2013; 46:162-4. [PMID: 22996737 PMCID: PMC3556468 DOI: 10.1007/s11262-012-0825-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/13/2012] [Indexed: 11/25/2022]
Abstract
Presentation of pyrosequencing data and phylogenetic analysis for the full genome of Ntaya virus, type virus of the Ntaya virus group of the Flaviviridae isolated in Cameroon in 1966.
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Affiliation(s)
- Meik Dilcher
- Department of Virology, University Medical Center Goettingen, Kreuzbergring 57, 37075 Goettingen, Germany
| | - Amadou A. Sall
- Institut Pasteur de Dakar, 36 Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Frank T. Hufert
- Department of Virology, University Medical Center Goettingen, Kreuzbergring 57, 37075 Goettingen, Germany
| | - Manfred Weidmann
- Department of Virology, University Medical Center Goettingen, Kreuzbergring 57, 37075 Goettingen, Germany
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34
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Abstract
We present pyrosequencing data and phylogenetic analysis for the full genome of Yug Bogdanovac virus (YBV), a member of the Vesicular stomatitis virus serogroup of the Rhabdoviridae isolated from a pool of Phlebotomus perfiliewi sandflies collected in Serbia in 1976. YBV shows very low nucleotide identities to other members of the Vesicular stomatitis virus serogroup and does not contain a reading frame for C′/C proteins.
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35
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Dilcher M, Weidmann M. Confusions in orbivirus protein classification. Virol J 2012; 9:166. [PMID: 22909086 PMCID: PMC3494582 DOI: 10.1186/1743-422x-9-166] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 07/24/2012] [Indexed: 11/24/2022] Open
Abstract
An extensive comparative analysis of orbivirus genomes revealed four cases of unclear numeration and protein designation, due to confused reference to protein size or segment size by which they are encoded. A concise nomenclature based on type species, sequence homology and functional characteristics independent of segment or protein size is suggested.
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Affiliation(s)
- Meik Dilcher
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
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36
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Genetic characterization of Erve virus, a European Nairovirus distantly related to Crimean-Congo hemorrhagic fever virus. Virus Genes 2012; 45:426-32. [PMID: 22864548 PMCID: PMC3519980 DOI: 10.1007/s11262-012-0796-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 07/20/2012] [Indexed: 01/26/2023]
Abstract
Erve virus (ERVEV) is a European Nairovirus that is suspected to cause severe headache (thunderclap headache) and intracerebral hemorrhage. The mode of transmission to humans (ticks or mosquitoes) is still unknown. Currently, no standardized testing method for ERVEV exists and only a small partial sequence of the polymerase gene is available. Here, we present the first complete genome sequence of ERVEV S, M, and L segments. Phylogenetic comparison of the amino acid sequence of the L-protein (RNA-dependent RNA polymerase) revealed only 48 % homology to available L-protein sequences of other Nairoviruses like Crimean-Congo hemorrhagic fever virus, Nairobi sheep disease virus, Hazara virus, Kupe virus, and Dugbe virus. Among themselves, these Nairoviruses show 62–89 % homology in the L-protein sequences. Therefore, ERVEV seems to be only distantly related to other Nairoviruses. The new sequence data can be used for the development of diagnostic methods and the identification of the natural vector.
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37
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Dilcher M, Alves MJ, Finkeisen D, Hufert F, Weidmann M. Genetic characterization of Bhanja virus and Palma virus, two tick-borne phleboviruses. Virus Genes 2012; 45:311-5. [PMID: 22806684 DOI: 10.1007/s11262-012-0785-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 07/04/2012] [Indexed: 02/02/2023]
Abstract
The genomes of Bhanja virus (BHAV) and Palma virus (PALV) two tick-borne viruses hitherto grouped into the Bhanja virus antigenic complex of the Bunyaviridae were determined by pyrosequencing. Phylogenetic analysis groups all three segments of BHAV and PALV into a distinct clade of tick-borne phleboviruses together with the newly described severe fever with thrombocytopenia syndrome virus and Uukuniemi virus. The terminal signature sequences which are signatures for taxonomic grouping and important for virus replication and RNA transcription show marked differences in the L- and S-segments.
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Affiliation(s)
- Meik Dilcher
- Department of Virology, University Medical Center Goettingen, Kreuzbergring 57, 37075 Göttingen, Germany
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