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Rosani U, Sollitto M, Fogal N, Salata C. Comparative analysis of Presence-Absence gene Variations in five hard tick species: impact and functional considerations. Int J Parasitol 2024; 54:147-156. [PMID: 37806426 DOI: 10.1016/j.ijpara.2023.08.004] [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: 01/25/2023] [Revised: 08/06/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023]
Abstract
Tick species are vectors of harmful human and animal diseases, and their expansion is raising concerns under the global environmental changes' scenario. Ticks host and transmit bacteria, protozoa and viruses, making the understanding of host-pathogen molecular pathways critical to development of effective disease control strategies. Despite the considerable sizes and repeat contents of tick genomes, individual tick genomics is perhaps the most effective approach to reveal genotypic traits of interest. Presence-Absence gene Variations (PAVs) can contribute to individual differences within species, with dispensable genes carried by subsets of individuals possibly underpinning functional significance at individual or population-levels. We exploited 350 resequencing datasets of Dermacentor silvarum, Haemaphysalis longicornis, Ixodes persulcatus, Rhipicephalus microplus and Rhipicephalus sanguineus hard tick specimens to reveal the extension of PAV and the conservation of dispensable genes among individuals and, comparatively, between species. Overall, we traced 550-3,346 dispensable genes per species and were able to reconstruct 5.3-7 Mb of genomic regions not included in the respective reference genomes, as part of the tick pangenomes. Both dispensable genes and de novo predicted genes indicated that PAVs preferentially impacted mobile genetic elements in these tick species.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Marco Sollitto
- Department of Life Science, University of Trieste, 34100 Trieste, Italy; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Nicolò Fogal
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
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Xu X, Gao Z, Wu Y, Yin H, Ren Q, Zhang J, Liu Y, Yang S, Bayasgalan C, Tserendorj A, Yang X, Chen Z. Discovery and vertical transmission analysis of Dabieshan Tick Virus in Haemaphysalis longicornis ticks from Chengde, China. Front Microbiol 2024; 15:1365356. [PMID: 38468853 PMCID: PMC10925692 DOI: 10.3389/fmicb.2024.1365356] [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: 01/04/2024] [Accepted: 02/01/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Ticks are important blood-sucking ectoparasites that can transmit various pathogens, posing significant threats to the wellbeing of humans and livestock. Dabieshan tick virus (DBTV) was initially discovered in 2015 in Haemaphysalis longicornis ticks from the Dabieshan mountain region in Hubei Province, China. In recent years, DBTV has been discovered in various regions of China, including Shandong, Zhejiang, Liaoning, Hubei, Yunnan, and Guizhou Provinces. However, the researches on tick-borne transmission of DBTV are scarce. Methods This study utilized the small RNA sequencing (sRNA-seq) method to identify tick-associated viruses in ticks collected from Chengde in Hebei Province and Yongcheng in Henan Province, leading to the discovery of a new DBTV strain in Hebei. The complete coding genome of DBTV Hebei strain was obtained through RNA-seq and Sanger sequencing. Furthermore, the transmission experiment of DBTV in H. longicornis was examined in laboratory for the first time. Results DBTV was detected in newly molted adult H. longicornis ticks collected in Chengde, Hebei Province. Additionally, DBTV was also detected in both unfed nymphs and engorged females of H. longicornis collected from Chengde, with a positive rate of 20% and 56.25%, respectively. The complete coding genome of DBTV (OP682840 and OP716696) were obtained, and phylogenetic analysis revealed that the DBTV Hebei strain clustered with previously reported DBTV strains. Furthermore, this virus was observed in engorged females, eggs, and larvae of the subsequent generation. Discussion It is necessary to expand the scope of DBTV investigation, particularly in northern China. This study demonstrated that DBTV can be transmitted from engorged females to larvae of the next generation. Moreover, the detection of DBTV in unfed nymphs and adults (which moulted from engorged nymphs) collected from the filed of Chengde suggests that H. longicornis serves as a potential transmission host and reservoir for DBTV through transstadial and transovarial transmission. However, there remains a lack of research on the isolation and pathogenicity of DBTV, highlighting the need for further studies to mitigate potential harm to the health of animals and humans.
