1
|
López Y, Thomas R, Muñoz-Leal S, López-Mejia Y, Galeano K, Garcia A, Romero L, la Hoz DED, Martinez C, Calderón A, Gastelbondo B, Contreras H, Olivieri G, Rubiano L, Paternina L, Hoyos-López R, Ortiz A, Garay E, Alemán-Santos M, Rivero R, Miranda J, Florez L, Ballesteros J, Contreras V, Tique V, Fragoso P, Guzman C, Arrieta G, Mattar S. Hard ticks (Ixodida: Ixodidae) in the Colombian Caribbean harbor the Jingmen tick virus: an emerging arbovirus of public health concern. Parasit Vectors 2024; 17:268. [PMID: 38918818 PMCID: PMC11202343 DOI: 10.1186/s13071-024-06362-x] [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: 02/22/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Ticks are obligate hematophagous ectoparasites involved in transmitting viruses of public health importance. The objective of this work was to identify the Jingmen tick virus in hard ticks from the Colombian Caribbean, an arbovirus of importance for public health. METHODS Ticks were collected in rural areas of Córdoba and Cesar, Colombia. Taxonomic identification of ticks was carried out, and pools of 13 individuals were formed. RNA extraction was performed. Library preparation was performed with the MGIEasy kit, and next-generation sequencing (NGS) with MGI equipment. Bioinformatic analyses and taxonomic assignments were performed using the Galaxy platform, and phylogenetic analyses were done using IQ-TREE2. RESULTS A total of 766 ticks were collected, of which 87.33% (669/766) were Rhipicephalus microplus, 5.4% (42/766) Dermacentor nitens, 4.2% (32/766) Rhipicephalus linnaei, and 3.0% (23/766) Amblyomma dissimile. Complete and partial segments 1, 2, 3, and 4 of Jingmen tick virus (JMTV) were detected in the metatranscriptome of the species R. microplus, D. nitens, and A. dissimile. The JMTVs detected are phylogenetically related to JMTVs detected in Aedes albopictus in France, JMTVs detected in R. microplus in Trinidad and Tobago, JMTVs in R. microplus and A. variegatum in the French Antilles, and JMTVs detected in R. microplus in Colombia. Interestingly, our sequences clustered closely with JMTV detected in humans from Kosovo. CONCLUSIONS JMTV was detected in R. microplus, D. nitens, and A. dissimile. JMTV could pose a risk to humans. Therefore, it is vital to establish epidemiological surveillance measures to better understand the possible role of JMTV in tropical diseases.
Collapse
Affiliation(s)
- Yesica López
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Richard Thomas
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Sebastián Muñoz-Leal
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Yeimi López-Mejia
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Ketty Galeano
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Alejandra Garcia
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Luis Romero
- Universidad de Sucre, Investigaciones Biomédicas, Sucre, Colombia
| | | | - Caty Martinez
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Alfonso Calderón
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Bertha Gastelbondo
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Montería, Colombia
- Grupo de Salud Pública y Auditoría en Salud, Corporación Universitaria del Caribe- CECAR, Sincelejo, Colombia
| | - Héctor Contreras
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Gino Olivieri
- Grupo de Investigación Parasitología y Agroecología Milenio, Universidad Popular del Cesar, Valledupar Cesar, Colombia
| | - Luis Rubiano
- Grupo de Investigación Parasitología y Agroecología Milenio, Universidad Popular del Cesar, Valledupar Cesar, Colombia
| | - Luis Paternina
- Universidad de Sucre, Investigaciones Biomédicas, Sucre, Colombia
| | - Richard Hoyos-López
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Anggie Ortiz
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Evelyn Garay
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Maira Alemán-Santos
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Ricardo Rivero
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Jorge Miranda
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Luis Florez
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Jolaime Ballesteros
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Verónica Contreras
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Vaneza Tique
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Pedro Fragoso
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - Camilo Guzman
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
| | - German Arrieta
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia
- Grupo de Salud Pública y Auditoría en Salud, Corporación Universitaria del Caribe- CECAR, Sincelejo, Colombia
| | - Salim Mattar
- Instituto de Investigaciones Biológicas del Trópico, Universidad de Córdoba, Córdoba, Colombia.
| |
Collapse
|
2
|
Wang X, Jing X, Shi J, Liu Q, Shen S, Cheung PPH, Wu J, Deng F, Gong P. A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase. Nucleic Acids Res 2024; 52:3278-3290. [PMID: 38296832 PMCID: PMC11014250 DOI: 10.1093/nar/gkae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous to flavivirus NS5. NSP1 comprises both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) modules playing essential roles in viral genome replication and capping. Here we solved a 1.8-Å resolution crystal structure of the NSP1 RdRP module from Jingmen tick virus (JMTV), the type species of jingmenviruses. The structure highly resembles flavivirus NS5 RdRP despite a sequence identity less than 30%. NSP1 RdRP enzymatic properties were dissected in a comparative setting with several representative Flaviviridae RdRPs included. Our data indicate that JMTV NSP1 produces characteristic 3-mer abortive products similar to the hepatitis C virus RdRP, and exhibits the highest preference of terminal initiation and shorter-primer usage. Unlike flavivirus NS5, JMTV RdRP may require the MTase for optimal transition from initiation to elongation, as an MTase-less NSP1 construct produced more 4-5-mer intermediate products than the full-length protein. Taken together, this work consolidates the evolutionary relationship between the jingmenvirus group and the Flaviviridae family, providing a basis to the further understanding of their viral replication/transcription process.
Collapse
Affiliation(s)
- Xinyu Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuping Jing
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Junming Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Qiaojie Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
| | - Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin 300350, China
| |
Collapse
|
3
|
Xiao J, Yao X, Guan X, Xiong J, Fang Y, Zhang J, Zhang Y, Moming A, Su Z, Jin J, Ge Y, Wang J, Fan Z, Tang S, Shen S, Deng F. Viromes of Haemaphysalis longicornis reveal different viral abundance and diversity in free and engorged ticks. Virol Sin 2024; 39:194-204. [PMID: 38360150 PMCID: PMC11074643 DOI: 10.1016/j.virs.2024.02.003] [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: 10/09/2023] [Accepted: 02/08/2024] [Indexed: 02/17/2024] Open
Abstract
Haemaphysalis longicornis ticks, commonly found in East Asia, can transmit various pathogenic viruses, including the severe fever with thrombocytopenia syndrome virus (SFTSV) that has caused febrile diseases among humans in Hubei Province. However, understanding of the viromes of H. longicornis was limited, and the prevalence of viruses among H. longicornis ticks in Hubei was not well clarified. This study investigates the viromes of both engorged (fed) and free (unfed) H. longicornis ticks across three mountainous regions in Hubei Province from 2019 to 2020. RNA-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging to unclassified viruses and seven RNA viral families, namely Chuviridae, Nairoviridae, Orthomyxoviridae, Parvoviridae, Phenuiviridae, Rhabdoviridae, and Totiviridae. Viral abundance and diversity in these ticks were analysed, and phylogenetic characteristics of the Henan tick virus (HNTV), Dabieshan tick virus (DBSTV), Okutama tick virus (OKTV), and Jingmen tick virus (JMTV) were elucidated based on their full genomic sequences. Prevalence analysis demonstrated that DBSTV was the most common virus found in individual H. longicornis ticks (12.59%), followed by HNTV (0.35%), whereas JMTV and OKTV were not detected. These results improve our understanding of H. longicornis tick viromes in central China and highlight the role of tick feeding status and geography in shaping the viral community. The findings of new viral strains and their potential impact on public health raise the need to strengthen surveillance efforts for comprehensively assessing their spillover potentials.
Collapse
Affiliation(s)
- Jian Xiao
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xuan Yao
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430070, China
| | - Xuhua Guan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430070, China
| | - Jinfeng Xiong
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430070, China
| | - Yaohui Fang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jingyuan Zhang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - You Zhang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Current address: Department of Medical Laboratory, The Second Affiliated Hospital, Hainan Medical University, Haikou, 57000, China
| | - Abulimiti Moming
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Xinjiang Key Laboratory of Vector-borne Infectious Diseases, Urumqi, 830002, China
| | - Zhengyuan Su
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiayin Jin
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yingying Ge
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jun Wang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhaojun Fan
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shuang Tang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shu Shen
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China; Xinjiang Key Laboratory of Vector-borne Infectious Diseases, Urumqi, 830002, China.
| | - Fei Deng
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
4
|
Li Y, Bai Y, Liu W, Li J, Tian F, Han X, Liu L, Tong Y. Diversity analysis of tick-associated viruses in northeast China. Virol Sin 2023; 38:961-965. [PMID: 37832718 PMCID: PMC10786652 DOI: 10.1016/j.virs.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023] Open
Abstract
•This study identified eleven tick-borne viruses in Liaoning Province and Inner Mongolia. •Tacheng tick virus 2 is for the first time detected outside Xinjiang and in a novel tick species D. niveus. •The Alongshan virus and Tacheng tick virus 2 identified in this study can be considered as novel species.
Collapse
Affiliation(s)
- Yang Li
- Jiamusi University School of Basic Medicine, Jiamusi, 154007, China; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yu Bai
- Jiamusi University School of Basic Medicine, Jiamusi, 154007, China; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wenli Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Institute of Analysis and Testing, Beijing Academy of Science and Technology (Beijing Center for Physical & Chemical Analysis), Beijing, 100094, China
| | - Jing Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fengjuan Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaohu Han
- Shenyang Agricultural University, Shenyang, 110866, China.
| | - Lei Liu
- Jiamusi University School of Basic Medicine, Jiamusi, 154007, China.
| | - Yigang Tong
- Jiamusi University School of Basic Medicine, Jiamusi, 154007, China; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
5
|
Stegmüller S, Qi W, Torgerson PR, Fraefel C, Kubacki J. Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens. PLoS One 2023; 18:e0290942. [PMID: 37956168 PMCID: PMC10642849 DOI: 10.1371/journal.pone.0290942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Ticks play an important role in transmitting many different emerging zoonotic pathogens that pose a significant threat to human and animal health. In Switzerland and abroad, the number of tick-borne diseases, in particular tick-borne encephalitis (TBE), has been increasing over the last few years. Thus, it remains essential to investigate the pathogen spectrum of ticks to rapidly detect emerging pathogens and initiate the necessary measures. To assess the risk of tick-borne diseases in different regions of Switzerland, we collected a total of 10'286 ticks from rural and urban areas in ten cantons in 2021 and 2022. Ticks were pooled according to species, developmental stage, gender, and collection site, and analyzed using next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). The metagenomic analysis revealed for the first time the presence of Alongshan virus (ALSV) in Swiss ticks. Interestingly, the pool-prevalence of ALSV was higher than that of tick-borne encephalitis virus (TBEV). Furthermore, several TBEV foci have been identified and pool prevalence of selected non-viral pathogens determined.
Collapse
Affiliation(s)
- Stefanie Stegmüller
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Paul R. Torgerson
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, Bern, Switzerland
| |
Collapse
|
6
|
Li W, Li R, Tang X, Cheng J, Zhan L, Shang Z, Wu J. Genomics evolution of Jingmen viruses associated with ticks and vertebrates. Genomics 2023; 115:110734. [PMID: 37890641 DOI: 10.1016/j.ygeno.2023.110734] [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: 08/30/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Jingmen virus (JMV) associated with ticks and vertebrates have been found to be related to human disease. We obtained the genome of a Jingmen tick virus (JMTV) strain from Rhipicephalus microplus in Guizhou province and compared the genomes of seven JMV species associated with ticks and vertebrates to understand the evolutionary relationships. The topology of the phylogenetic tree of segment 1 and segment 3 is similar, and segment 2 and segment 4 formed two different topologies, with the main differences being between Alongshan virus (ALSV), Takachi virus, Yanggou tick virus and Pteropus lylei jingmen virus (PLJV), and the possibility of genetic reassortment among these viruses. Moreover, we detected recombination within JMTV and between PLJV and ALSV. The genetic reassortment and recombination that occurs during cross-species transmission of these JMV associated with ticks and vertebrates not only complicates their evolutionary relationships, but also raises the risk of these viruses to humans.
Collapse
Affiliation(s)
- Weiyi Li
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Rongting Li
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Xiaomin Tang
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Jinzhi Cheng
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Lin Zhan
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, China
| | - Zhengling Shang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Jiahong Wu
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China.
| |
Collapse
|
7
|
Barnes M, Price DC. Endogenous Viral Elements in Ixodid Tick Genomes. Viruses 2023; 15:2201. [PMID: 38005880 PMCID: PMC10675110 DOI: 10.3390/v15112201] [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: 08/10/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
The documentation of endogenous viral elements (EVEs; virus-derived genetic material integrated into the genome of a nonviral host) has offered insights into how arthropods respond to viral infection via RNA interference pathways. Small non-coding RNAs derived from EVE loci serve to direct RNAi pathways in limiting replication and infection from cognate viruses, thus benefiting the host's fitness and, potentially, vectorial capacity. Here we use informatic approaches to analyze nine available genome sequences of hard ticks (Acari: Ixodidae; Rhipicephalus sanguineus, R. microplus, R. annulatus, Ixodes ricinus, I. persulcatus, I. scapularis, Hyalomma asiaticum, Haemaphysalis longicornis, and Dermacentor silvarum) to identify endogenous viral elements and to illustrate the shared ancestry of all elements identified. Our results highlight a broad diversity of viral taxa as having given rise to 1234 identified EVEs in ticks, with Mononegavirales (specifically Rhabdoviridae) well-represented in this subset of hard ticks. Further investigation revealed extensive adintovirus integrations in several Ixodes species, the prevalence of Bunyavirales EVEs (notably not observed in mosquitoes), and the presence of several elements similar to known emerging human and veterinary pathogens. These results will inform subsequent work on current and past associations with tick species with regard to the viruses from which their "viral fossils" are derived and may serve as a reference for quality control of various tick-omics data that may suffer from misidentification of EVEs as viral genetic material.
