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Hu G, Jiang F, Luo Q, Zong K, Dong L, Mei G, Du H, Dong H, Song Q, Song J, Xia Z, Gao C, Han J. Diversity Analysis of Tick-Borne Viruses from Hedgehogs and Hares in Qingdao, China. Microbiol Spectr 2023; 11:e0534022. [PMID: 37074196 PMCID: PMC10269667 DOI: 10.1128/spectrum.05340-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/12/2023] [Indexed: 04/20/2023] Open
Abstract
Tick-borne viruses (TBVs) have attracted increasingly global public health attention. In this study, the viral compositions of five tick species, Haemaphysalis flava, Rhipicephalus sanguineus, Dermacentor sinicus, Haemaphysalis longicornis, and Haemaphysalis campanulata, from hedgehogs and hares in Qingdao, China, were profiled via metagenomic sequencing. Thirty-six strains of 10 RNA viruses belonging to 4 viral families, including 3 viruses of Iflaviridae, 4 viruses of Phenuiviridae, 2 viruses of Nairoviridae, and 1 virus of Chuviridae, were identified in five tick species. Three novel viruses of two families, namely, Qingdao tick iflavirus (QDTIFV) of the family of Iflaviridae and Qingdao tick phlebovirus (QDTPV) and Qingdao tick uukuvirus (QDTUV) of the family of Phenuiviridae, were found in this study. This study shows that ticks from hares and hedgehogs in Qingdao harbored diverse viruses, including some that can cause emerging infectious diseases, such as Dabie bandavirus. Phylogenetic analysis revealed that these tick-borne viruses were genetically related to viral strains isolated previously in Japan. These findings shed new light on the cross-sea transmission of tick-borne viruses between China and Japan. IMPORTANCE Thirty-six strains of 10 RNA viruses belonging to 4 viral families, including 3 viruses of Iflaviridae, 4 viruses of Phenuiviridae, 2 viruses of Nairoviridae, and 1 virus of Chuviridae, were identified from five tick species in Qingdao, China. A diversity of tick-borne viruses from hares and hedgehogs in Qingdao was found in this study. Phylogenetic analysis showed that most of these TBVs were genetically related to Japanese strains. These findings indicate the possibility of the cross-sea transmission of TBVs between China and Japan.
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Affiliation(s)
- Geng Hu
- 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
| | - Fachun Jiang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Qin Luo
- 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
| | - Kexin Zong
- 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
| | - Liyan Dong
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Guoyong Mei
- 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
| | - Haijun Du
- 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
| | - Hongming Dong
- 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
| | - Qinqin Song
- 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
| | - Juan Song
- 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
| | - Zhiqiang Xia
- 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
| | - Chen Gao
- 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
| | - Jun Han
- 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
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Guo Y, Ji N, Bai L, Ma J, Li Z. Aphid Viruses: A Brief View of a Long History. FRONTIERS IN INSECT SCIENCE 2022; 2:846716. [PMID: 38468755 PMCID: PMC10926426 DOI: 10.3389/finsc.2022.846716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/31/2022] [Indexed: 03/13/2024]
Abstract
Aphids are common agricultural pests with a wide range of hosts from agriculture to forestry plants. As known, aphids also serve as the major vectors to transmit plant viruses. Although numerous studies have focused on interactions between aphids and plant viruses, little is known about the aphid viruses, i.e., the insect viruses that are infectious to aphids. In the past four decades, several aphid viruses have been identified in diverse aphid species. In this review, we present a brief view of the aphid pathogenic viruses from several aspects, including classification of aphid viruses and characters of the viral genome, integration of viral sequences in host genomes, infection symptoms and influence on aphids, as well as host range and transmission modes. Taken together, these studies have increased our understanding of the rarely known aphid viruses, and will potentially contribute to the development of new strategies for controlling aphid populations.
