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Kobayashi D, Inoue Y, Suzuki R, Matsuda M, Shimoda H, Faizah AN, Kaku Y, Ishijima K, Kuroda Y, Tatemoto K, Virhuez-Mendoza M, Harada M, Nishino A, Inumaru M, Yonemitsu K, Kuwata R, Takano A, Watanabe M, Higa Y, Sawabe K, Maeda K, Isawa H. Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles. Proc Natl Acad Sci U S A 2024; 121:e2319400121. [PMID: 38687787 PMCID: PMC11087778 DOI: 10.1073/pnas.2319400121] [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: 11/06/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yusuke Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama City, Tokyo208-0011, Japan
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama City, Tokyo208-0011, Japan
| | - Hiroshi Shimoda
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Astri Nur Faizah
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Keita Ishijima
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yudai Kuroda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Kango Tatemoto
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Milagros Virhuez-Mendoza
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Michiko Harada
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ayano Nishino
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Mizue Inumaru
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Kenzo Yonemitsu
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ryusei Kuwata
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari City, Ehime794-8555, Japan
| | - Ai Takano
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Mamoru Watanabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yukiko Higa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
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2
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Tajima S, Kataoka M, Takamatsu Y, Ebihara H, Lim CK. Mutations in the 3' non-coding region of a no-known vector flavivirus Yokose virus increased its replication ability in mosquito C6/36 cells. Virology 2024; 589:109928. [PMID: 37949004 DOI: 10.1016/j.virol.2023.109928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Yokose virus (YOKV) is a bat-associated no-known vector flavivirus group member. We investigated the replication ability of YOKV in mosquito-derived C6/36 cells. YOKV grew in C6/36 cells, but its kinetics of YOKV was markedly slower than those of other mosquito-borne flaviviruses. Transmission electron microscopy indicated an extremely small number of viral particles in YOKV-infected C6/36 cells. Mosquito-borne Japanese encephalitis virus prM-E-bearing chimeric YOKV failed to propagate efficiently in C6/36 cells. We isolated C6/36-adapted YOKV and identified nucleotide mutations in the adapted YOKV. Mutations detected in the 3' non-coding region of the adapted YOKV were critical for the enhanced proliferation ability of the virus. Moreover, the growth of the original and adapted YOKV in C6/36 cells was remarkably increased by shifting the culture temperature from 28 to 36 °C. Thus, our results demonstrate the potential of YOKV to propagate in mosquito cells and support its classification as a mosquito-borne flavivirus.
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Affiliation(s)
- Shigeru Tajima
- Department of Virology 1, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan.
| | - Michiyo Kataoka
- Department of Pathology, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan
| | - Yuki Takamatsu
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Hideki Ebihara
- Department of Virology 1, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan
| | - Chang-Kweng Lim
- Department of Virology 1, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan
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3
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Weinberg M, Yovel Y. Revising the paradigm: Are bats really pathogen reservoirs or do they possess an efficient immune system? iScience 2022; 25:104782. [PMID: 35982789 PMCID: PMC9379578 DOI: 10.1016/j.isci.2022.104782] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While bats are often referred to as reservoirs of viral pathogens, a meta-analysis of the literature reveals many cases in which there is not enough evidence to claim so. In many cases, bats are able to confront viruses, recover, and remain immune by developing a potent titer of antibodies, often without becoming a reservoir. In other cases, bats might have carried an ancestral virus that at some time point might have mutated into a human pathogen. Moreover, bats exhibit a balanced immune response against viruses that have evolved over millions of years. Using genomic tools, it is now possible to obtain a deeper understanding of that unique immune system and its variability across the order Chiroptera. We conclude, that with the exception of a few viruses, bats pose little zoonotic danger to humans and that they operate a highly efficient anti-inflammatory response that we should strive to understand.
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Affiliation(s)
- Maya Weinberg
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Corresponding author
| | - Yossi Yovel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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4
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Mishra B, Aduri R. The RNA Secondary Structure Analysis Reveals Potential for Emergence of Pathogenic Flaviviruses. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:10-29. [PMID: 34694573 DOI: 10.1007/s12560-021-09502-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
The Flavivirus genus is divided into four groups: Mosquito-borne flaviviruses, Tick-borne flaviviruses, no-known vector flaviviruses, and Insect specific flaviviruses. Millions of people are affected worldwide every year due to the flaviviral infections. The 5' UTR of the RNA genome plays a critical role in the biology of flaviviruses. To explore any correlation between the topology of the 5' UTR and pathogenesis, a global scale study of the RNA secondary structure of different groups of flaviviruses has been conducted. We found that most of the pathogenic flaviviruses, irrespective of their mode of transmission, tend to form a Y shaped topology in the Stem loop A of the 5' UTR. Some of the current non-pathogenic flaviviruses were also observed to form Y shaped structure. Based on this study, it has been proposed that the flaviviruses having the Y shaped topology in their 5' UTR regions may have the potential to become pathogenic.
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Affiliation(s)
- Bibhudutta Mishra
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa campus, Zuarinagar, South Goa, 403726, India
- Department of Zoology, Centurion University of Technology and Management, Bhubaneswar Campus, Khurda, Jatni, 752050, Odisha, India
| | - Raviprasad Aduri
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa campus, Zuarinagar, South Goa, 403726, India.
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5
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Charles J, Tangudu CS, Nunez-Avellaneda D, Brault AC, Blitvich BJ. The host range restriction of bat-associated no-known-vector flaviviruses occurs post-entry. J Gen Virol 2021; 102. [PMID: 34486974 PMCID: PMC8567430 DOI: 10.1099/jgv.0.001647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Most flaviviruses are transmitted horizontally between vertebrate hosts by haematophagous arthropods. Others exhibit host ranges restricted to vertebrates or arthropods. Vertebrate-specific flaviviruses are commonly referred to as no-known-vector (NKV) flaviviruses and can be separated into bat- and rodent-associated NKV flaviviruses. Rio Bravo virus (RBV) is one of eight recognized bat-associated NKV (B-NKV) flaviviruses. Studies designed to identify the genetic determinants that condition the host range restriction of B-NKV flaviviruses have never been performed. To investigate whether the host range restriction occurs at the level of attachment or entry, chimeric flaviviruses were created by inserting the pre-membrane and envelope protein genes of RBV into the genetic backbones of yellow fever virus (YFV) and Zika virus (ZIKV), two mosquito-borne flaviviruses associated with human disease. The chimeric viruses infected both vertebrate and mosquito cells. In vertebrate cells, all viruses produced similar mean peak titres, but the chimeric viruses grew more slowly than their parental viruses during early infection. In mosquito cells, the chimeric virus of YFV and RBV grew more slowly than YFV at early post-inoculation time points, but reached a similar mean peak titre. In contrast, the chimeric virus of ZIKV and RBV produced a mean peak titre that was approximately 10-fold lower than ZIKV. The chimeric virus of YFV and RBV produced an intermediate plaque phenotype, while the chimeric virus of ZIKV and RBV produced smaller plaques than both parental viruses. To conclude, we provide evidence that the structural glycoproteins of RBV permit entry into both mosquito and vertebrate cells, indicating that the host range restriction of B-NKV flaviviruses is mediated by a post-attachment/entry event.