Collapse
Affiliation(s)
| | - Dana C. Price
- Center for Vector Biology, Department of Entomology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA;
| |
Collapse
|
8
|
Wu Z, Zhang M, Zhang Y, Lu K, Zhu W, Feng S, Qi J, Niu G. Jingmen tick virus: an emerging arbovirus with a global threat. mSphere 2023; 8:e0028123. [PMID: 37702505 PMCID: PMC10597410 DOI: 10.1128/msphere.00281-23] [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] [Indexed: 09/14/2023] Open
Abstract
Jingmen tick virus (JMTV), belonging to the Flaviviridae family, is a novel segmented RNA virus identified in 2014 in the Jingmen region of Hubei Province, China. Up to now, JMTV has been detected in a variety of countries or regions in Asia, Europe, Africa, and the Americas, involving a wide range of arthropods and mammals, and even humans. The JMTV genome is composed of four linear RNA segments, two of which are derived from flaviviruses, while the other two segments are unique to JMTV and has no matching virus. Currently, JMTV has been shown to have a pathogenic effect on humans. Humans who had been infected would develop viremia and variable degrees of clinical symptoms. However, the pathogenic mechanism of JMTV has not been elucidated yet. Therefore, it is crucial to strengthen the epidemiological surveillance and laboratory studies of JMTV.
Collapse
Affiliation(s)
- Zhen Wu
- WeiFang Medical University, Weifang, Shandong, China
| | - Ming Zhang
- WeiFang Medical University, Weifang, Shandong, China
| | - Yuli Zhang
- WeiFang Medical University, Weifang, Shandong, China
| | - Ke Lu
- WeiFang Medical University, Weifang, Shandong, China
| | - Wenbing Zhu
- WeiFang Medical University, Weifang, Shandong, China
| | - Shuo Feng
- WeiFang Medical University, Weifang, Shandong, China
| | - Jun Qi
- Tianjin Customs Port Out-Patient Department, Tianjin International Travel Healthcare Center, Tianjin, Hebei, China
| | - Guoyu Niu
- WeiFang Medical University, Weifang, Shandong, China
| |
Collapse
|
9
|
Litov AG, Okhezin EV, Kholodilov IS, Polienko AE, Karganova GG. Quantitative Polymerase Chain Reaction System for Alongshan Virus Detection. Methods Protoc 2023; 6:79. [PMID: 37736962 PMCID: PMC10514782 DOI: 10.3390/mps6050079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The recently discovered Jingmenvirus group includes viruses with a segmented genome, RNA of a positive polarity, and several proteins with distant homology to the proteins of the members of the genus Orthoflavivirus. Some Jingmenvirus group members, namely the Alongshan virus (ALSV) and Jingmen tick virus, are reported to be tick-borne human pathogens that can cause a wide variety of symptoms. The ALSV is widely distributed in Eurasia, yet no reliable assay that can detect it exists. We describe a qPCR system for ALSV detection. Our data showed that this system can detect as little as 104 copies of the ALSV in a sample. The system showed no amplification of the common tick-borne viruses circulating in Eurasia, i.e., the Yanggou tick virus-which is another Jingmenvirus group member-or some known members of the genus Orthoflavivirus. The qPCR system was tested and had no nonspecific signal for the Ixodes ricinus, I. persulcatus, Dermacentor reticulatus, D. marginatus, Haemaphysalis concinna, and H. japonica ticks. The qPCR system had no nonspecific signal for human and sheep serum as well. Overall, the qPCR system described here can be used for reliable and quantitative ALSV detection.
Collapse
Affiliation(s)
- Alexander G. Litov
- Laboratory of Biology of Arboviruses, FSASI “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS” (Institute of Poliomyelitis), 108819 Moscow, Russia; (E.V.O.); (I.S.K.); (A.E.P.); (G.G.K.)
| | - Egor V. Okhezin
- Laboratory of Biology of Arboviruses, FSASI “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS” (Institute of Poliomyelitis), 108819 Moscow, Russia; (E.V.O.); (I.S.K.); (A.E.P.); (G.G.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, FSASI “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS” (Institute of Poliomyelitis), 108819 Moscow, Russia; (E.V.O.); (I.S.K.); (A.E.P.); (G.G.K.)
| | - Alexandra E. Polienko
- Laboratory of Biology of Arboviruses, FSASI “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS” (Institute of Poliomyelitis), 108819 Moscow, Russia; (E.V.O.); (I.S.K.); (A.E.P.); (G.G.K.)
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, FSASI “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS” (Institute of Poliomyelitis), 108819 Moscow, Russia; (E.V.O.); (I.S.K.); (A.E.P.); (G.G.K.)
| |
Collapse
|
10
|
Mohamed Ali S, Rakotonirina A, Heng K, Jacquemet E, Volant S, Temmam S, Boyer S, Eloit M. Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia. Viruses 2023; 15:1831. [PMID: 37766237 PMCID: PMC10535147 DOI: 10.3390/v15091831] [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: 08/03/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae, along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown.
Collapse
Affiliation(s)
- Souand Mohamed Ali
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Antsa Rakotonirina
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Kimly Heng
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Elise Jacquemet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Sebastien Boyer
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
- Ecology and Emergence of Arthropod-Borne Diseases, Institut Pasteur, 75015 Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 94704 Maisons-Alfort, France
| |
Collapse
|
11
|
Huang L, Liu S, Chen L, Wang F, Ye P, Xia L, Jiang B, Tang H, Zhang Q, Ruan X, Chen W, Jiang J. Identification of novel Jingmen tick virus from parasitic ticks fed on a giant panda and goats in Sichuan Province, southwestern China. Front Microbiol 2023; 14:1179173. [PMID: 37389347 PMCID: PMC10305807 DOI: 10.3389/fmicb.2023.1179173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/12/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction Tick-borne viruses (TBVs) pose a significant risk to the health of humans and other vertebrates. A class of multisegmented flavi-like viruses, Jingmen tick virus (JMTV) was first discovered in Rhipicephalus microplus ticks collected from Jingmen of Hubei Province, China in 2010. JMTV has been confirmed to have a relatively wide distribution in vectors and hosts and is associated with human diseases. Methods Parasitic and host-seeking ticks were collected in Wolong Nature Reserve, Sichuan Province. Total RNA was extracted and then enriched the viral RNA. The DNA library was constructed and then were sequenced with MGI High-throughput Sequencing Set (PE150). After the adaptor sequences,low-quality bases and host genome were removed, resulting reads classified as a virus were subsequently de novo assembled into contigs, which were then compared to the NT database. Those annotated under the kingdom virus were initially identified as potential virus-associated sequences. Phylogenetic and Reassortment analysis of sequences were performed using MEGA and SimPlot software, respectively. Results and discussion Two host-seeking ticks and 17 ticks that fed on giant pandas and goats were collected. Through high-throughput sequencing, whole virus genomes were attained from four tick samples (PC-13, PC-16, PC-18, and PC-19) that shared 88.7-96.3% similarity with known JMTV. Phylogenetic tree showed that it was a novel JMTV-like virus, referred to as Sichuan tick virus, which also had the signals of reassortment with other JMTV strains, suggesting a cross-species transmission and co-infection of segmented flavi-like viruses among multiple tick hosts. Conclusion We discovered and confirmed one new Jingmen tick virus, Sichuan tick virus. Further investigation is required to determine the pathogenicity of Sichuan tick virus to humans and animals, as well as its epidemiological characteristics in nature.
Collapse
Affiliation(s)
- Lin Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shunshuai Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lu Chen
- Beijing Macro & Micro-test Bio-Tech Co., Ltd., Beijing, China
| | - Fei Wang
- Sichuan Forestry and Grassland Pest Control and Quarantine Station, Chengdu, China
| | - Ping Ye
- Wolong National Natural Reserve Administration Bureau, Wenchuan, China
| | - Luoyuan Xia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Baogui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hao Tang
- Wolong National Natural Reserve Administration Bureau, Wenchuan, China
| | - Qingyu Zhang
- Wolong National Natural Reserve Administration Bureau, Wenchuan, China
| | - Xiangdong Ruan
- Academy of Inventory and Planning, National Forestry and Grassland Administration, Beijing, China
| | - Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiafu Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| |
Collapse
|
12
|
Ergunay K, Dincer E, Justi SA, Bourke BP, Nelson SP, Liao HM, Timurkan MO, Oguz B, Sahindokuyucu I, Gokcecik OF, Reinbold-Wasson DD, Jiang L, Achee NL, Grieco JP, Linton YM. Impact of nanopore-based metagenome sequencing on tick-borne virus detection. Front Microbiol 2023; 14:1177651. [PMID: 37323891 PMCID: PMC10267750 DOI: 10.3389/fmicb.2023.1177651] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction We evaluated metagenomic nanopore sequencing (NS) in field-collected ticks and compared findings from amplification-based assays. Methods Forty tick pools collected in Anatolia, Turkey and screened by broad-range or nested polymerase chain reaction (PCR) for Crimean-Congo Hemorrhagic Fever Virus (CCHFV) and Jingmen tick virus (JMTV) were subjected to NS using a standard, cDNA-based metagenome approach. Results Eleven viruses from seven genera/species were identified. Miviruses Bole tick virus 3 and Xinjiang mivirus 1 were detected in 82.5 and 2.5% of the pools, respectively. Tick phleboviruses were present in 60% of the pools, with four distinct viral variants. JMTV was identified in 60% of the pools, where only 22.5% were PCR-positive. CCHFV sequences characterized as Aigai virus were detected in 50%, where only 15% were detected by PCR. NS produced a statistically significant increase in detection of these viruses. No correlation of total virus, specific virus, or targeted segment read counts was observed between PCR-positive and PCR-negative samples. NS further enabled the initial description of Quaranjavirus sequences in ticks, where human and avian pathogenicity of particular isolates had been previously documented. Discussion NS was observed to surpass broad-range and nested amplification in detection and to generate sufficient genome-wide data for investigating virus diversity. It can be employed for monitoring pathogens in tick vectors or human/animal clinical samples in hot-spot regions for examining zoonotic spillover.
Collapse
Affiliation(s)
- Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States
- Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara, Türkiye
| | - Ender Dincer
- Department of Virology, Faculty of Veterinary Medicine, Dokuz Eylül University, Izmir, Türkiye
| | - Silvia A. Justi
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States
| | - Brian P. Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States
| | - Suppaluck P. Nelson
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States
| | - Hsiao-Mei Liao
- Naval Medical Research Center (NMRC), Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Mehmet Ozkan Timurkan
- Department of Virology, Faculty of Veterinary Medicine, Ataturk University, Yakutiye, Erzurum, Türkiye
| | - Bekir Oguz
- Department of Parasitology, Faculty of Veterinary Medicine, Van Yuzuncu Yil University, Van, Türkiye
| | - Ismail Sahindokuyucu
- Bornova Veterinary Control Institute, Veterinary Control Institute Directorates, Ministry of Agriculture and Forestry, Izmir, Türkiye
| | - Omer Faruk Gokcecik
- Bornova Veterinary Control Institute, Veterinary Control Institute Directorates, Ministry of Agriculture and Forestry, Izmir, Türkiye
| | | | - Le Jiang
- Naval Medical Research Center (NMRC), Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Nicole L. Achee
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - John P. Grieco
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States
| |
Collapse
|
13
|
Qu L, Li X, Huang B, Liu Y, Li Q, Shah T, Ning Y, Li J, Lu Y, Yan L, Wang B, Xia X. Identification and Characterization of Jingmen Tick Virus in Ticks from Yunnan Imported Cattle. Vector Borne Zoonotic Dis 2023; 23:298-302. [PMID: 37172285 DOI: 10.1089/vbz.2022.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Jingmen tick virus (JMTV) is a tick-borne segmented positive-sense ssRNA virus that can cause human disease. This virus has been confirmed to be widespread, having a wide host range. In human it can cause fever, headache, lymphadenopathy, and asthenia. Therefore, JMTV poses a threat to public health. In this study, we collected 478 ticks from imported cattle on three quarantine farms near the Yunnan border to detect medically significant tick-borne viruses. Our findings show that JMTV was the only detected virus, with an incidence rate of 56.67%. Phylogenetic analysis showed that our JMTV is more closely related to previously reported JMTV strains from Yunnan Province and neighboring Laos, implying that the tick-borne virus was most likely imported from Laos. In conclusion, we identified and characterized a novel JMTV strain in tick (Rhipicephalus microplus) from Yunnan imported cattle, emphasizing the importance of arbovirus quarantine of livestock imports.