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Affiliation(s)
- Xiaofeng Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhihua Gao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Youhong Wu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hong Yin
- State Key Laboratory of Animal Disease Prevention and Control, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Qiaoyun Ren
- State Key Laboratory of Animal Disease Prevention and Control, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Jie Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yongsheng Liu
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Shunli Yang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | | | - Ariunaa Tserendorj
- School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | - Xiaolong Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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3
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Ye RZ, Li YY, Xu DL, Wang BH, Wang XY, Zhang MZ, Wang N, Gao WY, Li C, Han XY, Du LF, Xia LY, Song K, Xu Q, Liu J, Cheng N, Li ZH, Du YD, Yu HJ, Shi XY, Jiang JF, Sun Y, Cui XM, Ding SJ, Zhao L, Cao WC. Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis. MICROBIOME 2024; 12:35. [PMID: 38378577 PMCID: PMC10880243 DOI: 10.1186/s40168-024-01753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Haemaphysalis longicornis is drawing attentions for its geographic invasion, extending population, and emerging disease threat. However, there are still substantial gaps in our knowledge of viral composition in relation to genetic diversity of H. longicornis and ecological factors, which are important for us to understand interactions between virus and vector, as well as between vector and ecological elements. RESULTS We conducted the meta-transcriptomic sequencing of 136 pools of H. longicornis and identified 508 RNA viruses of 48 viral species, 22 of which have never been reported. Phylogenetic analysis of mitochondrion sequences divided the ticks into two genetic clades, each of which was geographically clustered and significantly associated with ecological factors, including altitude, precipitation, and normalized difference vegetation index. The two clades showed significant difference in virome diversity and shared about one fifth number of viral species that might have evolved to "generalists." Notably, Bandavirus dabieense, the pathogen of severe fever with thrombocytopenia syndrome was only detected in ticks of clade 1, and half number of clade 2-specific viruses were aquatic-animal-associated. CONCLUSIONS These findings highlight that the virome diversity is shaped by internal genetic evolution and external ecological landscape of H. longicornis and provide the new foundation for promoting the studies on virus-vector-ecology interaction and eventually for evaluating the risk of H. longicornis for transmitting the viruses to humans and animals. Video Abstract.
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Affiliation(s)
- Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yu-Yu Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Da-Li Xu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Department of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China
| | - Bai-Hui Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Yang Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ke Song
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Qing Xu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Jing Liu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Nuo Cheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Ze-Hui Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Yi-Di Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Hui-Jun Yu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiao-Yu Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
| | - Shu-Jun Ding
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Department of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China.
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China.
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
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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.
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Affiliation(s)
| | - Dana C. Price
- Center for Vector Biology, Department of Entomology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA;
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5
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Cai X, Cai X, Xu Y, Shao Y, Fu L, Men X, Zhu Y. Virome analysis of ticks and tick-borne viruses in Heilongjiang and Jilin Provinces, China. Virus Res 2023; 323:199006. [PMID: 36414189 PMCID: PMC10194156 DOI: 10.1016/j.virusres.2022.199006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
Abstract
Ticks transmit diverse human and animal pathogens, leading to an increasing number of public health concerns. In the forest area of northeast China, the spread of tick-borne diseases (TBDs) is severe; however, little is known about the tick virome composition and evolution. Herein, we investigate the geographical distribution of tick species and related viruses in Heilongjiang and Jilin Provinces in Northeast China. To reveal the diversity of tick-borne viruses in parts of Heilongjiang and Jilin, ticks were collected at 9 collection points in these provinces in 2018. Morphology and molecular biology were used to identify tick species, and 1411 ticks from nine sampling sites were collected and analysed by next-generation sequencing (NGS). Four Ixodidae were identified, including Ixodes persulcatus, Haemaphysalis japonica, Dermacentor silvarum, and Haemaphysalis concinna. After removal of host genome sequences, 13,003 high-quality NGS reads were obtained and annotated as viruses. Further phylogenetic analysis based on amplicons revealed that these viral sequences belong to Beiji nairovirus, Alongshan virus, bovine parvovirus-2, and tick-associated circovirus; some distinct sequences are closely related to Songling virus, Changping tick virus, Norway luteo-like virus 2, and Norway partiti-like virus 1. In summary, this study describes the prevalence of local ticks and variety of tick-borne viruses in northeastern China, providing a basis for further research on tick-borne viruses in the future.
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Affiliation(s)
- Xianglong Cai
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Xiaojing Cai
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Yongkang Xu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Yi Shao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Lian Fu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Xiaoyu Men
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Yan Zhu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China.