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Affiliation(s)
- Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Daniel Nunez-Avellaneda
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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6
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Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, Clark TG, Campino S. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasit Vectors 2021; 14:332. [PMID: 34174947 PMCID: PMC8235865 DOI: 10.1186/s13071-021-04828-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
Mosquitoes of the genus Aedes are the main vectors of many viruses, e.g. dengue and Zika, which affect millions of people each year and for which there are limited treatment options. Understanding how Aedes mosquitoes tolerate high viral loads may lead to better disease control strategies. Elucidating endogenous viral elements (EVEs) within vector genomes may give exploitable biological insights. Previous studies have reported the presence of a large number of EVEs in Aedes genomes. Here we investigated if flavivirus EVEs are conserved across populations and different Aedes species by using ~ 500 whole genome sequence libraries from Aedes aegypti and Aedes albopictus, sourced from colonies and field mosquitoes across continents. We found that nearly all flavivirus EVEs in the Ae. aegypti reference genome originate from four separate putative viral integration events, and that they are highly conserved across geographically diverse samples. By contrast, flavivirus EVEs in the Ae. albopictus reference genome originate from up to nine distinct integration events and show low levels of conservation, even within samples from narrow geographical ranges. Our analysis suggests that flaviviruses integrated as long sequences and were subsequently fragmented and shuffled by transposable elements. Given that EVEs of Ae. aegypti and Ae. albopictus belong to different phylogenetic clades and have very differing levels of conservation, they may have different evolutionary origins and potentially different functional roles.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Lara Ferrero Gomez
- Unidade de Ciências da Natureza, da Vida e do Ambiente, Universidade Jean Piaget de Cabo Verde, Praia, Cabo Verde
| | - Fady Mohareb
- School of Water, Energy and Environment, Cranfield University, Bedford, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
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7
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Update on Potentially Zoonotic Viruses of European Bats. Vaccines (Basel) 2021; 9:vaccines9070690. [PMID: 34201666 PMCID: PMC8310327 DOI: 10.3390/vaccines9070690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses.
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8
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Braun BA, Schein CH, Braun W. DGraph Clusters Flaviviruses and β-Coronaviruses According to Their Hosts, Disease Type, and Human Cell Receptors. Bioinform Biol Insights 2021; 15:11779322211020316. [PMID: 34163149 PMCID: PMC8188974 DOI: 10.1177/11779322211020316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/05/2021] [Indexed: 01/11/2023] Open
Abstract
Motivation There is a need for rapid and easy-to-use, alignment-free methods to cluster large groups of protein sequence data. Commonly used phylogenetic trees based on alignments can be used to visualize only a limited number of protein sequences. DGraph, introduced here, is an application developed to generate 2-dimensional (2D) maps based on similarity scores for sequences. The program automatically calculates and graphically displays property distance (PD) scores based on physico-chemical property (PCP) similarities from an unaligned list of FASTA files. Such "PD-graphs" show the interrelatedness of the sequences, whereby clusters can reveal deeper connectivities. Results Property distance graphs generated for flavivirus (FV), enterovirus (EV), and coronavirus (CoV) sequences from complete polyproteins or individual proteins are consistent with biological data on vector types, hosts, cellular receptors, and disease phenotypes. Property distance graphs separate the tick- from the mosquito-borne FV, cluster viruses that infect bats, camels, seabirds, and humans separately. The clusters correlate with disease phenotype. The PD method segregates the β-CoV spike proteins of severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Middle East respiratory syndrome (MERS) sequences from other human pathogenic CoV, with clustering consistent with cellular receptor usage. The graphs also suggest evolutionary relationships that may be difficult to determine with conventional bootstrapping methods that require postulating an ancestral sequence.
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Affiliation(s)
- Benjamin A Braun
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
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9
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Braun BA, Schein CH, Braun W. D-graph clusters flaviviruses and β-coronaviruses according to their hosts, disease type and human cell receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32817945 PMCID: PMC7430575 DOI: 10.1101/2020.08.13.249649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Motivation: There is a need for rapid and easy to use, alignment free methods to cluster large groups of protein sequence data. Commonly used phylogenetic trees based on alignments can be used to visualize only a limited number of protein sequences. DGraph, introduced here, is a dynamic programming application developed to generate 2D-maps based on similarity scores for sequences. The program automatically calculates and graphically displays property distance (PD) scores based on physico-chemical property (PCP) similarities from an unaligned list of FASTA files. Such “PD-graphs” show the interrelatedness of the sequences, whereby clusters can reveal deeper connectivities. Results: PD-Graphs generated for flavivirus (FV), enterovirus (EV), and coronavirus (CoV) sequences from complete polyproteins or individual proteins are consistent with biological data on vector types, hosts, cellular receptors and disease phenotypes. PD-graphs separate the tick- from the mosquito-borne FV, clusters viruses that infect bats, camels, seabirds and humans separately and the clusters correlate with disease phenotype. The PD method segregates the β-CoV spike proteins of SARS, SARS-CoV-2, and MERS sequences from other human pathogenic CoV, with clustering consistent with cellular receptor usage. The graphs also suggest evolutionary relationships that may be difficult to determine with conventional bootstrapping methods that require postulating an ancestral sequence.
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10
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Rathore APS, St John AL. Cross-Reactive Immunity Among Flaviviruses. Front Immunol 2020; 11:334. [PMID: 32174923 PMCID: PMC7054434 DOI: 10.3389/fimmu.2020.00334] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses consist of significant human pathogens responsible for hundreds of millions of infections each year. Their antigenic relationships generate immune responses that are cross-reactive to multiple flaviviruses and their widespread and overlapping geographical distributions, coupled with increases in vaccination coverage, increase the likelihood of exposure to multiple flaviviruses. Depending on the antigenic properties of the viruses to which a person is exposed, flavivirus cross-reactivity can be beneficial or could promote immune pathologies. In this review we describe our knowledge of the functional immune outcomes that arise from varied flaviviral immune statuses. The cross-reactive antibody and T cell immune responses that are protective versus pathological are also addressed.
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Affiliation(s)
- Abhay P S Rathore
- Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Ashley L St John
- Department of Pathology, Duke University Medical Center, Durham, NC, United States.,Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,SingHealth Duke-National University of Singapore Global Health Institute, Singapore, Singapore
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11
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Calderón A, Guzmán C, Mattar S, Rodriguez V, Martínez C, Violet L, Martínez J, Figueiredo LTM. Dengue Virus in Bats from Córdoba and Sucre, Colombia. Vector Borne Zoonotic Dis 2019; 19:747-751. [PMID: 31211661 PMCID: PMC6765209 DOI: 10.1089/vbz.2018.2324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural infection of dengue virus (DENV) in bats is an unexplored field in Colombia. To detect the presence of DENV in bats, a descriptive prospective study using a nonprobabilistic sampling was carried out; 286 bats in 12 sites were caught. Sample tissues of different animals were obtained; the RNA was obtained from tissues and a nested-RT-PCR was carried out and detected amplicons of 143 fragment of the NS5 gene were sequenced by the Sanger method. In nonhematophagous bats Carollia perspicillata and Phyllostomus discolor captured in Ayapel and San Carlos (Córdoba), respectively, an amplicon corresponding to NS5 was detected. The amplicons showed a high similarity with serotype-2 dengue virus (DENV-2). This is the first evidence of the DENV-2 genome in bats in from the Colombian Caribbean.