Collapse
Affiliation(s)
- Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Xiaofei Li
- The Third People's Hospital of Kunming, Kunming, P.R. China
| | - Baoyang Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Yufu Liu
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Yuting Ning
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Jie Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Yunlan Lu
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Linghua Yan
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| |
Collapse
|
14
|
Rong Lee M, Kim JC, Eun Park S, Kim WJ, Su Kim J. Detection of Viral Genes in Metarhizium anisopliae JEF-290-infected longhorned tick, Haemaphysalis longicornis using transcriptome analysis. J Invertebr Pathol 2023; 198:107926. [PMID: 37087092 DOI: 10.1016/j.jip.2023.107926] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023]
Abstract
Ticks are carriers of viruses that can cause disease in humans and animals. The longhorned ticks (Haemaphysalis longicornis; LHT), for example, mediates the severe fever with thrombocytopenia syndrome virus (SFTSV) in humans, and the population of ticks is growing due to increases in temperature caused by climate change. As ticks carry primarily RNA viruses, there is a need to study the possibility of detecting new viruses through tick virome analysis. In this study, viruses in LHTs collected in Korea were investigated and virus titers in ticks exposed to the entomopathogenic fungus Metarhizium anisopliae JEF-290 were analyzed. Total RNA was extracted from the collected ticks, and short reads were obtained from Illumina sequencing. A total of 50,024 contigs with coding capacity were obtained after de novo assembly of the reads in the metaSPAdes genome assembler. A series of BLAST-based analyses using the GenBank database was performed to screen viral contigs, and three putative virus species were identified from the tick meta-transcriptome, such as Alongshan virus (ALSV), Denso virus and Taggert virus. Measurements of virus-expression levels of infected and non-infected LHTs failed to detect substantial differences in expression levels. However, we suggest that LHT can spread not only SFTSV, but also various other disease-causing viruses over large areas of the world. From the phylogenetic analysis of ALSV glycoproteins, genetic differences in the ALSV could be due to host differences as well as regional differences. Viral metagenome analysis can be used as a tool to manage future outbreaks of disease caused by ticks by detecting unknown viruses.
Collapse
Affiliation(s)
- Mi Rong Lee
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54596, Korea
| | - Jong-Cheol Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54596, Korea
| | - So Eun Park
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54596, Korea
| | | | - Jae Su Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54596, Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54596, Republic of Korea.
| |
Collapse
|
15
|
Litov AG, Okhezin EV, Kholodilov IS, Belova OA, Karganova GG. Conserved Sequences in the 5' and 3' Untranslated Regions of Jingmenvirus Group Representatives. Viruses 2023; 15:v15040971. [PMID: 37112951 PMCID: PMC10141212 DOI: 10.3390/v15040971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The Jingmenvirus group (JVG), with members such as Jingmen tick virus (JMTV), Alongshan virus (ALSV), Yanggou tick virus (YGTV), and Takachi virus (TAKV), is drawing attention due to evidence of it causing disease in humans and its unique genome architecture. In the current work, complete untranslated regions (UTRs) of four strains of ALSV and eight strains of YGTV were obtained. An analysis of these sequences, as well as JVG sequences from GenBank, uncovered several regions within viral UTRs that were highly conserved for all the segments and viruses. Bioinformatics predictions suggested that the UTRs of all the segments of YGTV, ALSV, and JMTV could form similar RNA structures. The most notable feature of these structures was a stable stem-loop with one (5' UTR) or two (3' UTR) AAGU tetraloops on the end of a hairpin.
Collapse
Affiliation(s)
- Alexander G Litov
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Egor V Okhezin
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan S Kholodilov
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Oxana A Belova
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Galina G Karganova
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| |
Collapse
|
16
|
Luan Y, Gou J, Zhong D, Ma L, Yin C, Shu M, Liu G, Lin Q. The Tick-Borne Pathogens: An Overview of China's Situation. Acta Parasitol 2023; 68:1-20. [PMID: 36642777 PMCID: PMC9841149 DOI: 10.1007/s11686-023-00658-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/02/2023] [Indexed: 01/17/2023]
Abstract
BACKGROUND Ticks are important medical arthropods that can transmit hundreds of pathogens, such as parasites, bacteria, and viruses, leading to serious public health burdens worldwide. Unexplained fever is the most common clinical manifestation of tick-borne diseases. Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the surge of coronavirus disease 2019 (COVID-19) cases led to the hospital overload and fewer laboratory tests for tick-borne diseases. Therefore, it is essential to review the tick-borne pathogens and further understand tick-borne diseases. PURPOSE The geographic distribution and population of ticks in the Northern hemisphere have expanded while emerging tick-borne pathogens have been introduced to China continuously. This paper focused on the tick-borne pathogens that are threatening public health in the world. Their medical significant tick vectors, as well as the epidemiology, clinical manifestations, diagnosis, treatment, prevention, and control measures, are emphasized in this document. METHODS In this study, all required data were collected from articles indexed in English databases, including Scopus, PubMed, Web of Science, Science Direct, and Google Scholar. RESULTS Ticks presented a great threat to the economy and public health. Although both infections by tick-borne pathogens and SARS-CoV-2 have fever symptoms, the history of tick bite and its associated symptoms such as encephalitis or eschar could be helpful for the differential diagnosis. Additionally, as a carrier of vector ticks, migratory birds may play a potential role in the geographical expansion of ticks and tick-borne pathogens during seasonal migration. CONCLUSION China should assess the risk score of vector ticks and clarify the potential role of migratory birds in transmitting ticks. Additionally, the individual and collective protection, vector control, comprehensive surveillance, accurate diagnosis, and symptomatic treatment should be carried out, to meet the challenge.
Collapse
Affiliation(s)
- Yuxuan Luan
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Jingmin Gou
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dongjie Zhong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Li Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chuansong Yin
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Minfeng Shu
- School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Qing Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.
| |
Collapse
|
17
|
Ebert CL, Söder L, Kubinski M, Glanz J, Gregersen E, Dümmer K, Grund D, Wöhler AS, Könenkamp L, Liebig K, Knoll S, Hellhammer F, Topp AK, Becher P, Springer A, Strube C, Nagel-Kohl U, Nordhoff M, Steffen I, Bauer BU, Ganter M, Feige K, Becker SC, Boelke M. Detection and Characterization of Alongshan Virus in Ticks and Tick Saliva from Lower Saxony, Germany with Serological Evidence for Viral Transmission to Game and Domestic Animals. Microorganisms 2023; 11:microorganisms11030543. [PMID: 36985117 PMCID: PMC10055853 DOI: 10.3390/microorganisms11030543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
The newly discovered group of Jingmenviruses has been shown to infect a wide range of hosts and has been associated with febrile illness in humans. During a survey for Jingmenviruses in ticks from Lower Saxony, Germany, Alongshan virus (ALSV) was identified in Ixodes spp. ticks. Additional virus screenings revealed the presence of ALSV in the bodies and saliva of ticks collected at several locations in Lower Saxony. Vector competence studies that included Ixodes ricinus and Dermacentor reticulatus validated the replication of ALSV within those tick species. In vitro feeding experiments with ALSV-injected Ixodes ricinus demonstrated effective viral transmission during blood feeding. To evaluate the potential viral transmission during a natural blood meal, sera from wild game and domestic animals were investigated. One serum sample from a red deer was found to be positive for ALSV RNA, while serological screenings in game and domestic animals revealed the presence of ALSV-specific antibodies at different locations in Lower Saxony. Overall, those results demonstrate the broad distribution of ALSV in ticks in Lower Saxony and hypothesize frequent exposure to animals based on serological investigations. Hence, its potential risk to human and animal health requires further investigation.
Collapse
Affiliation(s)
- Cara Leonie Ebert
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Lars Söder
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Mareike Kubinski
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Julien Glanz
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Eva Gregersen
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Katrin Dümmer
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Domenic Grund
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Ann-Sophie Wöhler
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Laura Könenkamp
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
- Institute for Biochemistry, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Katrin Liebig
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Steffen Knoll
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Fanny Hellhammer
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Anna-Katharina Topp
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Paul Becher
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Andrea Springer
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Uschi Nagel-Kohl
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Braunschweig/Hannover, Eintrachtweg 17, 30173 Hanover, Germany
| | - Marcel Nordhoff
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Oldenburg, Philosophenweg 38, 26121 Oldenburg, Germany
| | - Imke Steffen
- Institute for Biochemistry, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Benjamin Ulrich Bauer
- Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hanover, Germany
| | - Martin Ganter
- Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hanover, Germany
| | - Karsten Feige
- Clinic for Horses, University of Veterinary Medicine Hannover, Buenteweg 9, 30559 Hanover, Germany
| | - Stefanie C. Becker
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
- Correspondence: (S.C.B.); (M.B.); Tel.: +49-511-953-8717 (S.C.B.)
| | - Mathias Boelke
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
- Correspondence: (S.C.B.); (M.B.); Tel.: +49-511-953-8717 (S.C.B.)
| |
Collapse
|
18
|
Kartashov MY, Gladysheva AV, Naidenova EV, Zakharov KS, Shvalov АN, Krivosheina EI, Senichkina AM, Bah MB, Ternovoi VA, Boumbaly S, Loktev VB. [Molecular and genetic characteristics of the multicomponent flavi-like Kindia tick virus (Flaviviridae) found in ixodes ticks on the territory of the Republic of Guinea]. Vopr Virusol 2023; 67:487-495. [PMID: 37264838 DOI: 10.36233/0507-4088-145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Indexed: 06/03/2023]
Abstract
INTRODUCTION Ixodes ticks are vectors for pathogens of many infectious diseases. Recently, during the study of Rhipicephalus geigyi ticks collected from livestock in the Republic of Guinea, a new multicomponent flavi-like RNA virus, called Kindia tick virus (KITV), was discovered with an unusual mechanism for the implementation of genetic information. The aim of the work is to detect and study the genetic diversity of KITV in ixodes ticks collected in the territory of the Kindia province of the Republic of Guinea. MATERIAL AND METHODS In 2021, 324 specimens of ticks of the species Amblyomma variegatum, Rh. geigyi, Rh. annulatus, Rh. decoloratus, Rh. senegalensis were collected from cattle. The detection of viral RNA was carried out in individual samples of ticks by RT-PCR, followed by the determination of the nucleotide sequence and phylogenetic analysis. RESULTS AND DISCUSSION KITV detection rates in ticks of the species Rh. geigyi was 12.2%, Rh. annulatus 4.4%, Rh. decoloratus 3.3%. However, the KITV genetic material has not been identified in Am. variegatum ticks, which are one of the dominant species in West Africa. For all virus isolates, a partial nucleotide sequences of each of the four viral segments (GenBank, OK345271OK345306) were determined. The phylogenetic analysis showed a high level of identity (98.599.8%) for each of the four segments of the viral genome with those previously found in the Republic of Guinea. The obtained KITV isolates are most genetically close to Mogiana tick virus, which was previously detected in South America in Rh. microplus ticks and significantly differed from other multicomponent viruses circulating in Europe and Asia, including the Russian Federation. CONCLUSION KITV genetic material was found in three species of ixodid ticks collected from livestock in a number of prefectures of the Republic of Guinea. The infection rate in ticks was 3.312.2%. The continuation of research in this direction remains relevant.
Collapse
Affiliation(s)
- M Y Kartashov
- State Research Center of Virology and Biotechnology «Vector»
| | - A V Gladysheva
- State Research Center of Virology and Biotechnology «Vector»
| | | | - K S Zakharov
- Russian Research Anti-Plague Institute «Microbe»
| | - А N Shvalov
- State Research Center of Virology and Biotechnology «Vector»
| | - E I Krivosheina
- State Research Center of Virology and Biotechnology «Vector»
| | | | - M B Bah
- Research Institute of Applied Biology of Guinea
| | - V A Ternovoi
- State Research Center of Virology and Biotechnology «Vector»
| | - S Boumbaly
- Research Institute of Applied Biology of Guinea
| | - V B Loktev
- State Research Center of Virology and Biotechnology «Vector»
| |
Collapse
|
19
|
A Search for Tick-Associated, Bronnoya-like Virus Spillover into Sheep. Microorganisms 2023; 11:microorganisms11010209. [PMID: 36677501 PMCID: PMC9865699 DOI: 10.3390/microorganisms11010209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the order Bunyavirales were discovered in numerous tick species. In this study, we used metatranscriptomics to detect the virome, including novel viruses, associated with Ixodes ricinus collected from Romania and France. A bunyavirus-like virus related to the Bronnoya virus was identified for the first time in these regions. It presents a high level of amino-acid conservation with Bronnoya-related viruses identified in I. ricinus ticks from Norway and Croatia and with the Ixodes scapularis bunyavirus isolated from a tick cell line in Japan in 2014. Phylogenetic analyses revealed that the Bronnoya viruses' sub-clade is distinct from several Bunyavirales families, suggesting that it could constitute a novel family within the order. To determine if Bronnoya viruses could constitute novel tick-borne arboviruses, a Luciferase immunoprecipitation assay for detecting antibodies in the viral glycoprotein of the Romanian Bronnoya virus was used to screen sera from small ruminants exposed to tick bites. No positive serum was detected, suggesting that this virus is probably not able to infect small ruminants. This study represents the first serological investigation of mammalian infections with a Bronnoya-like virus and an initial step in the identification of potential new emergences of tick-borne arboviruses.
Collapse
|
20
|
Wu Z, Chen J, Zhang L, Zhang Y, Liu L, Niu G. Molecular evidence for potential transovarial transmission of Jingmen tick virus in Haemaphysalis longicornis fed on cattle from Yunnan Province, China. J Med Virol 2023; 95:e28357. [PMID: 36443647 DOI: 10.1002/jmv.28357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne virus first identified from Jingmen city, Hubei Province of China in 2010. It has been proved that JMTV can cause human diseases and is widely distributed both inside and outside of China. However, the survival mode and transmission characteristics of JMTV still need further research, particularly in terms of transovarial transmission. In this study, an investigation was conducted to explore the presence of JMTV from engorged female ticks to their offspring. All engorged female adult ticks were collected from domestic cattle and allowed to lay eggs in appropriate humidity and temperature conditions. Maternal ticks, eggs and larvae were screened for JMTV RNA through real-time polymerase chain reaction (RT-PCR) and nested PCR methods. The results revealed the positive rate of 10.53% (10/95) in engorged ticks, 9.09% (2/22) in eggs and 8% (4/50) in larvae pools, respectively. Phylogenetic analysis confirmed that sequences from eggs and larvae had closer relationship with those isolates from maternal engorged ticks with more than 99.7% homology and JMTV manifested with evolutional conservatism. Our study has identified for the first time that JMTV could be transmitted from mother generation to offspring of Haemaphysalis Longicornis. Nonetheless, the efficiency of transovarial transmission in JMTV and the significance of ticks as amplification hosts still need to be further illustrated.