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Affiliation(s)
| | | | | | | | - Zhaofei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
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Kobayashi D, Murota K, Itokawa K, Ejiri H, Amoa-Bosompem M, Faizah AN, Watanabe M, Maekawa Y, Hayashi T, Noda S, Yamauchi T, Komagata O, Sawabe K, Isawa H. RNA virome analysis of questing ticks from Hokuriku District, Japan, and the evolutionary dynamics of tick-borne phleboviruses. Ticks Tick Borne Dis 2019; 11:101364. [PMID: 31928929 DOI: 10.1016/j.ttbdis.2019.101364] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/13/2019] [Accepted: 12/21/2019] [Indexed: 01/23/2023]
Abstract
Tick-borne viruses have emerged recently in many parts of the world, and the discoveries of novel tick-borne viruses have been accelerated by the development of high-throughput sequencing technology. In this study, a cost-efficient small benchtop next-generation sequencer, the Illumina MiniSeq, was used for the RNA virome analysis of questing ticks collected from Hokuriku District, Japan, and assessed for their potential utility in a tick-borne virus surveillance system. We detected two phleboviruses [Kabuto Mountain virus (KAMV) and Okutama tick virus (OKTV)], a coltivirus [Tarumizu tick virus (TarTV)], and a novel iflavirus [Hamaphysalis flava iflavirus (HfIFV)] from tick homogenates and/or cell culture supernatants after virus isolation processes. The number of sequence reads from KAMV and TarTV markedly increased when cell culture supernatants were used, indicating a successful isolation of these viruses. In contrast, OKTV and HfIFV were detected only in tick homogenates but not from cell culture supernatants, suggesting a failure to isolate these viruses. Furthermore, we performed genomic and phylogenetic analyzes of these detected viruses. OKTV and some phleboviruses discovered recently by NGS-based methods were probably deficient in the M genome segment, which are herein proposed as M segment-deficient phlebovirus (MdPV). A phylogenetic analysis of phleboviruses, including MdPV, suggested that Uukuniemi and Kaisodi group viruses and kabutoviruses evolved from an ancestral MdPV, which provides insights into the evolutionary dynamics of phleboviruses as emerging pathogens.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Research Promotion, Japan Agency for Medical Research and Development, 20F Yomiuri Shimbun Bldg. 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Katsunori Murota
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Kyushu Research Station, National Institute of Animal Health, NARO, 2702 Chuzan, Kagoshima 891-0105, Japan
| | - Kentaro Itokawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Pathogen genomics center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hiroko Ejiri
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Division of infectious Diseases Epidemiology and Control, National Defense Medical Research Institute, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Michael Amoa-Bosompem
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Astri Nur Faizah
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Mamoru Watanabe
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshihide Maekawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Toshihiko Hayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shinichi Noda
- Research Center for the Pacific Islands, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan
| | - Takeo Yamauchi
- Laboratory of Entomology, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan
| | - Osamu Komagata
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Discovery of a novel iflavirus sequence in the eastern paralysis tick Ixodes holocyclus. Arch Virol 2018; 163:2451-2457. [PMID: 29752559 DOI: 10.1007/s00705-018-3868-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/14/2018] [Indexed: 01/02/2023]
Abstract
Ixodes holocyclus, the eastern paralysis tick, is a significant parasite in Australia in terms of animal and human health. However, very little is known about its virome. In this study, next-generation sequencing of I. holocyclus salivary glands yielded a full-length genome sequence which phylogenetically groups with viruses classified in the Iflaviridae family and shares 45% amino acid similarity with its closest relative Bole hyalomma asiaticum virus 1. The sequence of this virus, provisionally named Ixodes holocyclus iflavirus (IhIV) has been identified in tick populations from northern New South Wales and Queensland, Australia and represents the first virus sequence reported from I. holocyclus.
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Dong Y, Chao J, Liu J, Rice A, Holdbrook R, Liu Y, Xu P. Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus. Arch Virol 2017; 163:571-574. [PMID: 29101538 DOI: 10.1007/s00705-017-3622-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/26/2017] [Indexed: 01/10/2023]
Abstract
The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.