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Affiliation(s)
- Alfonso Calderón
- Department of Bacterilogy, Faculty of Health Sciences, University of Córdoba, Montería, Colombia.,Doctorate in Tropical Medicine SUE-Caribe, University of Córdoba, Monteria, Colombia
| | - Camilo Guzmán
- Department of Bacterilogy, Faculty of Health Sciences, University of Córdoba, Montería, Colombia.,Doctorate in Tropical Medicine SUE-Caribe, University of Córdoba, Monteria, Colombia
| | - Salim Mattar
- Department of Bacterilogy, Faculty of Health Sciences, University of Córdoba, Montería, Colombia
| | - Virginia Rodriguez
- Institute of Virology, Faculty of Medicine, University São Paulo, Ribeirão Preto, Brazil
| | - Caty Martínez
- Department of Bacterilogy, Faculty of Health Sciences, University of Córdoba, Montería, Colombia
| | - Lina Violet
- Department of Bacterilogy, Faculty of Health Sciences, University of Córdoba, Montería, Colombia
| | - Jairo Martínez
- Department of Bacterilogy, Faculty of Health Sciences, University of Córdoba, Montería, Colombia
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12
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Shimoda H, Hayasaka D, Yoshii K, Yokoyama M, Suzuki K, Kodera Y, Takeda T, Mizuno J, Noguchi K, Yonemitsu K, Minami S, Kuwata R, Takano A, Maeda K. Detection of a novel tick-borne flavivirus and its serological surveillance. Ticks Tick Borne Dis 2019; 10:742-748. [PMID: 30902589 DOI: 10.1016/j.ttbdis.2019.03.006] [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] [Received: 07/10/2018] [Revised: 03/10/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
Tick-borne encephalitis virus (TBEV), a flavivirus that causes severe neurological symptoms in humans, has been found in Hokkaido, Japan. In the present study, we detected sequences from a novel tick-borne flavivirus, designated Yamaguchi virus (YGV), in liver and serum samples obtained from a wild boar in the Yamaguchi prefecture, Japan. Phylogenetic analysis revealed that YGV belongs to the TBEV complex and is closely related to Langat virus (LGTV). YGV was also detected by specific RT-PCR from 20 in 378 pools of ticks (2923 ticks) collected in Yamaguchi and Wakayama prefectures and from seven in 46 wild boar captured in Wakayama. The major ticks infected with YGV belong to the genus Haemaphysalis. Unfortunately, YGV could not be isolated from any samples from the RT-PCR positive wild boar or ticks. Therefore, ELISA for detection of antibodies against YGV was established using LGTV, and surveillance was performed among wild boar in 10 different prefectures on Honshu Island, the main island of Japan. The results showed that the seroprevalence of tick-borne flavivirus infection in the Wakayama and Hyogo prefectures of western Japan was significantly higher than that in the other prefectures, while antibodies against tick-borne flavivirus were not detected in any wild boar in the Tochigi prefecture in the eastern part of Japan. In addition, wild raccoons or masked palm civets in the Hyogo prefecture did not possess detectable antibodies against tick-borne flaviviruses. In conclusion, YGV appears to be maintained primarily among wild boar and ticks in the western part of Japan. YGV is the second flavivirus (after Japanese encephalitis virus) shown to be circulating on Honshu Island in Japan.
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Affiliation(s)
- Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Daisuke Hayasaka
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku Kita-18 Nishi-9, Sapporo, Hokkaido, 060-0818, Japan
| | - Mayumi Yokoyama
- Institute of Natural and Environmental Science, University of Hyogo, 940 Sawano, Aogaki-cho, Tamba, Hyogo, 669-3842, Japan
| | - Kazuo Suzuki
- Hikiiwa Park Center, 1629 Inari-cho, Tanabe, Wakayama, 646-0051, Japan
| | - Yuuji Kodera
- Center for Weed and Wildlife Management, Utsunomiya University, 350 Mine-machi, Utsunomioya, Tochigi, 321-8505, Japan
| | - Tsutomu Takeda
- Center for Weed and Wildlife Management, Utsunomiya University, 350 Mine-machi, Utsunomioya, Tochigi, 321-8505, Japan; Natural Parks Foundation Nikko National Park, Yumoto, Nikko, Tochigi, 321-1662, Japan
| | - Junko Mizuno
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Keita Noguchi
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Shohei Minami
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Ai Takano
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan.
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Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats ( Eonycteris spelaea). Viruses 2019; 11:v11030250. [PMID: 30871070 PMCID: PMC6466414 DOI: 10.3390/v11030250] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission. Here we investigate the diversity and abundance of viral communities from a colony of Eonycteris spelaea residing in Singapore. Our results detected 47 and 22 different virus families from bat fecal and urine samples, respectively. Among these, we identify a large number of virus families including Adenoviridae, Flaviviridae, Reoviridae, Papillomaviridae, Paramyxoviridae, Parvoviridae, Picornaviridae, and Polyomaviridae. In most cases, viral sequences from Eonycteris spelaea are genetically related to a group of bat viruses from other bat genera (e.g., Eidolon, Miniopterus, Rhinolophus and Rousettus). The results of this study improve our knowledge of the host range, spread and evolution of several important viral pathogens. More significantly, our findings provide a baseline to study the temporal patterns of virus shedding and how they correlate with bat phenological trends.
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Feng Y, Ren X, Xu Z, Fu S, Li X, Zhang H, Yang W, Zhang Y, Liang G. Genetic diversity of the Yokose virus, XYBX1332, isolated from bats (Myotis daubentonii) in China. Virol J 2019; 16:8. [PMID: 30634973 PMCID: PMC6330390 DOI: 10.1186/s12985-018-1107-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/11/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Yokose virus was first isolated from bats (Miniopterus fuliginosus) collected in Yokosuka, Japan, in 1971, and is a new member of the family Flaviviridae, genus Flavivirus. In this study, we isolated a Yokose virus from a serum sample of Myotis daubentonii (order Chiroptera, family Vespertilionidae) collected in Yunnan province, China in 2013. METHODS The serum specimens of bat were used to inoculate in BHK-21 and Vero E6 cells for virus isolation. Then the viral complete genome sequence was obtained and was used for phylogenetic analysis performed by BEAST software package. RESULTS The virus was shown to have cytopathic effects in mammalian cells (BHK-21 and Vero E6). Genome sequencing indicated that it has a single open reading frame (ORF), with a genome of 10,785 nucleotides in total. Phylogenetic analysis of the viral genome suggests that XYBX1332 is a Yokose virus (YOKV) of the genus Flavivirus. Nucleotide and amino acid homology levels of the ORF of XYBX1332 and Oita-36, the original strain of YOKV, were 72 and 82%, respectively. The ORFs of XYBX1332 and Oita-36 encode 3422 and 3425 amino acids, respectively. In addition, the non-coding regions (5'- and 3'-untranslated regions [UTRs]) of these two strains differ in length and the homology of the 5'- and 3'-UTRs was 81.5 and 78.3%, respectively. CONCLUSION The isolation of YOKV (XYBX1332) from inland China thousands of kilometers from Yokosuka, Japan, suggests that the geographical distribution of YOKV is not limited to the islands of Japan and that it can also exist in the inland areas of Asia. However, there are large differences between the Chinese and Japanese YOKV strains in viral genome.