Collapse
Affiliation(s)
- Zhen Wu
- School of Public Health, WeiFang Medical University, Weifang, China
| | - Junhao Chen
- School of Public Health, WeiFang Medical University, Weifang, China
| | | | - Yuli Zhang
- School of Public Health, WeiFang Medical University, Weifang, China
| | - Lin Liu
- Immune-Path Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Guoyu Niu
- School of Public Health, WeiFang Medical University, Weifang, China
| |
Collapse
|
21
|
Zhang J, Zheng YC, Chu YL, Cui XM, Wei R, Bian C, Liu HB, Yao NN, Jiang RR, Huo QB, Yuan TT, Li J, Zhao L, Li LF, Wang Q, Wei W, Zhu JG, Chen MC, Gao Y, Wang F, Ye JL, Song JL, Jiang JF, Lam TTY, Ni XB, Jia N. Skin infectome of patients with a tick bite history. Front Cell Infect Microbiol 2023; 13:1113992. [PMID: 36923591 PMCID: PMC10008932 DOI: 10.3389/fcimb.2023.1113992] [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: 12/02/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
Introduction Ticks are the most important obligate blood-feeding vectors of human pathogens. With the advance of high-throughput sequencing, more and more bacterial community and virome in tick has been reported, which seems to pose a great threat to people. Methods A total of 14 skin specimens collected from tick-bite patients with mild to severe symptoms were analyzed through meta-transcriptomic sequencings. Results Four bacteria genera were both detected in the skins and ticks, including Pseudomonas, Acinetobacter, Corynebacterium and Propionibacterium, and three tick-associated viruses, Jingmen tick virus (JMTV), Bole tick virus 4 (BLTV4) and Deer tick mononegavirales-like virus (DTMV) were identified in the skin samples. Except of known pathogens such as pathogenic rickettsia, Coxiella burnetii and JMTV, we suggest Roseomonas cervicalis and BLTV4 as potential new agents amplified in the skins and then disseminated into the blood. As early as 1 day after a tick-bite, these pathogens can transmit to skins and at most four ones can co-infect in skins. Discussion Advances in sequencing technologies have revealed that the diversity of tick microbiome and virome goes far beyond our previous understanding. This report not only identifies three new potential pathogens in humans but also shows that the skin barrier is vital in preventing horizontal transmissions of tick-associated bacteria or virus communities to the host. It is the first research on patients' skin infectome after a tick bite and demonstrates that more attention should be paid to the cutaneous response to prevent tick-borne illness.
Collapse
Affiliation(s)
- Jie Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan-Chun Zheng
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Yan-Li Chu
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ran Wei
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cai Bian
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Hong-Bo Liu
- Department of Infectious Diseases Control and Prevention, Chinese People's Liberation Army of China (PLA) Center for Disease Control and Prevention, Beijing, China
| | - Nan-Nan Yao
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Rui-Ruo Jiang
- Institute of Nuclear, Biological, and Chemical weapons (NBC) Defence, PLA Army, Beijing, China
| | - Qiu-Bo Huo
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | | | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lian-Feng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin-Guo Zhu
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Mei-Chao Chen
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Yan Gao
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Fei Wang
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Jin-Ling Ye
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Ju-Liang Song
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Na Jia, ; Xue-Bing Ni, ; Tommy Tsan-Yuk Lam,
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Na Jia, ; Xue-Bing Ni, ; Tommy Tsan-Yuk Lam,
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Na Jia, ; Xue-Bing Ni, ; Tommy Tsan-Yuk Lam,
| |
Collapse
|
22
|
Liu Z, Li L, Xu W, Yuan Y, Liang X, Zhang L, Wei Z, Sui L, Zhao Y, Cui Y, Yin Q, Li D, Li Q, Hou Z, Wei F, Liu Q, Wang Z. Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China. PLoS Negl Trop Dis 2022; 16:e0011017. [PMID: 36542659 PMCID: PMC9836300 DOI: 10.1371/journal.pntd.0011017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 01/12/2023] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ticks act as important vectors of infectious agents, and several emerging tick-borne viruses have recently been identified to be associated with human diseases in northeastern China. However, little is known about the tick virome in northeastern China. METHODS Ticks collected from April 2020 to July 2021 were pooled for metagenomic analysis to investigate the virome diversity in northeastern China. RESULTS In total, 22 RNA viruses were identified, including four each in the Nairoviridae and Phenuiviridae families, three each in the Flaviviridae, Rhabdoviridae, and Solemoviridae families, two in the Chuviridae family, and one each in the Partitiviridae, Tombusviridae families and an unclassified virus. Of these, eight viruses were of novel species, belonging to the Nairoviridae (Ji'an nairovirus and Yichun nairovirus), Phenuiviridae (Mudanjiang phlebovirus), Rhabdoviridae (Tahe rhabdovirus 1-3), Chuviridae (Yichun mivirus), and Tombusviridae (Yichun tombus-like virus) families, and five members were established human pathogens, including Alongshan virus, tick-borne encephalitis virus, Songling virus, Beiji nairovirus, and Nuomin virus. I. persulcatus ticks had significant higher number of viral species than H. japonica, H. concinna, and D. silvarum ticks. Significant differences in tick viromes were observed among Daxing'an, Xiaoxing'an and Changbai mountains. CONCLUSIONS These findings showed an extensive diversity of RNA viruses in ticks in northeastern China, revealing potential public health threats from the emerging tick-borne viruses. Further studies are needed to explain the natural circulation and pathogenicity of these viruses.
Collapse
Affiliation(s)
- Ziyan Liu
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
- Laboratory of Pathogen Microbiology and Immunology, College of Life Science, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Liang Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People’s Republic of China
| | - Wenbo Xu
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
| | - Yongxu Yuan
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Xiaojie Liang
- Laboratory of Pathogen Microbiology and Immunology, College of Life Science, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Li Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People’s Republic of China
| | - Zhengkai Wei
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, People’s Republic of China
| | - Liyan Sui
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
| | - Yinghua Zhao
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
| | - Yanyan Cui
- College of Food Science and Engineering, Tonghua Normal University, Tonghua, Jilin Province, People’s Republic of China
| | - Qing Yin
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
| | - Dajun Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Qianxue Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People’s Republic of China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Feng Wei
- Laboratory of Pathogen Microbiology and Immunology, College of Life Science, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Quan Liu
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People’s Republic of China
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, People’s Republic of China
- * E-mail: (ZW); (QL)
| | - Zedong Wang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin Province, People’s Republic of China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People’s Republic of China
- * E-mail: (ZW); (QL)
| |
Collapse
|
23
|
Kholodilov IS, Belova OA, Ivannikova AY, Gadzhikurbanov MN, Makenov MT, Yakovlev AS, Polienko AE, Dereventsova AV, Litov AG, Gmyl LV, Okhezin EV, Luchinina SV, Klimentov AS, Karganova GG. Distribution and Characterisation of Tick-Borne Flavi-, Flavi-like, and Phenuiviruses in the Chelyabinsk Region of Russia. Viruses 2022; 14:v14122699. [PMID: 36560703 PMCID: PMC9780909 DOI: 10.3390/v14122699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
In this work, we presented data from a two-year study of flavi-, flavi-like, and phenuiviruses circulation in the population of ixodid ticks in the Chelyabinsk region. We isolated three tick-borne encephalitis virus (TBEV) strains from I. persulcatus, which was not detected in the ticks of the genus Dermacentor. The virus prevalence ranged from 0.66% to 2.28%. The Yanggou tick virus (YGTV) is widespread in steppe and forest-steppe zones and is mainly associated with ticks of the genus Dermacentor. We isolated 26 strains from D. reticulatus, D. marginatus, and I. persulcatus ticks in the HAE/CTVM8 tick cell line. The virus prevalence ranged from 1.58% to 4.18% in D. reticulatus, ranged from 0.78% to 3.93% in D. marginatus, and was 0.66% in I. persulcatus. There was combined focus of TBEV and YGTV in the territory of the Chelyabinsk region. The Alongshan virus (ALSV) was found to be associated with I. persulcatus ticks and is spread in forest zone. We detected 12 amplicons and isolated 7 strains of ALSV in tick cells. The virus prevalence ranged from 1.13% to 6.00%. The phlebovirus Gomselga and unclassified phenuivirus Stavropol were associated with I. persulcatus and D. reticulatus ticks, respectively. Virus prevalence of the unclassified phenuivirus Stavropol in the Chelyabinsk region is lower than that in neighbouring regions.
Collapse
Affiliation(s)
- Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Anna Y. Ivannikova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Magomed N. Gadzhikurbanov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Marat T. Makenov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Alexander S. Yakovlev
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Alexandra E. Polienko
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Alena V. Dereventsova
- Laboratory of Biochemistry, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Alexander G. Litov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Egor V. Okhezin
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | - Alexander S. Klimentov
- Laboratory of Biochemistry, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
- Correspondence:
| |
Collapse
|
24
|
Colmant AMG, Charrel RN, Coutard B. Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses. Front Microbiol 2022; 13:997058. [PMID: 36299728 PMCID: PMC9589506 DOI: 10.3389/fmicb.2022.997058] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.
Collapse
|
25
|
Zhang Y, Li Z, Pang Z, Wu Z, Lin Z, Niu G. Identification of Jingmen tick virus (JMTV) in Amblyomma testudinarium from Fujian Province, southeastern China. Parasit Vectors 2022; 15:339. [PMID: 36167570 PMCID: PMC9513871 DOI: 10.1186/s13071-022-05478-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Background Jingmen tick virus (JMTV) is a newly discovered tick-borne virus that can cause disease in humans. This virus has been authenticated as being extremely widespread worldwide and as posing a significant threat to public health and safety. Methods We collected 35 ticks belonging to two tick species from wild boars in Nanping, Fujian Province, China. JMTV-specific genes were amplified by qRT-PCR and nested PCR to confirm the presence of this pathogen. Results More than one third of of all ticks collected (11/35) were positive for JMTV. Viral sequences were obtained from three of the JMTV-positive ticks, including the complete genomic sequence from one tick. This was the first time that JMTV was identified in the hard-bodied tick Amblyomma testudinarium. Phylogenetic analysis revealed that JMTV from Fujian Province shared > 90% identity with other isolates derived from China, but was distinct from those reported in France and Cambodia. Conclusions JMTV is characterized by relatively low mutations and has its own local adaptive characteristics in different regions. Our findings provide molecular evidence of the presence of JMTV in an overlooked tick species from an area not unrecognized as being endemic. They also suggest that JMTV occupies a wider geographical distribution than currently believed and is a potential disease vector. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05478-2.
Collapse
Affiliation(s)
- Yuli Zhang
- WeiFang Medical University, Weifang, 261053, China
| | - Zhenfeng Li
- Department of Public Health, Gaomi People's Hospital, Weifang, 261500, China
| | - Zheng Pang
- Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China
| | - Zhen Wu
- WeiFang Medical University, Weifang, 261053, China
| | - Zhijuan Lin
- WeiFang Medical University, Weifang, 261053, China.
| | - Guoyu Niu
- WeiFang Medical University, Weifang, 261053, China.
| |
Collapse
|
26
|
Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery. Viruses 2022; 14:v14091990. [PMID: 36146797 PMCID: PMC9500916 DOI: 10.3390/v14091990] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolutionary distances from known members of the Pneumoviridae family, were used. Results were compared to Chan Zuckerberg ID (CZ ID), a reference cloud-based mNGS pipeline. We show that Microseek reliably identifies known viral sequences and performs well for the detection of distant pseudoviral sequences, especially in complex samples such as in human plasma, while minimizing non-relevant hits.
Collapse
|
27
|
Integrated Jingmenvirus Polymerase Gene in Ixodes ricinus Genome. Viruses 2022; 14:v14091908. [PMID: 36146715 PMCID: PMC9501327 DOI: 10.3390/v14091908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Members of the jingmenviruses group have been found in arthropods and mammals on all continents except Australia and Antarctica. Two viruses of this group were isolated from patients with fever after a tick bite. Using a nested RT-PCR assay targeting a jingmenvirus polymerase gene fragment, we screened ticks collected in seven regions of Russia and found that the abundant jingmenvirus-positive were of Ixodes ricinus species, with the prevalence ranging from 19.8% to 34.3%. In all cases, DNase/RNase treatment suggested that the detected molecule was DNA and subsequent next generation sequencing (NGS) proved that the viral polymerase gene was integrated in the I. ricinus genome. The copy number of the integrated polymerase gene was quantified by qPCR relative to the ITS2 gene and estimated as 1.32 copies per cell. At least three different genetic variants of the integrated polymerase gene were found in the territory of Russia. Phylogenetic analysis of the integrated jingmenvirus polymerase gene showed the highest similarity with the sequence of the correspondent gene obtained in Serbia from I. ricinus.