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Bai Y, Li Y, Liu W, Li J, Tian F, Liu L, Han X, Tong Y. Analysis of the diversity of tick-borne viruses at the border areas in Liaoning Province, China. Front Microbiol 2023; 14:1179156. [PMID: 37200913 PMCID: PMC10187663 DOI: 10.3389/fmicb.2023.1179156] [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: 04/05/2023] [Indexed: 05/20/2023] Open
Abstract
Ticks play a significant role in transmitting arboviruses, which pose a risk to human and animal health. The region of Liaoning Province, China, with abundant plant resources with multiple tick populations, has reported several tick-borne diseases. However, there remains a scarcity of research on the composition and evolution of the tick virome. In this study, we conducted the metagenomic analysis of 561 ticks in the border area of Liaoning Province in China and identified viruses related to known diseases in humans and animals, including severe fever with thrombocytopenia syndrome virus (SFTSV) and nairobi sheep disease virus (NSDV). Moreover, the groups of tick viruses were also closely related to the families of Flaviviridae, Parvoviridae, Phenuiviridae, and Rhabdoviridae. Notably, the Dabieshan tick virus (DBTV) of the family Phenuiviridae was prevalent in these ticks, with the minimum infection rate (MIR) of 9.09%, higher than previously reported in numerous provinces in China. In addition, sequences of tick-borne viruses of the family Rhabdoviridae have first been reported from the border area of Liaoning Province, China, after being described from Hubei Province, China. This research furthered the insight into pathogens carried by ticks in the northeastern border areas of China, offering epidemiological information for possible forthcoming outbreaks of infectious diseases. Meanwhile, we provided an essential reference for assessing the risk of tick bite infection in humans and animals, as well as for exploring into the evolution of the virus and the mechanisms of species transmission.
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Affiliation(s)
- Yu Bai
- Jiamusi University School of Basic Medicine, Jiamusi, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yang Li
- Jiamusi University School of Basic Medicine, Jiamusi, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wenli Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fengjuan Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lei Liu
- Jiamusi University School of Basic Medicine, Jiamusi, China
- *Correspondence: Lei Liu,
| | - Xiaohu Han
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
- Xiaohu Han,
| | - Yigang Tong
- Jiamusi University School of Basic Medicine, Jiamusi, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Yigang Tong,
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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.
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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)
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8
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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Guo L, Ma J, Lin J, Chen M, Liu W, Zha J, Jin Q, Hong H, Huang W, Zhang L, Zhang K, Wei Z, Liu Q. Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China. Front Microbiol 2022; 13:966735. [PMID: 36033874 PMCID: PMC9403862 DOI: 10.3389/fmicb.2022.966735] [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: 06/11/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
Tick-borne viruses (TBVs) have increasingly caused a global public health concern. This study collected Rhipicephalus ticks in Guangdong, southern China to identify RNA viruses. Meta-transcriptome analysis revealed the virome in Rhipicephalus ticks, resulting in the discovery of 10 viruses, including Lihan tick virus, Brown dog tick phlebovirus 1 and 2 in the family Phenuiviridae, Mivirus and Wuhan tick virus 2 in the family Chuviridae, Wuhan tick virus 1 in the family Rhabdoviridae, bovine hepacivirus in the family Flaviviridae, Guangdong tick quaranjavirus (GTQV) in the family Orthomyxoviridae, Guangdong tick orbivirus (GTOV) in the family Reoviridae, and Guangdong tick Manly virus (GTMV) of an unclassified family. Phylogenetic analysis showed that most of these TBVs were genetically related to the strains in countries outside China, and GTQV, GTOV, and GTMV may represent novel viral species. These findings provided evidence of the long-distance spread of these TBVs in Guangdong, southern China, suggesting the necessity and importance of TBV surveillance.
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Affiliation(s)
- Luanying Guo
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jun Ma
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Junwei Lin
- Jieyang Animal Health Supervision Institute, Jieyang, China
| | - Meiyi Chen
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Wei Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jin Zha
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Qinqin Jin
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Hongrong Hong
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Weinan Huang
- Agricultural and Rural Bureau of Huilai County, Jieyang, China
| | - Li Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Ketong Zhang
- Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhengkai Wei
- School of Life Sciences and Engineering, Foshan University, Foshan, China
- Zhengkai Wei,
| | - Quan Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
- Center for Infectious Diseases and Pathogen Biology, International Center of Future Science, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital, Jilin University, Changchun, China
- *Correspondence: Quan Liu,
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10
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Detection of Gyrovirus galga 1 in Cryopreserved Organs from Two Commercial Broiler Flocks in Japan. Viruses 2022; 14:v14071590. [PMID: 35891569 PMCID: PMC9319249 DOI: 10.3390/v14071590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Gyrovirus galga 1 (GyVg1, previously recognized as avian gyrovirus 2), which was first reported in chicken in 2011, is a new member of the genus Gyrovirus. The presence of GyVg1 has also been confirmed in different regions of Europe, South America, Africa, and Asia, indicating its global distribution. However, because there are no reports of examining the distribution of GyVg1 in animals in Japan, the epidemiology of this virus is unknown. In this study, we attempted to retrospectively detect GyVg1 in cryopreserved chicken materials derived from different two commercial broiler flocks in 1997. The GyVg1 genome was detected in organ materials derived from both flocks by PCR. GyVg1 detected in both flocks was classified into four genetic groups by analyzing the nucleotide sequences of the detected PCR products. These results suggest that diverse GyVg1 strains were present in commercial chicken flocks as early as 1997 in Japan.
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