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Affiliation(s)
- Yun Feng
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Xiaojie Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ziqian Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Shihong Fu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaolong Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hailin Zhang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Weihong Yang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Yuzhen Zhang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Lv J, Fernández de Marco MDM, Goharriz H, Phipps LP, McElhinney LM, Hernández-Triana LM, Wu S, Lin X, Fooks AR, Johnson N. Detection of tick-borne bacteria and babesia with zoonotic potential in Argas (Carios) vespertilionis (Latreille, 1802) ticks from British bats. Sci Rep 2018; 8:1865. [PMID: 29382871 PMCID: PMC5789838 DOI: 10.1038/s41598-018-20138-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/12/2018] [Indexed: 11/20/2022] Open
Abstract
Ticks host a wide range of zoonotic pathogens and are a significant source of diseases that affect humans and livestock. However, little is known about the pathogens associated with bat ticks. We have collected ectoparasites from bat carcasses over a seven year period. Nucleic acids (DNA and RNA) were extracted from 296 ticks removed from bats and the species designation was confirmed in all ticks as Argas (Carios) vespertilionis. A subset of these samples (n = 120) were tested for the presence of zoonotic pathogens by molecular methods. Babesia species, Rickettsia spp., within the spotted fever group (SFG), and Ehrlichia spp. were detected in ticks removed from 26 bats submitted from 14 counties across England. The prevalence of Rickettsia spp. was found to be highest in Pipistrellus pipistrellus from southern England. This study suggests that the tick species that host B. venatorum may include the genus Argas in addition to the genus Ixodes. As A. vespertilionis has been reported to feed on humans, detection of B. venatorum and SFG Rickettsia spp. could present a risk of disease transmission in England. No evidence for the presence of flaviviruses or Issyk-Kul virus (nairovirus) was found in these tick samples.
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Affiliation(s)
- Jizhou Lv
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, P.R. China.,Animal and Plant Health Agency, Woodham Lane, Surrey, KT15 3NB, UK
| | | | - Hooman Goharriz
- Animal and Plant Health Agency, Woodham Lane, Surrey, KT15 3NB, UK
| | - L Paul Phipps
- Animal and Plant Health Agency, Woodham Lane, Surrey, KT15 3NB, UK
| | - Lorraine M McElhinney
- Animal and Plant Health Agency, Woodham Lane, Surrey, KT15 3NB, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | | | - Shaoqiang Wu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, P.R. China
| | - Xiangmei Lin
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, P.R. China
| | - Anthony R Fooks
- Animal and Plant Health Agency, Woodham Lane, Surrey, KT15 3NB, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Nicholas Johnson
- Animal and Plant Health Agency, Woodham Lane, Surrey, KT15 3NB, UK. .,Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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Abstract
Most viruses in the genus Flavivirus are horizontally transmitted between hematophagous arthropods and vertebrate hosts, but some are maintained in arthropod- or vertebrate-restricted transmission cycles. Flaviviruses maintained by vertebrate-only transmission are commonly referred to as no known vector (NKV) flaviviruses. Fourteen species and two subtypes of NKV flaviviruses are recognized by the International Committee on Taxonomy of Viruses (ICTV), and Tamana bat virus potentially belongs to this group. NKV flaviviruses have been isolated in nature almost exclusively from bats and rodents; exceptions are the two isolates of Dakar bat virus recovered from febrile humans and the recent isolations of Sokoluk virus from field-collected ticks, which raises questions as to whether it should remain classified as an NKV flavivirus. There is evidence to suggest that two other NKV flaviviruses, Entebbe bat virus and Yokose virus, may also infect arthropods in nature. The best characterized bat- and rodent-associated NKV flaviviruses are Rio Bravo and Modoc viruses, respectively, but both have received limited research attention compared to many of their arthropod-infecting counterparts. Herein, we provide a comprehensive review of NKV flaviviruses, placing a particular emphasis on their classification, host range, geographic distribution, replication kinetics, pathogenesis, transmissibility and molecular biology.
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Vicente-Santos A, Moreira-Soto A, Soto-Garita C, Chaverri LG, Chaves A, Drexler JF, Morales JA, Alfaro-Alarcón A, Rodríguez-Herrera B, Corrales-Aguilar E. Neotropical bats that co-habit with humans function as dead-end hosts for dengue virus. PLoS Negl Trop Dis 2017; 11:e0005537. [PMID: 28545090 PMCID: PMC5451070 DOI: 10.1371/journal.pntd.0005537] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 05/31/2017] [Accepted: 03/29/2017] [Indexed: 01/27/2023] Open
Abstract
Several studies have shown Dengue Virus (DENV) nucleic acids and/or antibodies present in Neotropical wildlife including bats, suggesting that some bat species may be susceptible to DENV infection. Here we aim to elucidate the role of house-roosting bats in the DENV transmission cycle. Bats were sampled in households located in high and low dengue incidence regions during rainy and dry seasons in Costa Rica. We captured 318 bats from 12 different species in 29 households. Necropsies were performed in 205 bats to analyze virus presence in heart, lung, spleen, liver, intestine, kidney, and brain tissue. Histopathology studies from all organs showed no significant findings of disease or infection. Sera were analyzed by PRNT90 for a seroprevalence of 21.2% (51/241), and by PCR for 8.8% (28/318) positive bats for DENV RNA. From these 28 bats, 11 intestine samples were analyzed by RT-PCR. Two intestines were DENV RNA positive for the same dengue serotype detected in blood. Viral isolation from all positive organs or blood was unsuccessful. Additionally, viral load analyses in positive blood samples by qRT-PCR showed virus concentrations under the minimal dose required for mosquito infection. Simultaneously, 651 mosquitoes were collected using EVS-CO2 traps and analyzed for DENV and feeding preferences (bat cytochrome b). Only three mosquitoes were found DENV positive and none was positive for bat cytochrome b. Our results suggest an accidental presence of DENV in bats probably caused from oral ingestion of infected mosquitoes. Phylogenetic analyses suggest also a spillover event from humans to bats. Therefore, we conclude that bats in these urban environments do not sustain DENV amplification, they do not have a role as reservoirs, but function as epidemiological dead end hosts for this virus. Dengue is the most important human vector-borne disease. Several studies have shown DENV presence in mammalian wildlife such as bats, thus considering them putative reservoirs or hosts. We aimed to elucidate if bats that cohabit in houses in close proximity with humans may be involved in a dengue transmission cycle. We sampled bats in low and high dengue incidence areas during the dry (low mosquito abundance) and wet (high mosquito abundance) seasons. We analyzed blood and several organs. As previously reported, we found DENV nucleic acid and neutralizing antibodies in a small percentage of blood samples, but virus detection in all organs was negative. We were able to show that dengue found in all positive samples was in low concentration and thus virus isolation was unsuccessful. We found positive intestine samples which may suggest infection through DENV-positive mosquito ingestion. Furthermore, mosquitoes sampled in close vicinity of bats’ roosting place were not feeding on these mammals. Virus sequence analysis from bats and humans show a spillover effect from humans to bats. Taken together, our results indicate that bats do not sustain sufficient virus amplification in order to function as reservoirs and exclude them as players in the dengue virus transmission cycle.
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Affiliation(s)
- Amanda Vicente-Santos
- Virology-CIET (Research Center for Tropical Diseases), Microbiology, University of Costa Rica, San José, Costa Rica
- Biology, University of Costa Rica, San José, Costa Rica
| | - Andres Moreira-Soto
- Virology-CIET (Research Center for Tropical Diseases), Microbiology, University of Costa Rica, San José, Costa Rica
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Claudio Soto-Garita
- Virology-CIET (Research Center for Tropical Diseases), Microbiology, University of Costa Rica, San José, Costa Rica
| | - Luis Guillermo Chaverri
- Exact and Natural Sciences School, National Distance Education University, San José, Costa Rica
| | - Andrea Chaves
- Biology, University of Costa Rica, San José, Costa Rica
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research, Bonn-Cologne, Germany
| | - Juan Alberto Morales
- Department of Pathology, School of Veterinary Medicine, National University, Heredia, Costa Rica
| | - Alejandro Alfaro-Alarcón
- Department of Pathology, School of Veterinary Medicine, National University, Heredia, Costa Rica
| | | | - Eugenia Corrales-Aguilar
- Virology-CIET (Research Center for Tropical Diseases), Microbiology, University of Costa Rica, San José, Costa Rica
- * E-mail:
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18
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Kading RC, Schountz T. Flavivirus Infections of Bats: Potential Role in Zika Virus Ecology. Am J Trop Med Hyg 2016; 95:993-996. [PMID: 27645783 PMCID: PMC5094249 DOI: 10.4269/ajtmh.16-0625] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/22/2016] [Indexed: 11/07/2022] Open
Abstract
Understanding the vector and nonhuman vertebrate species contributing to Zika virus (ZIKAV) transmission is critical to understanding the ecology of this emerging arbovirus and its potential to establish in new geographic areas. This minireview summarizes what is known regarding the association of bats with flaviviruses (Flaviviridae: Flavivirus) with a particular emphasis on the potential role of bats in the sylvatic transmission of ZIKAV. Key research directions that remain to be addressed are also discussed.