Collapse
|
28
|
Pang Z, Jin Y, Pan M, Zhang Y, Wu Z, Liu L, Niu G. Geographical distribution and phylogenetic analysis of Jingmen tick virus in China. iScience 2022; 25:105007. [PMID: 36097615 PMCID: PMC9463580 DOI: 10.1016/j.isci.2022.105007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne segmented RNA virus that is closely related to un-segmental RNA virus in evolution. It has been confirmed that JMTV could be a causative agent of human disease. In this study, a total of 3658 ticks were sampled from 7 provinces of China and then divided into 545 pools according to the location and species. QRT-PCR and nested PCR were performed to confirm the presence of JMTV. The results showed JMTV was identified in 5 out of 7 provinces with an average infection rate of 1.4% (51/3658). Phylogenetic analysis indicated that all JMTV strains identified in this study were closely related to each other and formed a well-supported sub-lineage. Our results provide molecular evidence of JMTV in different species of ticks from endemic and non-endemic regions and demonstrate that JMTV, as a natural foci pathogen, may be widely distributed all over China. JMTV was first identified in unrecognized endemic regions of China Two complete genomes and 13 partial S1 segments of JMTV were sequenced and analyzed JMTV was relatively conservative in evolution JMTV was widely distributed in China as a potential health threat to humans and animals
Collapse
|
29
|
Ergunay K, Mutinda M, Bourke B, Justi SA, Caicedo-Quiroga L, Kamau J, Mutura S, Akunda IK, Cook E, Gakuya F, Omondi P, Murray S, Zimmerman D, Linton YM. Metagenomic Investigation of Ticks From Kenyan Wildlife Reveals Diverse Microbial Pathogens and New Country Pathogen Records. Front Microbiol 2022; 13:932224. [PMID: 35847110 PMCID: PMC9283121 DOI: 10.3389/fmicb.2022.932224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Focusing on the utility of ticks as xenosurveillance sentinels to expose circulating pathogens in Kenyan drylands, host-feeding ticks collected from wild ungulates [buffaloes, elephants, giraffes, hartebeest, impala, rhinoceros (black and white), zebras (Grévy’s and plains)], carnivores (leopards, lions, spotted hyenas, wild dogs), as well as regular domestic and Boran cattle were screened for pathogens using metagenomics. A total of 75 host-feeding ticks [Rhipicephalus (97.3%) and Amblyomma (2.7%)] collected from 15 vertebrate taxa were sequenced in 46 pools. Fifty-six pathogenic bacterial species were detected in 35 pools analyzed for pathogens and relative abundances of major phyla. The most frequently observed species was Escherichia coli (62.8%), followed by Proteus mirabilis (48.5%) and Coxiella burnetii (45.7%). Francisella tularemia and Jingmen tick virus (JMTV) were detected in 14.2 and 13% of the pools, respectively, in ticks collected from wild animals and cattle. This is one of the first reports of JMTV in Kenya, and phylogenetic reconstruction revealed significant divergence from previously known isolates and related viruses. Eight fungal species with human pathogenicity were detected in 5 pools (10.8%). The vector-borne filarial pathogens (Brugia malayi, Dirofilaria immitis, Loa loa), protozoa (Plasmodium spp., Trypanosoma cruzi), and environmental and water-/food-borne pathogens (Entamoeba histolytica, Encephalitozoon intestinalis, Naegleria fowleri, Schistosoma spp., Toxoplasma gondii, and Trichinella spiralis) were detected. Documented viruses included human mastadenovirus C, Epstein-Barr virus and bovine herpesvirus 5, Trinbago virus, and Guarapuava tymovirus-like virus 1. Our findings confirmed that host-feeding ticks are an efficient sentinel for xenosurveillance and demonstrate clear potential for wildlife-livestock-human pathogen transfer in the Kenyan landscape.
Collapse
Affiliation(s)
- Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
- *Correspondence: Koray Ergunay,
| | | | - Brian Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
| | - Silvia A. Justi
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
| | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
| | - Joseph Kamau
- One Health Centre, Institute of Primate Research (IPR), Nairobi, Kenya
| | - Samson Mutura
- One Health Centre, Institute of Primate Research (IPR), Nairobi, Kenya
| | | | - Elizabeth Cook
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Francis Gakuya
- Wildlife Research and Training Institute (WRTI), Naivasha, Kenya
| | - Patrick Omondi
- Wildlife Research and Training Institute (WRTI), Naivasha, Kenya
| | - Suzan Murray
- Global Health Program, Smithsonian Conservation Biology Unit, Fort Royal, VA, United States
| | - Dawn Zimmerman
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, United States
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
| |
Collapse
|
30
|
Li LF, Zhang MZ, Zhu JG, Cui XM, Zhang CF, Niu TY, Li J, Sun Y, Wei W, Liu HB, Yuan TT, Wei R, Wang Q, Xia LY, Zhao L, Lesley BS, Jiang BG, Jiang JF, Frans J, Jia N, Cao WC. Dermacentor silvarum, a Medically Important Tick, May Not Be a Competent Vector to Transmit Jingmen Tick Virus. Vector Borne Zoonotic Dis 2022; 22:402-407. [PMID: 35834662 DOI: 10.1089/vbz.2021.0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Jingmen tick virus (JMTV) has attracted great attention due to its potential pathogenicity in humans and its transmission by ticks. Dermacentor silvarum (D. silvarum) is one of the dominant tick species in northeastern China, and can transmit many pathogens to humans and animals. However, there have been no report of transmission of JMTV by D. silvarum. Materials and Methods: Ticks were collected from vegetation at the Aershan Port in Inner Mongolia in April 2019. And we do attempt to infect D. silvarum with JMTV by the immersion technique in laboratory conditions. The transmission of JMTV was examined by reverse transcriptase PCR, fluorescence in situ hybridization, and indirect immunofluorescence assay. Statistical analysis was performed using SPSS 24.0. Results: We found that JMTV may only be maintained in the tick without replication, and could not be transmitted to a host following transstadial transmission. Moreover, no virus colonization was found in the midgut or salivary glands of unfed D. silvarum; therefore, D. silvarum may not be susceptible to JMTV infection and therefore unlikely to carry and transmit JMTV. Conclusion: Our study has to some extent filled the knowledge gap regarding the possibility of JMTV transmission by a medically important tick vector, D. silvarum.
Collapse
Affiliation(s)
- Lian-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, China
| | - Ming-Zhu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | - Jin-Guo Zhu
- ManZhouLi Customs District, Manzhouli, P.R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | | | | | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | - Wei- Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,Center for Medical Genetics and Genomics, The Second Afliated Hospital of Guangxi Medical University, Nanning, China
| | - Hong-Bo Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, China
| | - Ran Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Luo-Yuan Xia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lin Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China.,School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bell-Sakyi Lesley
- Department of Infection Biology and Microbiomes, Institute of Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | - Jongejan Frans
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, Onderstepoort, South Africa
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P.R. China
| |
Collapse
|
31
|
Colmant AMG, Furlong MJ, Etebari K. Discovery of a Novel Jingmenvirus in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2022; 14:v14061140. [PMID: 35746612 PMCID: PMC9229714 DOI: 10.3390/v14061140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 02/07/2023] Open
Abstract
In Australia, soldier flies are major pests of sugarcane, and they can cause significant yield losses in some areas, possibly due to the virus’ transmission to the plants. We sequenced fly larvae salivary glands and identified a novel jingmenvirus, putatively named Inopus flavus jingmenvirus 1 (IFJV1). Phylogenetic trees confirmed that IFJV1 groups with insect-associated jingmenviruses, newly identified flavivirus-like viruses with a segmented genome. After the design and the validation of molecular detection systems for IFJV1, larval homogenates were passaged on insect and vertebrate cells, but IFJV1 could only be detected in the first two passages in insect cells and not at all in vertebrate cells. Despite this lack of consistent replication in laboratory models, this virus does replicate in its host Inopus flavus, as sequenced, small RNA from the larvae matched the IFJV1 sequences. Moreover, they were found to be predominantly 21 nucleotides long and map to the whole sequences on both strands, which is typical of an actively replicating virus. This discovery confirms the worldwide presence of jingmenviruses which, until now, had only been detected on four continents. However, the study of IFJV1 tropism and the possible pathogenicity to its host or the sugarcane it parasitizes requires the development of a stable replication model.
Collapse
Affiliation(s)
- Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), 13005 Marseille, France;
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J. Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (M.J.F.); (K.E.)
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (M.J.F.); (K.E.)
| |
Collapse
|
32
|
Ogola EO, Kopp A, Bastos ADS, Slothouwer I, Marklewitz M, Omoga D, Rotich G, Getugi C, Sang R, Torto B, Junglen S, Tchouassi DP. Jingmen Tick Virus in Ticks from Kenya. Viruses 2022; 14:1041. [PMID: 35632782 PMCID: PMC9147648 DOI: 10.3390/v14051041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/29/2023] Open
Abstract
Jingmen tick virus (JMTV) is an arbovirus with a multisegmented genome related to those of unsegmented flaviviruses. The virus first described in Rhipicephalus microplus ticks collected in Jingmen city (Hubei Province, China) in 2010 is associated with febrile illness in humans. Since then, the geographic range has expanded to include Trinidad and Tobago, Brazil, and Uganda. However, the ecology of JMTV remains poorly described in Africa. We screened adult ticks (n = 4550, 718 pools) for JMTV infection by reverse transcription polymerase chain reaction (RT-PCR). Ticks were collected from cattle (n = 859, 18.88%), goats (n = 2070, 45.49%), sheep (n = 1574, 34.59%), and free-ranging tortoises (Leopard tortoise, Stigmochelys pardalis) (n = 47, 1.03%) in two Kenyan pastoralist-dominated areas (Baringo and Kajiado counties) with a history of undiagnosed febrile human illness. Surprisingly, ticks collected from goats (0.3%, 95% confidence interval (CI) 0.1-0.5), sheep (1.8%, 95% CI 1.2-2.5), and tortoise (74.5%, 95% CI 60.9-85.4, were found infected with JMTV, but ticks collected from cattle were all negative. JMTV ribonucleic acid (RNA) was also detected in blood from tortoises (66.7%, 95% CI 16.1-97.7). Intragenetic distance of JMTV sequences originating from tortoise-associated ticks was greater than that of sheep-associated ticks. Phylogenetic analyses of seven complete-coding genome sequences generated from tortoise-associated ticks formed a monophyletic clade within JMTV strains from other countries. In summary, our findings confirm the circulation of JMTV in ticks in Kenya. Further epidemiological surveys are needed to assess the potential public health impact of JMTV in Kenya.
Collapse
Affiliation(s)
- Edwin O. Ogola
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
- Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria 0028, South Africa;
| | - Anne Kopp
- Berlin Institute of Health, Institute of Virology, Charité—Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.); (M.M.)
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, 10117 Berlin, Germany
| | - Armanda D. S. Bastos
- Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria 0028, South Africa;
| | - Inga Slothouwer
- Berlin Institute of Health, Institute of Virology, Charité—Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.); (M.M.)
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, 10117 Berlin, Germany
| | - Marco Marklewitz
- Berlin Institute of Health, Institute of Virology, Charité—Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.); (M.M.)
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, 10117 Berlin, Germany
| | - Dorcus Omoga
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
| | - Gilbert Rotich
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
| | - Caroline Getugi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
- Kenya Medical Research Institute (KEMRI), Off Raila Odinga Way, Nairobi P.O. Box 54840-00200, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
- Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria 0028, South Africa;
| | - Sandra Junglen
- Berlin Institute of Health, Institute of Virology, Charité—Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.); (M.M.)
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, 10117 Berlin, Germany
| | - David P. Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (E.O.O.); (D.O.); (G.R.); (C.G.); (R.S.); (B.T.)
| |
Collapse
|
33
|
Bratuleanu BE, Temmam S, Munier S, Chrétien D, Bigot T, van der Werf S, Savuta G, Eloit M. Detection of Phenuiviridae, Chuviridae Members, and a Novel Quaranjavirus in Hard Ticks From Danube Delta. Front Vet Sci 2022; 9:863814. [PMID: 35498749 PMCID: PMC9044029 DOI: 10.3389/fvets.2022.863814] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The members of the Quaranjavirus genus are mainly associated with argas ticks but recent studies demonstrated the presence of novel quaranjaviruses-like in ixodid ticks. In 2020, 169 Rhipicephalus sanguineus ticks were collected in Southern Romania from small ruminants and analyzed by high-throughput transcriptome sequencing. Among the viral families that infect Romanian ticks, we have identified sequences from Phenuiviridae (Brown dog tick phlebovirus 1 [BDTPV1] and Brown dog tick phlebovirus 2 [BDTPV2]) and Chuviridae families (Cataloi mivirus [CTMV]), and numerous sequences from a new quaranjavirus-like, tentatively named Cataloi tick quaranjavirus (CTQV). Phylogenetic analyses performed on the five segments show that CTQV is phylogenetically positioned within a clade that encompasses Ixodidae-borne viruses associated with iguanas, small ruminants, seabirds, and penguins distributed across different geographical areas. Furthermore, CTQV is positioned differently depending on the segment considered. This is the first report on the detection of a quaranjavirus-like in Eastern Europe. Further investigations are needed to discern its infectivity and pathogenicity against vertebrates.