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Affiliation(s)
- Yonghao Dong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China.,College of Plant Protection, Shandong Agricultural University, Taian, P.R. China
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China
| | - Jinyan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China
| | - Annabel Rice
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Robert Holdbrook
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yongjie Liu
- College of Plant Protection, Shandong Agricultural University, Taian, P.R. China
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China. .,Lancaster Environment Centre, Lancaster University, Lancaster, UK.
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Abbà S, Galetto L, Vallino M, Rossi M, Turina M, Sicard A, Marzachì C. Genome sequence, prevalence and quantification of the first iflavirus identified in a phytoplasma insect vector. Arch Virol 2016; 162:799-809. [PMID: 27888410 DOI: 10.1007/s00705-016-3158-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 01/29/2023]
Abstract
The leafhopper Euscelidius variegatus is a natural vector of chrysanthemum yellows phytoplasma (CY) and an efficient vector of flavescence dorée phytoplasma (FD) under laboratory conditions. During a transcriptome sequencing (RNA-seq) project aimed at investigating the interactions between the insect and the two phytoplasmas, a 10,616-nucleotide-long contig with high sequence similarity to known picorna-like viruses was identified among the assembled insect transcripts. The discovery came totally unexpected, because insects from the laboratory colony did not show any evident symptom that could be related to the presence of a virus. The amino acid sequence, the shape and size of viral particles, and the results of phylogenetic analysis suggest that this virus, named Euscelidius variegatus virus 1 (EVV-1), can be considered a new member of a new species in the genus Iflavirus. EVV-1 was detected in all of the tested insects from the laboratory colony used for RNA-seq, both in phytoplasma-exposed and in non-exposed insects, but the viral load measured in FD-exposed samples was significantly lower than that in non-exposed insects. This result suggests the possible existence of an intriguing cross-talk among insects, endogenous bacteria, and viruses. The identification of two other E. variegatus laboratory colonies that were free of EVV-1 could represent the key to addressing some basic virological issues, e.g., viral replication and transmission mechanisms, and offer the opportunity to use infectious clones to express heterologous genes in the leafhopper and manipulate the expression of endogenous genes by promoting virus-induced gene silencing.
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Affiliation(s)
- Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy.
| | - Luciana Galetto
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Anne Sicard
- Department of Environmental Science, Policy and Management, University of California, 130 Mulford Hall, Berkeley, CA, 94720, USA
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
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Two novel viruses associated with the Apis mellifera pathogenic mite Varroa destructor. Sci Rep 2016; 6:37710. [PMID: 27883042 PMCID: PMC5121581 DOI: 10.1038/srep37710] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/03/2016] [Indexed: 12/21/2022] Open
Abstract
Varroa destructor infestation of Apis mellifera colonies carries and/or promotes replication of honey bee viruses like the Deformed wing virus, the Varroa destructor virus-1, the Acute bee paralysis virus, the Israeli acute bee paralysis virus and the Kashmir bee virus that have been well described and characterized; but viruses exclusively associated with Varroa were not found. To look for viruses that may associate with- or infect V. destructor we performed deep sequencing (RNA-seq) of RNA extracted from honey bees and mites in Varroa-infested untreated colonies. Comparative bioinformatic analysis of the two separate contig-assemblies generated from the sequences' reads annotated using Blastx enabled identification of new viruses unique to Varroa and absent in A. mellifera: an Iflavirus and a virus with homology to Ixodes scapularis associated virus 2, that we named Varroa destructor virus 2 (VDV-2) and 3(VDV-3), respectively. We validated these findings sequencing the mite- and honey bee-viromes and in separate mites and honey bees randomly sampled. The complete genomes of VDV-2 and VDV-3 bear 9576 nucleotides and 4202 nucleotides, respectively. Phylogenetic analysis of VDV-3 suggests that it belongs to a new group of viruses. Our results open venues for investigating the pathogenicity of these V. destructor viruses.
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