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Affiliation(s)
- Rebekah C Kading
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado.
| | - Tony Schountz
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
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Abstract
In this chapter, we describe 73 zoonotic viruses that were isolated in Northern Eurasia and that belong to the different families of viruses with a single-stranded RNA (ssRNA) genome. The family includes viruses with a segmented negative-sense ssRNA genome (families Bunyaviridae and Orthomyxoviridae) and viruses with a positive-sense ssRNA genome (families Togaviridae and Flaviviridae). Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Other viruses described in the chapter can cause epizootics in wild or domestic animals: Geta virus (GETV, Alphavirus), Influenza A virus (Influenzavirus A), Bhanja virus (BHAV, Phlebovirus) and more. The chapter also discusses both ecological peculiarities that promote the circulation of these viruses in natural foci and factors influencing the occurrence of epidemic and epizootic outbreaks
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20
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Abstract
UNLABELLED Equine hepacivirus (EHcV) has been identified as a closely related homologue of hepatitis C virus (HCV) in the United States, the United Kingdom, and Germany, but not in Asian countries. In this study, we genetically and serologically screened 31 serum samples obtained from Japanese-born domestic horses for EHcV infection and subsequently identified 11 PCR-positive and 7 seropositive serum samples. We determined the full sequence of the EHcV genome, including the 3' untranslated region (UTR), which had previously not been completely revealed. The polyprotein of a Japanese EHcV strain showed approximately 95% homology to those of the reported strains. HCV-like cis-acting RNA elements, including the stem-loop structures of the 3' UTR and kissing-loop interaction were deduced from regions around both UTRs of the EHcV genome. A comparison of the EHcV and HCV core proteins revealed that Ile(190) and Phe(191) of the EHcV core protein could be important for cleavage of the core protein by signal peptide peptidase (SPP) and were replaced with Ala and Leu, respectively, which inhibited intramembrane cleavage of the EHcV core protein. The loss-of-function mutant of SPP abrogated intramembrane cleavage of the EHcV core protein and bound EHcV core protein, suggesting that the EHcV core protein may be cleaved by SPP to become a mature form. The wild-type EHcV core protein, but not the SPP-resistant mutant, was localized on lipid droplets and partially on the lipid raft-like membrane in a manner similar to that of the HCV core protein. These results suggest that EHcV may conserve the genetic and biological properties of HCV. IMPORTANCE EHcV, which shows the highest amino acid or nucleotide homology to HCV among hepaciviruses, was previously reported to infect horses from Western, but not Asian, countries. We herein report EHcV infection in Japanese-born horses. In this study, HCV-like RNA secondary structures around both UTRs were predicted by determining the whole-genome sequence of EHcV. Our results also suggest that the EHcV core protein is cleaved by SPP to become a mature form and then is localized on lipid droplets and partially on lipid raft-like membranes in a manner similar to that of the HCV core protein. Hence, EHcV was identified as a closely related homologue of HCV based on its genetic structure as well as its biological properties. A clearer understanding of the epidemiology, genetic structure, and infection mechanism of EHcV will assist in elucidating the evolution of hepaciviruses as well as the development of surrogate models for the study of HCV.
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Detection of Quang Binh virus from mosquitoes in China. Virus Res 2013; 180:31-8. [PMID: 24342141 DOI: 10.1016/j.virusres.2013.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/24/2013] [Accepted: 12/04/2013] [Indexed: 11/24/2022]
Abstract
Flaviviruses present a wide range of genetic diversity and exhibit diverse host relationships. Mosquito-borne flaviviruses have recently been isolated and characterized worldwide. Yunnan Province of China is one of the richest areas of species diversity and is the center of multi-species evolution in mainland Asia, which supports the circulation of numerous arthropod-borne viruses (arboviruses). In a screening program of arboviruses, mosquitoes were collected during the mosquito activity season in the Yunnan Province from 2007 to 2010. Eleven flavivirus strains, named Yunnan Culex flaviviruses (YNCxFVs), were obtained from Culex tritaeniorhynchus and Anopheles sinensis specimens. Sequence analyses based on partial nonstructural protein (NS) 5 gene indicated that the YNCxFVs shared 92.8-99.6% nucleotide identity with each other and were similar to the Culex-related flaviviruses. The complete genome of one representative isolate, LSFlaviV-A20-09, was sequenced. The genome was 10,865 nucleotides long and contained a single, long open reading frame (ORF) of 10,080 nucleotides that encoded a 3360-aa polyprotein. This genome was most closely related to the Quang Binh virus (QBV) VN180 strain, an insect-specific flavivirus isolated from Culex mosquitoes in Vietnam, but only had 83.0% nucleotide and 93.8% amino acid identities for the ORF sequence. The genome has approximately 66.3%-68.5% nucleotide sequence and 69.3-73.3% amino acid sequence identities to other Culex flaviviruses, and only has 47.9-57.9% nucleotide sequence and 38.7-55.1% amino acid sequence identities to Coquillettidia-related, Mansonia-related and Aedes-related flaviviruses. Phylogenetic analyses revealed that the LSFlaviV-A20-09 fell into the Culex-related flavivirus clade. Our discoveries provide more information regarding the heterogeneity of viruses that infect mosquitoes.
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22
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Tang Y, Diao Y, Chen H, Ou Q, Liu X, Gao X, Yu C, Wang L. Isolation and genetic characterization of a tembusu virus strain isolated from mosquitoes in Shandong, China. Transbound Emerg Dis 2013; 62:209-16. [PMID: 23711093 DOI: 10.1111/tbed.12111] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 11/29/2022]
Abstract
Tembusu virus (TMUV) is a flavivirus, presumed to be a mosquito-borne flavivirus of the Ntaya virus subgroup. To date, however, there have been no reports indicating that mosquitoes are involved in the spread of TMUV. In this study, we report the first isolation of TMUV from Culex mosquitoes. We describe the isolation and characterization of a field strain of TMUV from mosquitoes collected in Shandong Province, China. The virus isolate, named TMUV-SDMS, grows well in mosquito cell line C6/36, in Vero and duck embryo fibroblast (DEF) cell lines, and causes significant cytopathic effects in these cell cultures. The TMUV-SDMS genome is a single-stranded RNA, 10 989 nt in length, consisting of a single open reading frame encoding a polyprotein of 3410 amino acids, with 5' and 3' untranslated regions of 142 and 617 nt, respectively. Phylogenetic analysis of the E and NS5 genes revealed that the TMUV-SDMS is closely related to the TMUV YY5 and BYD strains which cause severe egg-drop in ducks. The 3'NTR of TMUV-SDMS contains two pairs of tandem repeat CS and one non-duplicate CS, which have sequence similarities to the same repeats in the YY5 and BYD strains. Our findings indicate that mosquitoes carrying the TMUV may play an important role in the spread of this virus and in disease outbreak.