Collapse
Affiliation(s)
- Bianca Elena Bratuleanu
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Regional Center of Advanced Research for Emerging Diseases, Zoonoses and Food Safety (ROVETEMERG), “Ion Ionescu de la Brad”, University of Life Sciences, Iasi, Romania
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Institut Pasteur, OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France
| | - Sandie Munier
- Institut Pasteur, Molecular Genetics of RNA Viruses Unit, CNRS UMR 3569, Université de Paris, Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Institut Pasteur, OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France
| | - Thomas Bigot
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, Molecular Genetics of RNA Viruses Unit, CNRS UMR 3569, Université de Paris, Paris, France
- Institut Pasteur, National Reference Center for Respiratory Viruses, Paris, France
| | - Gheorghe Savuta
- Regional Center of Advanced Research for Emerging Diseases, Zoonoses and Food Safety (ROVETEMERG), “Ion Ionescu de la Brad”, University of Life Sciences, Iasi, Romania
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Institut Pasteur, OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France
- Alfort National Veterinary School, Maisons-Alfort, France
- *Correspondence: Marc Eloit
| |
Collapse
|
34
|
Li LJ, Ning NZ, Zheng YC, Chu YL, Cui XM, Zhang MZ, Guo WB, Wei R, Liu HB, Sun Y, Ye JL, Jiang BG, Yuan TT, Li J, Bian C, Bell-Sakyi L, Wang H, Jiang JF, Song JL, Cao WC, Tsan-Yuk Lam T, Ni XB, Jia N. Virome and Blood Meal-Associated Host Responses in Ixodes persulcatus Naturally Fed on Patients. Front Microbiol 2022; 12:728996. [PMID: 35250897 PMCID: PMC8891964 DOI: 10.3389/fmicb.2021.728996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
The long-lasting co-evolution of ticks with pathogens results in mutual adaptation. Blood-feeding is one of the critical physiological behaviors that have been associated with the tick microbiome; however, most knowledge was gained through the study of laboratory-reared ticks. Here we detached Ixodes persulcatus ticks at different stages of blood-feeding from human patients and performed high-throughput transcriptomic analysis on them to identify their virome and genes differentially expressed between flat and fully fed ticks. We also traced bloodmeal sources of those ticks and identified bats and three other potential mammalian hosts, highlighting the public health significance. We found Jingmen tick virus and 13 putative new viruses belonging to 11 viral families, three of which even exhibited high genetic divergence from viruses previously reported in the same tick species from the same geographic region. Furthermore, differential expression analysis suggested a downregulation of antioxidant genes in the fully fed I. persulcatus ticks, which might be related to bloodmeal-related redox homeostasis. Our work highlights the significance of active surveillance of tick viromes and suggests a role of reactive oxygen species (ROS) in modulating changes in the microbiome during blood-feeding.
Collapse
Affiliation(s)
- Liang-Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Nian-Zhi Ning
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yan-Li Chu
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ming-Zhu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wen-Bin Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ran Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hong-Bo Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin-Ling Ye
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Cai Bian
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hui Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ju-Liang Song
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Joint Institute of Virology (SU/HKU), Shantou University, Shantou, China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Xue-Bing Ni,
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Na Jia,
| |
Collapse
|
35
|
Dinçer E, Timurkan MÖ, Oğuz B, Şahindokuyucu İ, Şahan A, Ekinci M, Polat C, Ergünay K. Several Tick-Borne Pathogenic Viruses in Circulation in Anatolia, Turkey. Vector Borne Zoonotic Dis 2022; 22:148-158. [PMID: 35133905 DOI: 10.1089/vbz.2021.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Introduction: We screened host-collected ticks for tick-borne viruses, including those recently documented as human pathogens. Methods: During 2020-2021, ticks removed form cattle, sheep, dogs, and cats in 11 provinces in 5 geographically distinct regions of Anatolia were identified, pooled, and screened using pan-nairovirus, pan-flavivirus and individual assays for Jingmen tick virus (JMTV), and Tacheng tick virus 1 and 2 (TcTV-1 and TcTV-2). Results: A total of 901 tick specimens, comprising 6 species were included. Rhipicephalus sanguineus complex was the most abundant species (44.1%), followed by Rhipicephalus bursa (38.3%), Haemaphysalis parva (7.2%), and others. The specimens were screened in 158 pools with 12 pools (7.6%) being positive. Crimean-Congo hemorrhagic fever virus (CCHFV) lineage Europe 2 (genotype VI) sequences were detected in R. bursa in five (3.2%) of the pools, with similar prevalences in central and Mediterranean Anatolian provinces. JMTV was identified in four R. bursa and one Rhipicephalus turanicus pools, collected from Mediterranean and southeastern Anatolia, with a CCHFV and JMTV coinfected R. bursa pool. The JMTV segment 1 sequences formed a separate cluster with those from Turkey and the Balkan peninsula in the maximum likelihood analysis. TcTV-2 was detected in two Dermacentor marginatus specimens (1.3%) collected in central Anatolia, with nucleocapsid sequences forming a phylogenetically segregated group among viruses from humans and ticks from China and Kazakhstan. Discussion: CCHFV Europe 2 was initially documented in ticks from central Anatolian locations, where related orthonairoviruses had been previously recorded. Ongoing activity and a wider distribution of JMTV and TcTV-2 were observed. These viruses should be screened as potential etiological agents in human infections associated with tick bites.
Collapse
Affiliation(s)
- Ender Dinçer
- Department of Virology, Faculty of Veterinary Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Mehmet Özkan Timurkan
- Department of Virology, Faculty of Veterinary Medicine, Atatürk University, Erzurum, Turkey
| | - Bekir Oğuz
- Department of Parasitology, Faculty of Veterinary Medicine, Van Yuzuncu Yil University, Van, Turkey
| | - İsmail Şahindokuyucu
- Bornova Veterinary Control Institute, Veterinary Control Institute Directorates, Ministry of Agriculture and Forestry, Izmir, Turkey
| | - Adem Şahan
- Department of Internal Medicine, Faculty of Veterinary Medicine, Harran University, Şanlıurfa, Turkey
| | - Mustafa Ekinci
- Department of Animal Breeding, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Ceylan Polat
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| |
Collapse
|
36
|
Detection of Jingmenviruses in Japan with Evidence of Vertical Transmission in Ticks. Viruses 2021; 13:v13122547. [PMID: 34960816 PMCID: PMC8709010 DOI: 10.3390/v13122547] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 12/04/2022] Open
Abstract
Jingmen tick virus (JMTV) and the related jingmenvirus-termed Alongshan virus are recognized as globally emerging human pathogenic tick-borne viruses. These viruses have been detected in various mammals and invertebrates, although their natural transmission cycles remain unknown. JMTV and a novel jingmenvirus, tentatively named Takachi virus (TAKV), have now been identified during a surveillance of tick-borne viruses in Japan. JMTV was shown to be distributed across extensive areas of Japan and has been detected repeatedly at the same collection sites over several years, suggesting viral circulation in natural transmission cycles in these areas. Interestingly, these jingmenviruses may exist in a host tick species-specific manner. Vertical transmission of the virus in host ticks in nature was also indicated by the presence of JMTV in unfed host-questing Amblyomma testudinarium larvae. Further epidemiological surveillance and etiological studies are necessary to assess the status and risk of jingmenvirus infection in Japan.
Collapse
|
37
|
Xu L, Guo M, Hu B, Zhou H, Yang W, Hui L, Huang R, Zhan J, Shi W, Wu Y. Tick virome diversity in Hubei Province, China, and the influence of host ecology. Virus Evol 2021; 7:veab089. [PMID: 34804590 PMCID: PMC8599308 DOI: 10.1093/ve/veab089] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/14/2021] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
Ticks are important vector hosts of pathogens which cause human and animal
diseases worldwide. Diverse viruses have been discovered in ticks; however,
little is known about the ecological factors that affect the tick virome
composition and evolution. Herein, we employed RNA sequencing to study the
virome diversity of the Haemaphysalis longicornis and
Rhipicephalus microplus ticks sampled in Hubei Province in
China. Twelve RNA viruses with complete genomes were identified, which belonged
to six viral families: Flaviviridae, Matonaviridae, Peribunyaviridae,
Nairoviridae, Phenuiviridae, and Rhabdoviridae.
These viruses showed great diversity in their genome organization and evolution,
four of which were proposed to be novel species. The virome diversity and
abundance of R. microplus ticks fed on cattle were evidently
high. Further ecological analyses suggested that host species and feeding status
may be key factors affecting the tick virome structure. This study described a
number of novel viral species and variants from ticks and, more importantly,
provided insights into the ecological factors shaping the virome structures of
ticks, although it clearly warrants further investigation.
Collapse
Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271016, China
| | - Moujian Guo
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Bing Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Wei Yang
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Lixia Hui
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Rui Huang
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jianbo Zhan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Weifeng Shi
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271016, China
| | - Ying Wu
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| |
Collapse
|
38
|
Pérez-Sautu U, Wiley MR, Prieto K, Chitty JA, Haddow AD, Sánchez-Lockhart M, Klein TA, Kim HC, Chong ST, Kim YJ, Choi BS, Palacios GF. Novel viruses in hard ticks collected in the Republic of Korea unveiled by metagenomic high-throughput sequencing analysis. Ticks Tick Borne Dis 2021; 12:101820. [PMID: 34555711 DOI: 10.1016/j.ttbdis.2021.101820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/25/2022]
Abstract
Ticks are vectors of a wide range of zoonotic viruses of medical and veterinary importance. Recently, metagenomics studies demonstrated that they are also the source of potentially pathogenic novel viruses. During the period from 2015 to 2017, questing ticks were collected by dragging the vegetation from geographically distant locations in the Republic of Korea (ROK) and a target-independent high-throughput sequencing method was utilized to study their virome. A total of seven viruses, including six putative novel viral entities, were identified. Genomic analysis showed that the novel viruses were most closely related to members in the orders Jingchuvirales and Bunyavirales. Phylogenetic reconstruction showed that the Bunyavirales-like viruses grouped in the same clade with other viruses within the Nairovirus and Phlebovirus genera, while the novel Jingchuvirales-like virus grouped together with other viruses within the family Chuviridae. Real-time RT-PCR was used to determine the geographic distribution and prevalence of these viruses in adult ticks. These novel viruses have a wide geographic distribution in the ROK with prevalences ranging from 2% to 18%. Our study expands the knowledge about the composition of the tick virome and highlights the wide diversity of viruses they harbor in the ROK. The discovery of novel viruses associated with ticks in the ROK highlights the need for an active tick-borne disease surveillance program to identify possible reservoirs of putative novel human pathogens.
Collapse
Affiliation(s)
- Unai Pérez-Sautu
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; College of Public Health, University of Nebraska Medical Center, Omaha, 68198, Nebraska, USA
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; College of Public Health, University of Nebraska Medical Center, Omaha, 68198, Nebraska, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA
| | - Andrew D Haddow
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, 30144, Georgia, USA
| | - Mariano Sánchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; Department of Pathology & Microbiology, University of Nebraska Medical Centre, Omaha, 68198, Nebraska, USA
| | - Terry A Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea /65(th) Medical Brigade, Unit 15281, APO AP 96271, USA
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea /65(th) Medical Brigade, Unit 15281, APO AP 96271, USA
| | - Sung-Tae Chong
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea /65(th) Medical Brigade, Unit 15281, APO AP 96271, USA
| | - Yu-Jin Kim
- Army Headquarters, Gyeryong-si, 32800, Republic of Korea
| | | | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA
| |
Collapse
|
39
|
Parry R, James ME, Asgari S. Uncovering the Worldwide Diversity and Evolution of the Virome of the Mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms 2021; 9:1653. [PMID: 34442732 PMCID: PMC8398489 DOI: 10.3390/microorganisms9081653] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
Aedes aegypti, the yellow fever mosquito, and Aedes albopictus, the Asian tiger mosquito, are the most significant vectors of dengue, Zika, and Chikungunya viruses globally. Studies examining host factors that control arbovirus transmission demonstrate that insect-specific viruses (ISVs) can modulate mosquitoes' susceptibility to arbovirus infection in both in vivo and in vitro co-infection models. While research is ongoing to implicate individual ISVs as proviral or antiviral factors, we have a limited understanding of the composition and diversity of the Aedes virome. To address this gap, we used a meta-analysis approach to uncover virome diversity by analysing ~3000 available RNA sequencing libraries representing a worldwide geographic range for both mosquitoes. We identified ten novel viruses and previously characterised viruses, including mononegaviruses, orthomyxoviruses, negeviruses, and a novel bi-segmented negev-like group. Phylogenetic analysis suggests close relatedness to mosquito viruses implying likely insect host range except for one arbovirus, the multi-segmented Jingmen tick virus (Flaviviridae) in an Italian colony of Ae. albopictus. Individual mosquito transcriptomes revealed remarkable inter-host variation of ISVs within individuals from the same colony and heterogeneity between different laboratory strains. Additionally, we identified striking virus diversity in Wolbachia infected Aedes cell lines. This study expands our understanding of the virome of these important vectors. It provides a resource for further assessing the ecology, evolution, and interaction of ISVs with their mosquito hosts and the arboviruses they transmit.
Collapse
Affiliation(s)
- Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Maddie E James
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (M.E.J.); (S.A.)
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (M.E.J.); (S.A.)
| |
Collapse
|
40
|
Guo WB, Shi WQ, Wang Q, Pan YS, Chang QC, Jiang BG, Cheng JX, Cui XM, Zhou YH, Wei JT, Sun Y, Jiang JF, Jia N, Cao WC. Distribution of Dermacentor silvarum and Associated Pathogens: Meta-Analysis of Global Published Data and a Field Survey in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094430. [PMID: 33921917 PMCID: PMC8122522 DOI: 10.3390/ijerph18094430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/29/2021] [Accepted: 04/18/2021] [Indexed: 12/30/2022]
Abstract
Dermacentor silvarum is an obligate blood sucking arthropod and transmits various pathogens to humans and domestic animals. Recently several new viruses were detected in D. silvarum as an emerging disease threat. In this study, we aimed to analyze its geographical distribution and associated pathogens. Data were collected from multiple sources, including a field survey, reference book, and literature review. We searched various electronic databases with the terms “Dermacentor silvarum” OR “D. silvarum” for studies published since 1963 and the positive rates for Dermacentor silvarum-associated pathogens were estimated by meta-analysis. D. silvarum was found only in four countries in Eurasia, ranging from 22° N to 57° N latitude. At least 20 human pathogens were associated with D. silvarum, including five species of spotted fever group rickettsiae, three species in the family of Anaplasmataceae, three genospecies in the complex Borrelia burgdorferi sensu lato, Francisella tularensis, Babesia venatorum, Coxiella buenetii, Borrelia miyamotoi, and five species of virus. Among them, Rickettsia raoultii was widely detected in D. silvarum, showing the highest pooled positive rate (25.15%; 95% CI 13.31–39.27). Our work presents the most comprehensive data and analysis (to our knowledge) for the geographical distribution of D. silvarum and associated pathogens, revealing an emerging threat to public health and stocking farming. Continued surveillance and further investigations should be enhanced.
Collapse
Affiliation(s)
- Wen-Bin Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Wen-Qiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yu-Sheng Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Jing-Xia Cheng
- Department of Vector Control, Shanxi Provence Center for Disease Control and Prevention, Taiyuan 030012, China;
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Yu-Hao Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Jia-Te Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
- Correspondence: (N.J.); (W.-C.C.)
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (W.-B.G.); (W.-Q.S.); (Q.W.); (Y.-S.P.); (B.-G.J.); (X.-M.C.); (Y.-H.Z.); (J.-T.W.); (Y.S.); (J.-F.J.)
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Correspondence: (N.J.); (W.-C.C.)
| |
Collapse
|
41
|
Bratuleanu BE, Temmam S, Chrétien D, Regnault B, Pérot P, Bouchier C, Bigot T, Savuța G, Eloit M. The virome of Rhipicephalus, Dermacentor and Haemaphysalis ticks from Eastern Romania includes novel viruses with potential relevance for public health. Transbound Emerg Dis 2021; 69:1387-1403. [PMID: 33840161 DOI: 10.1111/tbed.14105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 12/22/2022]
Abstract
Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The composition of viral communities in ticks and their interactions with pathogens, is poorly understood, particularly in Eastern Europe, an area that represents a major hub for animal-arthropod vectors exchanges (e.g., via bird migrations). The aim of this study was to describe the virome of Dermacentor sp., Rhipicephalus sp. and Haemaphysalis sp. ticks collected from relatively little studied regions of Romania (Iasi and Tulcea counties) located at the intersection of various biotopes, countries and routes of migrations. We also focused the study on viruses that could potentially have relevance for human and animal health. In 2019, more than 500 ticks were collected from the vegetation and from small ruminants and analysed by high-throughput transcriptome sequencing. Among the viral communities infecting Romanian ticks, viruses belonging to the Flaviviridae, Phenuiviridae and Nairoviridae families were identified and full genomes were derived. Phylogenetic analyses placed them in clades where mammalian isolates are found, suggesting that these viruses could constitute novel arboviruses. The characterization of these communities increase the knowledge of the diversity of viruses in Eastern Europe and provides a basis for further studies about the interrelationship between ticks and tick-borne viruses.
Collapse
Affiliation(s)
- Bianca Elena Bratuleanu
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,Regional Center of Advanced Research for Emerging Diseases, Zoonoses and Food Safety (ROVETEMERG), "Ion Ionescu de la Brad", University of Agricultural Sciences and Veterinary Medicine, Iasi, Romania
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France
| | - Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France
| | | | - Thomas Bigot
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - Gheorghe Savuța
- Regional Center of Advanced Research for Emerging Diseases, Zoonoses and Food Safety (ROVETEMERG), "Ion Ionescu de la Brad", University of Agricultural Sciences and Veterinary Medicine, Iasi, Romania
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France.,Department of Pharmaceutical and Biological Sciences, Alfort National Veterinary School, Maisons-Alfort, France
| |
Collapse
|
42
|
Paraskevopoulou S, Käfer S, Zirkel F, Donath A, Petersen M, Liu S, Zhou X, Drosten C, Misof B, Junglen S. Viromics of extant insect orders unveil the evolution of the flavi-like superfamily. Virus Evol 2021; 7:veab030. [PMID: 34026271 PMCID: PMC8129625 DOI: 10.1093/ve/veab030] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insects are the most diversified and species-rich group of animals and harbor an immense diversity of viruses. Several taxa in the flavi-like superfamily, such as the genus Flavivirus, are associated with insects; however, systematic studies on insect virus genetic diversity are lacking, limiting our understanding of the evolution of the flavi-like superfamily. Here, we examined the diversity of flavi-like viruses within the most complete and up-to-date insect transcriptome collection comprising 1,243 insect species by employing a Flaviviridae RdRp profile hidden Markov model search. We identified seventy-six viral sequences in sixty-one species belonging to seventeen insect, one entognathan, and one arachnidan orders. Phylogenetic analyses revealed that twenty-seven sequences fell within the Flaviviridae phylogeny but did not group with established genera. Despite the large diversity of insect hosts studied, we only detected one virus in a blood-feeding insect, which branched within the genus Flavivirus, indicating that this genus likely diversified only in hematophagous arthropods. Nine new jingmenviruses with novel host associations were identified. One of the jingmenviruses established a deep rooting lineage additional to the insect- and tick-associated clades. Segment co-segregation phylogenies support the separation of tick- and insect-associated groups within jingmenviruses, with evidence for segment reassortment. In addition, fourteen viruses grouped with unclassified flaviviruses encompassing genome length of up to 20 kb. Species-specific clades for Hymenopteran- and Orthopteran-associated viruses were identified. Forty-nine viruses populated three highly diversified clades in distant relationship to Tombusviridae, a plant-infecting virus family, suggesting the detection of three previously unknown insect-associated families that contributed to tombusvirus evolution.
Collapse
Affiliation(s)
- Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Simon Käfer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical Center, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Malte Petersen
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 17 Qinghua E Rd, Haidian District, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 17 Qinghua E Rd, Haidian District, Beijing, China
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), partner site Charité, Chariteplatz 1, 10117 Berlin, Germany
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), partner site Charité, Chariteplatz 1, 10117 Berlin, Germany
| |
Collapse
|
43
|
Kholodilov IS, Belova OA, Morozkin ES, Litov AG, Ivannikova AY, Makenov MT, Shchetinin AM, Aibulatov SV, Bazarova GK, Bell-Sakyi L, Bespyatova LA, Bugmyrin SV, Chernetsov N, Chernokhaeva LL, Gmyl LV, Khaisarova AN, Khalin AV, Klimentov AS, Kovalchuk IV, Luchinina SV, Medvedev SG, Nafeev AA, Oorzhak ND, Panjukova EV, Polienko AE, Purmak KA, Romanenko EN, Rozhdestvenskiy EN, Saryglar AA, Shamsutdinov AF, Solomashchenko NI, Trifonov VA, Volchev EG, Vovkotech PG, Yakovlev AS, Zhurenkova OB, Gushchin VA, Karan LS, Karganova GG. Geographical and Tick-Dependent Distribution of Flavi-Like Alongshan and Yanggou Tick Viruses in Russia. Viruses 2021; 13:458. [PMID: 33799742 PMCID: PMC7998622 DOI: 10.3390/v13030458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
The genus Flavivirus includes related, unclassified segmented flavi-like viruses, two segments of which have homology with flavivirus RNA-dependent RNA polymerase NS5 and RNA helicase-protease NS3. This group includes such viruses as Jingmen tick virus, Alongshan virus, Yanggou tick virus and others. We detected the Yanggou tick virus in Dermacentor nuttalli and Dermacentor marginatus ticks in two neighbouring regions of Russia. The virus prevalence ranged from 0.5% to 8.0%. We detected RNA of the Alongshan virus in 44 individuals or pools of various tick species in eight regions of Russia. The virus prevalence ranged from 0.6% to 7.8%. We demonstrated the successful replication of the Yanggou tick virus and Alongshan virus in IRE/CTVM19 and HAE/CTVM8 tick cell lines without a cytopathic effect. According to the phylogenetic analysis, we divided the Alongshan virus into two groups: an Ixodes persulcatus group and an Ixodes ricinus group. In addition, the I. persulcatus group can be divided into European and Asian subgroups. We found amino acid signatures specific to the I. ricinus and I. persulcatus groups and also distinguished between the European and Asian subgroups of the I. persulcatus group.
Collapse
Affiliation(s)
- Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Evgeny S. Morozkin
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Alexander G. Litov
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Anna Y. Ivannikova
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Marat T. Makenov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Alexey M. Shchetinin
- Pathogenic Microorganisms Variability Laboratory, Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.M.S.); (V.A.G.)
| | - Sergey V. Aibulatov
- Laboratory of Parasitic Arthropods, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (S.V.A.); (A.V.K.); (S.G.M.)
| | - Galina K. Bazarova
- Laboratory of Bacteriology, Altai Antiplague Station of Rospotrebnadzor, 649000 Gorno-Altaisk, Russia;
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK;
| | - Liubov A. Bespyatova
- Laboratory for Animal and Plant Parasitology, Institute of Biology of Karelian Research Centre, Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (L.A.B.); (S.V.B.)
| | - Sergey V. Bugmyrin
- Laboratory for Animal and Plant Parasitology, Institute of Biology of Karelian Research Centre, Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (L.A.B.); (S.V.B.)
| | - Nikita Chernetsov
- Laboratory of Ornithology, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Department of Vertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Liubov L. Chernokhaeva
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Anna N. Khaisarova
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, 432005 Ulyanovsk, Russia; (A.N.K.); (A.A.N.); (P.G.V.)
| | - Alexei V. Khalin
- Laboratory of Parasitic Arthropods, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (S.V.A.); (A.V.K.); (S.G.M.)
| | - Alexander S. Klimentov
- Laboratory of Biochemistry, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia;
- Laboratory of Biology and Indication of Arboviruses, Department Ivanovsky Institute of Virology, Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Irina V. Kovalchuk
- Office of Rospotrebnadzor in the Stavropol Territory, 355008 Stavropol, Russia; (I.V.K.); (N.I.S.)
- Stavropol State Medical University, 355017 Stavropol, Russia
| | | | - Sergey G. Medvedev
- Laboratory of Parasitic Arthropods, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (S.V.A.); (A.V.K.); (S.G.M.)
| | - Alexander A. Nafeev
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, 432005 Ulyanovsk, Russia; (A.N.K.); (A.A.N.); (P.G.V.)
| | | | - Elena V. Panjukova
- Institute of Biology, Komi Science Center, Ural Branch of Russian Academy of Sciences, 167982 Syktyvkar, Russia;
| | - Alexandra E. Polienko
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Kristina A. Purmak
- FBIH “Center for Hygiene and Epidemiology in the Stavropol kray”, 355008 Stavropol, Russia; (K.A.P.); (E.N.R.)
| | - Evgeniya N. Romanenko
- FBIH “Center for Hygiene and Epidemiology in the Stavropol kray”, 355008 Stavropol, Russia; (K.A.P.); (E.N.R.)
| | | | - Anna A. Saryglar
- Infectious Disease Hospital, 667003 Kyzyl, Russia; (N.D.O.); (A.A.S.)
| | - Anton F. Shamsutdinov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, 420015 Kazan, Russia; (A.F.S.); (V.A.T.)
| | - Nataliya I. Solomashchenko
- Office of Rospotrebnadzor in the Stavropol Territory, 355008 Stavropol, Russia; (I.V.K.); (N.I.S.)
- FBIH “Center for Hygiene and Epidemiology in the Stavropol kray”, 355008 Stavropol, Russia; (K.A.P.); (E.N.R.)
| | - Vladimir A. Trifonov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, 420015 Kazan, Russia; (A.F.S.); (V.A.T.)
- Kazan State Medical Academy—Branch Campus of the FSBEI FPE «Russian Medical Academy of Continuous Postgraduate Education» of the Ministry of Healthcare of the Russian Federation, 420012 Kazan, Russia
| | - Evgenii G. Volchev
- Institute of Living Systems Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia;
| | - Pavel G. Vovkotech
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, 432005 Ulyanovsk, Russia; (A.N.K.); (A.A.N.); (P.G.V.)
| | - Alexander S. Yakovlev
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Olga B. Zhurenkova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Vladimir A. Gushchin
- Pathogenic Microorganisms Variability Laboratory, Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.M.S.); (V.A.G.)
- Faculty of Biology, Lomonosov MSU, 119991 Moscow, Russia
| | - Lyudmila S. Karan
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
- Institute for Translational Medicine and Biotechnology, Sechenov University, 119146 Moscow, Russia
| |
Collapse
|
44
|
Meta-Transcriptomic Analysis Reveals the Virome and Viral Genomic Evolution of Medically Important Mites. J Virol 2021; 94:JVI.01686-20. [PMID: 33208452 PMCID: PMC8092686 DOI: 10.1128/jvi.01686-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Mites are notorious for being vectors transmitting infectious pathogens and source of allergens causing allergic conditions in animals and humans. However, despite their huge impact on public health, the virome of mites remains unknown. Here we characterized the virus diversity and abundance of 14 species of medically important mites based on total RNA sequencing data sets generated in this study as well as those deposited in the Sequence Read Archive (SRA) database. A total of 47 genetically distinct viruses were identified and classified into 17 virus families or virus super-groups, and the viral sequences accounted for as much as 29.67% of total non-rRNA transcriptome in one mite library. The most commonly identified viruses are members of Picornavirales, among which we revealed more than one type of viruses that are evolutionarily related to dicistronic viruses but contain a single open reading frame, thus likely representing a recent example of host (i.e., mite)-related parallel evolution from dicistronic to monocistronic genomic form within the family Dicistroviridae To our best knowledge, this is the first time to perform comprehensive and systematic screening of RNA virome in medically important mites including house dust mites (HDM). Overall, the RNA virome identified here provides not only significant insights into the diversity and evolution of RNA viruses in mites, but also a solid knowledge base for studying their roles in human diseases.IMPORTANCE Mites are important group of arthropods that are associated with a variety of human diseases including scrub typhus and asthma. However, it remains unclear whether or not mites carry viruses that might play a role in human infections or allergic disease. In this study, we used a total transcriptomics approach to characterize and compare the complete RNA virome within mites that are relevant to human health and diseases. Specifically, our data revealed a large diversity, a high abundance, and a flexible genomic evolution for these viruses. Although most of the viruses identified here are unknown to associate with human infectious disease, the abundant presence of viral RNAs may play an immunomodulatory role in the development of allergic reactions such as asthma during environmental exposure to mite allergens, and therefore provide important insights into the mite-induced allergy and preparation of mite allergen vaccines.