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Affiliation(s)
- Y Tang
- Institute of Poultry Disease, Shan Dong Agricultural University, Taian, Shan Dong Province, China
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Tang Y, Diao Y, Gao X, Yu C, Chen L, Zhang D. Analysis of the complete genome of Tembusu virus, a flavivirus isolated from ducks in China. Transbound Emerg Dis 2011; 59:336-43. [PMID: 22103739 DOI: 10.1111/j.1865-1682.2011.01275.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
During investigations into the outbreak of duck viral infection in 2010 in China, with a severe drop in egg production, a flavivirus was isolated from the affected ducks. It was characterized as a Tembusu virus (TMUV). In this study, we obtained a complete genome sequence of Tembusu virus using RT-PCR and RACE techniques. TMUV genome is a singled-stranded RNA, with 10,990 nucleotides in length, and contains a single open reading frame (3410 amino acids) encoding 11 viral proteins with 5'and 3'non-translated regions (NTRs) of 142 and 618 nt, respectively. We characterized the open reading frame (ORF) with respect to gene sizes, cleavage sites and potential glycosylation sites. The different genomic regions of the virus were also compared with those of six other flaviviruses including Japanese encephalitis virus, West Nile virus (WNV), dengue-2 virus, yellow fever virus, tick-borne encephalitis virus (TBEV) and Bagaza virus. TMUV demonstrated the highest similarity to Bagaza virus. The result of entire ORF scanning shows that TMUV was close to Bagaza viruses in genetic relatedness. These data demonstrate that TMUV is a unique virus among the mosquito-borne flaviviruses and also provide a useful reference for a critically important study to determine why TMUV is a serious pathogen for ducks.
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Affiliation(s)
- Y Tang
- Zoology Institute, Agricultural University of Shan Dong Province, Shan Dong Province, China
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Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat. J Virol 2010; 84:13004-18. [PMID: 20926577 DOI: 10.1128/jvi.01255-10] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Effective prediction of future viral zoonoses requires an in-depth understanding of the heterologous viral population in key animal species that will likely serve as reservoir hosts or intermediates during the next viral epidemic. The importance of bats as natural hosts for several important viral zoonoses, including Ebola, Marburg, Nipah, Hendra, and rabies viruses and severe acute respiratory syndrome-coronavirus (SARS-CoV), has been established; however, the large viral population diversity (virome) of bats has been partially determined for only a few of the ∼1,200 bat species. To assess the virome of North American bats, we collected fecal, oral, urine, and tissue samples from individual bats captured at an abandoned railroad tunnel in Maryland that is cohabitated by 7 to 10 different bat species. Here, we present preliminary characterization of the virome of three common North American bat species, including big brown bats (Eptesicus fuscus), tricolored bats (Perimyotis subflavus), and little brown myotis (Myotis lucifugus). In samples derived from these bats, we identified viral sequences that were similar to at least three novel group 1 CoVs, large numbers of insect and plant virus sequences, and nearly full-length genomic sequences of two novel bacteriophages. These observations suggest that bats encounter and disseminate a large assortment of viruses capable of infecting many different animals, insects, and plants in nature.
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Bollati M, Alvarez K, Assenberg R, Baronti C, Canard B, Cook S, Coutard B, Decroly E, de Lamballerie X, Gould EA, Grard G, Grimes JM, Hilgenfeld R, Jansson AM, Malet H, Mancini EJ, Mastrangelo E, Mattevi A, Milani M, Moureau G, Neyts J, Owens RJ, Ren J, Selisko B, Speroni S, Steuber H, Stuart DI, Unge T, Bolognesi M. Structure and functionality in flavivirus NS-proteins: perspectives for drug design. Antiviral Res 2010; 87:125-48. [PMID: 19945487 PMCID: PMC3918146 DOI: 10.1016/j.antiviral.2009.11.009] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/08/2009] [Accepted: 11/21/2009] [Indexed: 12/28/2022]
Abstract
Flaviviridae are small enveloped viruses hosting a positive-sense single-stranded RNA genome. Besides yellow fever virus, a landmark case in the history of virology, members of the Flavivirus genus, such as West Nile virus and dengue virus, are increasingly gaining attention due to their re-emergence and incidence in different areas of the world. Additional environmental and demographic considerations suggest that novel or known flaviviruses will continue to emerge in the future. Nevertheless, up to few years ago flaviviruses were considered low interest candidates for drug design. At the start of the European Union VIZIER Project, in 2004, just two crystal structures of protein domains from the flaviviral replication machinery were known. Such pioneering studies, however, indicated the flaviviral replication complex as a promising target for the development of antiviral compounds. Here we review structural and functional aspects emerging from the characterization of two main components (NS3 and NS5 proteins) of the flavivirus replication complex. Most of the reviewed results were achieved within the European Union VIZIER Project, and cover topics that span from viral genomics to structural biology and inhibition mechanisms. The ultimate aim of the reported approaches is to shed light on the design and development of antiviral drug leads.
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Affiliation(s)
- Michela Bollati
- Department of Biomolecular Sciences and Biotechnology, University of Milano, Via Celoria 26, 20133 Milano, Italy
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26
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Evolution of the sequence composition of Flaviviruses. INFECTION GENETICS AND EVOLUTION 2010; 10:129-36. [DOI: 10.1016/j.meegid.2009.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 10/26/2009] [Accepted: 11/03/2009] [Indexed: 11/20/2022]
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Grard G, Moureau G, Charrel RN, Holmes EC, Gould EA, de Lamballerie X. Genomics and evolution of Aedes-borne flaviviruses. J Gen Virol 2009; 91:87-94. [PMID: 19741066 DOI: 10.1099/vir.0.014506-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We analysed the complete coding sequences of all recognized species of Aedes-borne flavivirus, including previously uncharacterized viruses within the yellow fever virus (YFV), Spondweni virus (SPOV) and dengue virus (DENV) groups. Two major phylogenetic lineages were revealed: one included the YFV and Entebbe bat virus groups, and the other included the DENV, SPOV and Culex-borne flavivirus groups. This analysis supported previous evidence that Culex-borne flaviviruses have evolved from ancestral Aedes-borne viruses. However, the topology at the junction between these lineages remains complex and may be refined by the discovery of viruses related to the Kedougou virus. Additionally, viral evolution was found to be associated with the appearance of new biological characteristics; mutations that may modify the envelope protein structure were identified for seven viruses within the YFV group, and an expansion of host-vector range was identified in the two major evolutionary lineages, which in turn may facilitate the emergence of mosquito-borne flaviviruses.
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Affiliation(s)
- Gilda Grard
- Unité des Virus Emergents, UMR 190 Pathologies Virales Emergentes, Institut de Recherche pour le Développement-Université de la Méditerranée, Faculté de Médecine de Marseille, 27 boulevard Jean Moulin, 13005 Marseille, France.
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Mackenzie JS, Williams DT. The Zoonotic Flaviviruses of Southern, South-Eastern and Eastern Asia, and Australasia: The Potential for Emergent Viruses. Zoonoses Public Health 2009; 56:338-56. [DOI: 10.1111/j.1863-2378.2008.01208.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Hoshino K, Isawa H, Tsuda Y, Sawabe K, Kobayashi M. Isolation and characterization of a new insect flavivirus from Aedes albopictus and Aedes flavopictus mosquitoes in Japan. Virology 2009; 391:119-29. [PMID: 19580982 DOI: 10.1016/j.virol.2009.06.025] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 05/04/2009] [Accepted: 06/13/2009] [Indexed: 11/17/2022]
Abstract
We isolated a new flavivirus from Aedes albopictus mosquito and a related species in Japan. The virus, designated Aedes flavivirus (AEFV), only replicated in a mosquito cell line and produced a mild cytopathic effect. The AEFV genome was positive-sense, single-stranded RNA, 11,064 nucleotides in length and contained a single open reading frame encoding a polyprotein of 3341 amino acids with 5' and 3' untranslated regions (UTRs) of 96 and 945 nucleotides, respectively. Genetic and phylogenetic analyses classified AEFV with the insect flavivirus, but distinct from Cell fusing agent (CFA), Kamiti river virus and Culex flavivirus. Interestingly, a partial sequence of AEFV showed significant similarity to that of Cell silent agent (CSA), the insect flavivirus-related nucleotide sequence integrated in the genome of A. albopictus. These results suggest that AEFV is a new member of the insect flaviviruses, which are intimately associated with Aedes mosquitoes and may share a common origin with CSA.
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Affiliation(s)
- Keita Hoshino
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
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Crystal structure of a methyltransferase from a no-known-vector Flavivirus. Biochem Biophys Res Commun 2009; 382:200-4. [PMID: 19275894 DOI: 10.1016/j.bbrc.2009.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 03/04/2009] [Indexed: 12/30/2022]
Abstract
Presently known flaviviruses belong to three major evolutionary branches: tick-borne viruses, mosquito-borne viruses and viruses with no known vector. Here we present the crystal structure of the Yokose virus methyltransferase at 1.7A resolution, the first structure of a methyltransferase of a Flavivirus with no known vector. Structural comparison of three methyltransferases representative of each of the Flavivirus branches shows that fold and structures are closely conserved, most differences being related to surface loops flexibility. Analysis of the conserved residues throughout all the sequenced flaviviral methyltransferases reveals that, besides the central cleft hosting the substrate and cofactor binding sites, a second, almost continuous, patch is conserved and points away from active site towards the back of the protein. The high level of structural conservation in this region could be functional for the methyltransferase/RNA interaction and stabilization of the ensuing complex.
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Watanabe S, Omatsu T, Miranda MEG, Masangkay JS, Ueda N, Endo M, Kato K, Tohya Y, Yoshikawa Y, Akashi H. Epizootology and experimental infection of Yokose virus in bats. Comp Immunol Microbiol Infect Dis 2008; 33:25-36. [PMID: 18789527 PMCID: PMC7112705 DOI: 10.1016/j.cimid.2008.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2008] [Indexed: 11/01/2022]
Abstract
To reveal whether bats serve as an amplifying host for Yokose virus (YOKV), we conducted a serological survey and experimentally infected fruit bats with YOKV isolated from microbats in Japan. YOKV belongs to the Entebbe bat virus group of vector unknown group within the genus Flavivirus and family Flaviviridae. To detect antibodies against YOKV, we developed an enzyme-linked immunosorbent assay (ELISA) using biotinylated anti-bat IgG rabbit sera. Serological surveillance was conducted with samples collected in the Philippines and the sera supplied from Malaysia. One of the 36 samples from the Philippines (2.7%) and 5 of the 26 samples from Malaysia (19%) had detectable ELISA antibodies. In the experimental infections, no clinical signs of disease were observed. Moreover, no significant viral genome amplification was detected. These findings revealed that YOKV replicates poorly in the fruit bat, suggesting that fruit bats do not seem to serve as an amplifying host for YOKV.
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Affiliation(s)
- Shumpei Watanabe
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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32
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Watanabe S, Mizutani T, Sakai K, Kato K, Tohya Y, Fukushi S, Saijo M, Yoshikawa Y, Kurane I, Morikawa S, Akashi H. Ligation-mediated amplification for effective rapid determination of viral RNA sequences (RDV). J Clin Virol 2008; 43:56-9. [PMID: 18595773 PMCID: PMC7108420 DOI: 10.1016/j.jcv.2008.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/23/2008] [Accepted: 05/08/2008] [Indexed: 11/25/2022]
Abstract
Background Emerging infectious diseases pose a significant risk to public health. Methods for rapid detection of pathogens are needed to effectively treat these diseases. Recently, we developed new methods for the rapid determination of viral RNA sequences, RDV ver1.0 and ver2.0. We demonstrated that these methods were able to simultaneously detect cDNA fragments of many different viruses without using sequence specific primers. However, some species of viruses, including the Yokose virus (YOKV), a flavivirus, could not be detected using the conventional procedures. Objective The RDV method was further modified to reduce the candidate PCR primer sets. Study design Primer sets were reduced to 256 sets in the improved RDV ver3.0, and theoretically, all viral cDNA fragments ligated by two kinds of adaptors after digestion by two restriction enzymes could be amplified in the PCR step for direct sequencing. Results We succeeded in obtaining 118 YOKV cDNA fragments of the 141 sequence fragments. The cDNA fragments covered diverse range of viral genome. Conclusion We were able to reduce the combinations of PCR primer sets used in the RDV method. This RDV method ver3.0 has a potential to detect viral cDNA fragments of both known and unknown RNA viruses rapidly and conveniently.
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Affiliation(s)
- Shumpei Watanabe
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Omatsu T, Watanabe S, Akashi H, Yoshikawa Y. Biological characters of bats in relation to natural reservoir of emerging viruses. Comp Immunol Microbiol Infect Dis 2007; 30:357-74. [PMID: 17706776 PMCID: PMC7112585 DOI: 10.1016/j.cimid.2007.05.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 05/30/2007] [Indexed: 12/19/2022]
Abstract
Many investigators focused on bats (Chiroptera) for their specific character, i.e. echolocation system, phylogenic tree, food practice and unique reproduction. However, most of basic information about the vital functions related to anti-viral activity has been unclear. For evaluating some animals as a natural reservoir or host of infectious pathogens, it is necessary that not only their immune system but also their biology, the environment of their living, food habits and physiological features should be clarified and they should be analyzed from these multi-view points. The majority of current studies on infectious diseases have been conducted for the elucidation of viral virulence using experimental animals or viral gene function in vitro, but in a few case, researchers focused on wild animal itself. In this paper, we described basic information about bats as follows; genetic background, character of the immunological factors, histological character of immune organs, the physiological function and sensitivity of bat cells to viral infection.
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Affiliation(s)
- Tsutomu Omatsu
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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Silva PAGC, Molenkamp R, Dalebout TJ, Charlier N, Neyts JH, Spaan WJM, Bredenbeek PJ. Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3' stem-loop structure is not required for replication. J Gen Virol 2007; 88:1738-1747. [PMID: 17485534 DOI: 10.1099/vir.0.82811-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pentanucleotide (PN) sequence 5'-CACAG-3' at the top of the 3' stem-loop structure of the flavivirus genome is well conserved in the arthropod-borne viruses but is more variable in flaviviruses with no known vector. In this study, the sequence requirements of the PN motif for yellow fever virus 17D (YFV) replication were determined. In general, individual mutations at either the second, third or fourth positions were tolerated and resulted in replication-competent virus. Mutations at the fifth position were lethal. Base pairing of the nucleotide at the first position of the PN motif and a nucleotide four positions downstream of the PN (ninth position) was a major determinant for replication. Despite the fact that the majority of the PN mutants were able to replicate efficiently, they were outcompeted by parental YFV-17D virus following repeated passages in double-infected cell cultures. Surprisingly, some of the virus mutants at the first and/or the ninth position that maintained the possibility of forming a base pair were found to have a similar fitness to YFV-17D under these conditions. Overall, these experiments suggest that YFV is less dependent on sequence conservation of the PN motif for replication in animal cells than West Nile virus. However, in animal cell culture, YFV has a preference for the wt CACAG PN sequence. The molecular mechanisms behind this preference remain to be elucidated.