Collapse
|
45
|
Yang J, Jing X, Yi W, Li XD, Yao C, Zhang B, Zheng Z, Wang H, Gong P. Crystal structure of a tick-borne flavivirus RNA-dependent RNA polymerase suggests a host adaptation hotspot in RNA viruses. Nucleic Acids Res 2021; 49:1567-1580. [PMID: 33406260 PMCID: PMC7897508 DOI: 10.1093/nar/gkaa1250] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 01/07/2023] Open
Abstract
The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By solving the RdRP crystal structure of the tick-borne encephalitis virus (TBEV), a tick-borne flavivirus, and comparing the structural and sequence features with mosquito-borne flavivirus RdRPs, we found that a region between RdRP catalytic motifs B and C, namely region B-C, clearly bears host-related diversity. Inter-virus substitutions of region B-C sequence were designed in both TBEV and mosquito-borne Japanese encephalitis virus backbones. While region B-C substitutions only had little or moderate effect on RdRP catalytic activities, virus proliferation was not supported by these substitutions in both virus systems. Importantly, a TBEV replicon-derived viral RNA replication was significantly reduced but not abolished by the substitution, suggesting the involvement of region B-C in viral and/or host processes beyond RdRP catalysis. A systematic structural analysis of region B-C in viral RdRPs further emphasizes its high level of structure and length diversity, providing a basis to further refine its relevance in RNA virus-host interactions in a general context.
Collapse
Affiliation(s)
| | | | - Wenfu Yi
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, Hubei 430071, China
| | - Xiao-Dan Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, Hubei 430071, China
| | - Chen Yao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Correspondence may also be addressed to Bo Zhang.
| | - Zhenhua Zheng
- Correspondence may also be addressed to Zhenhua Zheng.
| | | | - Peng Gong
- To whom correspondence should be addressed. Tel: +86 27 87197578; Fax: +86 27 87197578;
| |
Collapse
|
46
|
Ergünay K, Polat C, Özkul A. Vector-borne viruses in Turkey: A systematic review and bibliography. Antiviral Res 2020; 183:104934. [PMID: 32949637 DOI: 10.1016/j.antiviral.2020.104934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 11/25/2022]
Abstract
Turkey serves as a natural hub for the dissemination of vector-borne viruses and provides many suitable habitats with diverse ecologies for introduction and establishment of new pathogens. This manuscript provides an updated systematic review and meta-analysis of the vector-borne viruses documented in Turkey. Following web-based identification, screening and eligibility evaluation, 291 published reports were reviewed. The publications were categorized and listed as a supplementary bibliography accompanying the manuscript. In brief, Crimean-Congo hemorrhagic fever virus (CCHFV) and West Nile virus (WNV) are currently documented as prominent tick and mosquito-borne viral pathogens in Turkey. CCHFV produces a significant number of infections annually, with severe outcome or death in a portion of cases. WNV gained attention following the clustering of cases in 2010. Exposure and infections with sandfly-borne phleboviruses, such as Toscana virus, are indigenous and widespread. Epidemiology, risk factors, symptomatic infections in susceptible hosts, vectors and reservoirs for these pathogens have been explored in detail. Detection of novel viruses in mosquitoes, sandflies and ticks from several regions is of particular interest, despite scarce information on their epidemiology and pathogenicity in vertebrates. Introduction and emergence of viruses transmitted by invasive Aedes mosquitoes constitute a threat, albeit only imported infections have so far been documented. Detection of Rift valley fever virus exposure is also of concern, due to its detrimental effects on livestock and spillover infections in humans. Vigilance to identify and diagnose probable cases as well as vector surveillance for established and potential pathogens is therefore, imperative.
Collapse
Affiliation(s)
- Koray Ergünay
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, 06100, Turkey.
| | - Ceylan Polat
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, 06100, Turkey
| | - Aykut Özkul
- Ankara University, Faculty of Veterinary Medicine, Department of Virology, Ankara, 06110, Turkey
| |
Collapse
|
47
|
Stanojević M, Li K, Stamenković G, Ilić B, Paunović M, Pešić B, Maslovara IĐ, Šiljić M, Ćirković V, Zhang Y. Depicting the RNA Virome of Hematophagous Arthropods from Belgrade, Serbia. Viruses 2020; 12:v12090975. [PMID: 32887342 PMCID: PMC7552015 DOI: 10.3390/v12090975] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 01/21/2023] Open
Abstract
Hematophagous arthropods are important vectors for zoonotic pathogens. To date, a huge number of viruses have been identified in these arthropods, with a considerable proportion of them being human pathogens. However, the viromes of hematophagous arthropods are still largely unresearched. In this study, a number of arthropods were collected from Belgrade, Serbia including mosquitoes, ticks and bedbugs. The viromes of these arthropods were identified and characterized using Illumina MiSeq sequencing. In total, 21 viruses belonging to 11 families were characterized, with 11 of them representing novel species. These results may contribute to our knowledge of RNA viruses in arthropods and the discovery of novel human pathogens.
Collapse
Affiliation(s)
- Maja Stanojević
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, 11000 Belgrade, Serbia; (M.S.); (M.Š.); (V.C.)
| | - Kun Li
- Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing 102206, China;
| | - Gorana Stamenković
- Department for Genetic Research, Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia;
| | - Bojan Ilić
- Department of Animal Development, Faculty of Biology, Institute of Zoology, University of Belgrade, 11000 Belgrade, Serbia;
| | - Milan Paunović
- Natural History Museum in Belgrade, 11000 Belgrade, Serbia;
| | - Branislav Pešić
- Institute for Biocides and Medical Ecology, 11000 Belgrade, Serbia; (B.P.); (I.Đ.M.)
| | - Ivana Đurić Maslovara
- Institute for Biocides and Medical Ecology, 11000 Belgrade, Serbia; (B.P.); (I.Đ.M.)
| | - Marina Šiljić
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, 11000 Belgrade, Serbia; (M.S.); (M.Š.); (V.C.)
| | - Valentina Ćirković
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, 11000 Belgrade, Serbia; (M.S.); (M.Š.); (V.C.)
| | - Yongzhen Zhang
- Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing 102206, China;
- Shanghai Public Health Clinical Center & Institute of Biomedical Sciences, Fudan University, Shanghai 200432, China
- Correspondence:
| |
Collapse
|
48
|
Guo JJ, Lin XD, Chen YM, Hao ZY, Wang ZX, Yu ZM, Lu M, Li K, Qin XC, Wang W, Holmes EC, Hou W, Zhang YZ. Diversity and circulation of Jingmen tick virus in ticks and mammals. Virus Evol 2020; 6:veaa051. [PMID: 33976906 PMCID: PMC8097133 DOI: 10.1093/ve/veaa051] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents, and primates. To better understand the diversity, evolution, and transmission of JMTV, we sampled 215 ticks, 104 cattle bloods, 216 bats, and 119 rodents in Wenzhou city, Zhejiang Province, China as well as 240 bats from Guizhou and Henan Provinces. JMTV was identified in 107 ticks (from two species), 54 bats (eleven species), 8 rodents (three species), and 10 cattle, with prevalence levels of 49.8, 11.8, 6.7, and 9.6 per cent, respectively, suggesting that bats may be a natural reservoir of JMTV. Phylogenetic analyses revealed that all the newly identified JMTVs were closely related to each other and to previously described viruses. Additionally, all tick and mammalian JMTV sampled in Wenzhou shared a consistent genomic structure, suggesting that the virus can cocirculate between ticks and mammals without observable variation in genome organization. All JMTVs sampled globally could be divided into two phylogenetic groups, Mantel tests suggested that geographic isolation, rather than host species, may be the main driver of JMTV diversity. However, the exact geographical origin of JMTV was difficult to determine, suggesting that this virus has a complex evolutionary history.
Collapse
Affiliation(s)
- Jing-Jing Guo
- State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, 325001,China
| | - Yan-Mei Chen
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, 201052, China
| | - Zong-Yu Hao
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, 450000, China
| | - Zhao-Xiao Wang
- GGuizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, 550000, China and
| | - Zhu-Mei Yu
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Miao Lu
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Kun Li
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xin-Cheng Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, 201052, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Wei Hou
- State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yong-Zhen Zhang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, 201052, China
| |
Collapse
|
49
|
Yu ZM, Chen JT, Qin J, Guo JJ, Li K, Xu QY, Wang W, Lu M, Qin XC, Zhang YZ. Identification and characterization of Jingmen tick virus in rodents from Xinjiang, China. INFECTION GENETICS AND EVOLUTION 2020; 84:104411. [PMID: 32531517 PMCID: PMC7283072 DOI: 10.1016/j.meegid.2020.104411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 05/30/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022]
Abstract
Jingmen tick virus (JMTV) is a recently identified virus which provides an unexpected connection between segmented and unsegmented RNA viruses. Recent investigations reveal that JMTV including JMTV-like virus (Alongshan virus) could be associated with human disease, suggesting the significance of JMTV in public health. To better understand the genetic diversity and host range of JMTV, a total of 164 rodents representing 8 species were collected in Qapqal Xibe county of Xinjiang Uygur Autonomous Region, China, and were screened for JMTVs using RT- PCR. Consequently, JMTV was identified in 42 rodents including 23 Microtus arvalis voles (24.5%), 9 Apodemus uralensis mice (29.0%), 5 Mus musculus mice, 1 Rhombomys opimus gerbil, 1 Meriones tamariscinus gerbil, 1 Meriones libycus gerbil, 1 Cricetulus migratorius hamster and 1 Microtus gregalis vole. Interestingly, nearly complete genome sequences were successfully recovered from 7 JMTV positive samples. Although the newly identified rodent JMTVs were closely related to those previously identified in ticks from China, based on the phylogenetic analysis of the S1, S2 and S3 segments, the newly identified rodent viruses clustered into two genetic groups. One group comprised of viruses only found in M. arvalis, while another group included viruses from A. uralensis, C. migratorius and M. gregalis. However, all rodent viruses clustered together in the S4 tree. Considering rodents live in close proximity to humans, more efforts are needed to investigate the role of rodents in the evolution and transmission of JMTV in nature. Jingmen tick virus (JMTV) was found in 8 species of rodents from Xinjiang of China. Two sub-lineages of JMTVs were co-circulating in these rodents in Xinjiang. One sub-lineage of viruses was only identified in Microtus arvalis voles. Our data indicate that rodents are one of the natural hosts of JMTV.
Collapse
Affiliation(s)
- Zhu-Mei Yu
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Jin-Tao Chen
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Jing Qin
- Yili Prefecture Center for Disease Control and Prevention, Yili 835000, China
| | - Jing-Jing Guo
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Kun Li
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Qi-Yi Xu
- Yili Prefecture Center for Disease Control and Prevention, Yili 835000, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Miao Lu
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Xin-Cheng Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Yong-Zhen Zhang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Shanghai Public Health Clinical Center, Institute of Biomedical Science, Fudan University, Shanghai, China.
| |
Collapse
|
50
|
Kondo H, Fujita M, Hisano H, Hyodo K, Andika IB, Suzuki N. Virome Analysis of Aphid Populations That Infest the Barley Field: The Discovery of Two Novel Groups of Nege/Kita-Like Viruses and Other Novel RNA Viruses. Front Microbiol 2020; 11:509. [PMID: 32318034 PMCID: PMC7154061 DOI: 10.3389/fmicb.2020.00509] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Aphids (order Hemiptera) are important insect pests of crops and are also vectors of many plant viruses. However, little is known about aphid-infecting viruses, particularly their diversity and relationship to plant viruses. To investigate the aphid viromes, we performed deep sequencing analyses of the aphid transcriptomes from infested barley plants in a field in Japan. We discovered virus-like sequences related to nege/kita-, flavi-, tombus-, phenui-, mononega-, narna-, chryso-, partiti-, and luteoviruses. Using RT-PCR and sequence analyses, we determined almost complete sequences of seven nege/kitavirus-like virus genomes; one of which was a variant of the Wuhan house centipede virus (WHCV-1). The other six seem to belong to four novel viruses distantly related to Wuhan insect virus 9 (WhIV-9) or Hubei nege-like virus 4 (HVLV-4). We designated the four viruses as barley aphid RNA virus 1 to 4 (BARV-1 to -4). Moreover, some nege/kitavirus-like sequences were found by searches on the transcriptome shotgun assembly (TSA) libraries of arthropods and plants. Phylogenetic analyses showed that BARV-1 forms a clade with WHCV-1 and HVLV-4, whereas BARV-2 to -4 clustered with WhIV-9 and an aphid virus, Aphis glycines virus 3. Both virus groups (tentatively designated as Centivirus and Aphiglyvirus, respectively), together with arthropod virus-like TSAs, fill the phylogenetic gaps between the negeviruses and kitaviruses lineages. We also characterized the flavi/jingmen-like and tombus-like virus sequences as well as other RNA viruses, including six putative novel viruses, designated as barley aphid RNA viruses 5 to 10. Interestingly, we also discovered that some aphid-associated viruses, including nege/kita-like viruses, were present in different aphid species, raising a speculation that these viruses might be distributed across different aphid species with plants being the reservoirs. This study provides novel information on the diversity and spread of nege/kitavirus-related viruses and other RNA viruses that are associated with aphids.
Collapse
Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| |
Collapse
|