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Affiliation(s)
- Patrícia A G C Silva
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Richard Molenkamp
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Tim J Dalebout
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Nathalie Charlier
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Johan H Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Willy J M Spaan
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Peter J Bredenbeek
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
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Wong S, Lau S, Woo P, Yuen K. Bats as a continuing source of emerging infections in humans. Rev Med Virol 2007; 17:67-91. [PMID: 17042030 PMCID: PMC7169091 DOI: 10.1002/rmv.520] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 08/08/2006] [Accepted: 08/29/2006] [Indexed: 12/25/2022]
Abstract
Amongst the 60 viral species reported to be associated with bats, 59 are RNA viruses, which are potentially important in the generation of emerging and re-emerging infections in humans. The prime examples of these are the lyssaviruses and Henipavirus. The transmission of Nipah, Hendra and perhaps SARS coronavirus and Ebola virus to humans may involve intermediate amplification hosts such as pigs, horses, civets and primates, respectively. Understanding of the natural reservoir or introductory host, the amplifying host, the epidemic centre and at-risk human populations are crucial in the control of emerging zoonosis. The association between the bat coronaviruses and certain lyssaviruses with particular bat species implies co-evolution between specific viruses and bat hosts. Cross-infection between the huge number of bat species may generate new viruses which are able to jump the trans-mammalian species barrier more efficiently. The currently known viruses that have been found in bats are reviewed and the risks of transmission to humans are highlighted. Certain families of bats including the Pteropodidae, Molossidae, Phyllostomidae, and Vespertilionidae are most frequently associated with known human pathogens. A systematic survey of bats is warranted to better understand the ecology of these viruses.
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Affiliation(s)
- Samson Wong
- Department of Microbiology, Research Centre of Infection and Immunology, The University of Hong Kong, 4/F University Pathology Building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
| | - Susanna Lau
- Department of Microbiology, Research Centre of Infection and Immunology, The University of Hong Kong, 4/F University Pathology Building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
| | - Patrick Woo
- Department of Microbiology, Research Centre of Infection and Immunology, The University of Hong Kong, 4/F University Pathology Building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
| | - Kwok‐Yung Yuen
- Department of Microbiology, Research Centre of Infection and Immunology, The University of Hong Kong, 4/F University Pathology Building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
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36
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Gritsun TS, Gould EA. Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission. Adv Virus Res 2007; 69:203-48. [PMID: 17222695 DOI: 10.1016/s0065-3527(06)69005-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.
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Affiliation(s)
- T S Gritsun
- Centre for Ecology and Hydrology, Oxford, 0X1 3SR, United Kingdom
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HAMANO M, LIM C, TAKAGI H, SAWABE K, KUWAYAMA M, KISHI N, KURANE I, TAKASAKI T. Detection of antibodies to Japanese encephalitis virus in the wild boars in Hiroshima prefecture, Japan. Epidemiol Infect 2007; 135:974-7. [PMID: 17217550 PMCID: PMC2870655 DOI: 10.1017/s0950268806007710] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Serum specimens were collected from 25 wild boars in Hiroshima prefecture located in the western region of Japan from November 2004 to February 2005. The sera were tested for antibodies to Japanese encephalitis virus (JEV) by IgM capture and IgG enzyme-linked immunosorbent assays (ELISA), and plaque reduction neutralization test. Seventeen samples (68%) were positive for neutralizing antibody to JEV. All the neutralizing antibody-positive samples were positive for IgG-ELISA. One was also positive for IgM. The results indicate that approximately 70% of the wild boars were positive for anti-JEV antibody, and raises the possibility that wild boars may play a role in the infectious cycle of JEV in this region.
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Affiliation(s)
- M. HAMANO
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - C. K. LIM
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - H. TAKAGI
- Division of Biosafety Control and Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - K. SAWABE
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
| | - M. KUWAYAMA
- Division of Microbiology II, Hiroshima Prefectural Institute of Health and Environment, Hiroshima, Japan
| | - N. KISHI
- Hiroshima Prefectural Livestock Technological Research Center, Hiroshima, Japan
| | - I. KURANE
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
- Author for correspondence: I. Kurane M.D., Department of Virology 1, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan. ()
| | - T. TAKASAKI
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan
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38
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Gritsun TS, Gould EA. Direct repeats in the 3' untranslated regions of mosquito-borne flaviviruses: possible implications for virus transmission. J Gen Virol 2006; 87:3297-3305. [PMID: 17030864 DOI: 10.1099/vir.0.82235-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Direct repeats (DRs) of 20-45 nucleotide conserved sequences (CS) and repeated CS (RCS), separated by non-conserved sequences up to 100 nucleotides long, were previously described in the 3' untranslated region (3'UTR) of the three major mosquito-borne flavivirus (MBFV) subgroups, represented by Japanese encephalitis virus, Yellow fever virus and Dengue virus. Each subgroup exhibits a specific pattern of DRs, the biological significance of which has not yet been adequately addressed. The DRs were originally identified using conventional alignment programs based on the assumption that genetic variation is driven primarily by nucleotide substitutions. Since there are no recognized alignment programs that can adequately accommodate very divergent sequences, a method has been devised to construct and analyse a substantially improved 3'UTR alignment between these highly divergent viruses, based on the concept that deletions and/or insertions, in addition to substitutions, are important drivers of 3'UTR evolution. This 'robust alignment' approach demonstrated more extensive homologies in the 3'UTR than had been recognized previously and revealed the presence of similar DRs, either intact or as sequence 'remnants', in all the MBFV subgroups. The relevance of these observations is discussed in relation to (i) the function of DRs as elements of replication enhancement, (ii) the evolution of RNA secondary structures and (iii) the significance of DRs and secondary structures in MBFV transmissibility between vertebrate and invertebrate hosts.
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Affiliation(s)
- T S Gritsun
- Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, UK
| | - E A Gould
- Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, UK
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39
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Hoshino K, Isawa H, Tsuda Y, Yano K, Sasaki T, Yuda M, Takasaki T, Kobayashi M, Sawabe K. Genetic characterization of a new insect flavivirus isolated from Culex pipiens mosquito in Japan. Virology 2006; 359:405-14. [PMID: 17070886 DOI: 10.1016/j.virol.2006.09.039] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 07/26/2006] [Accepted: 09/22/2006] [Indexed: 11/19/2022]
Abstract
We found a new flavivirus that is widespread in Culex pipiens and other Culex mosquitoes in Japan. The virus isolate, named Culex flavivirus (CxFV), multiplied only in mosquito cell lines producing a moderate cytopathic effect, but did not grow in mammalian cells. The CxFV genome is single-stranded RNA, 10,834 nt in length and containing a single open reading frame encoding a polyprotein of 3362 aa with 5' and 3' untranslated regions (UTRs) of 91 and 657 nt, respectively. Phylogenetic analyses revealed that CxFV is closely related to the insect flaviviruses associated with Aedes mosquitoes, Cell fusing agent (CFA) and Kamiti River virus (KRV). The 3' UTR of CxFV contains four tandem repeats, which have sequence similarities to the two direct repeats in the CFA and KRV 3' UTRs. These results suggest that CxFV may be a new group of insect flaviviruses.
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Affiliation(s)
- Keita Hoshino
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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