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Bakker JW, Esser HJ, Sprong H, Godeke GJ, Hoornweg TE, de Boer WF, Pijlman GP, Koenraadt CJM. Differential susceptibility of geographically distinct Ixodes ricinus populations to tick-borne encephalitis virus and louping ill virus. Emerg Microbes Infect 2024; 13:2321992. [PMID: 38484290 PMCID: PMC10946273 DOI: 10.1080/22221751.2024.2321992] [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] [Indexed: 03/19/2024]
Abstract
Tick-borne encephalitis virus (TBEV) is an emerging pathogen in the Netherlands. Multiple divergent viral strains are circulating and the focal distribution of TBEV remains poorly understood. This may, however, be explained by differences in the susceptibility of tick populations for specific viruses and viral strains, and by viral strains having higher infection success in their local tick population. We investigated this hypothesis by exposing Dutch Ixodes ricinus ticks to two different TBEV strains: TBEV-NL from the Netherlands and TBEV-Neudoerfl from Austria. In addition, we exposed ticks to louping Ill virus (LIV), which is endemic to large parts of the United Kingdom and Ireland, but has not been reported in the Netherlands. Ticks were collected from two locations in the Netherlands: one location without evidence of TBEV circulation and one location endemic for the TBEV-NL strain. Ticks were infected in a biosafety level 3 laboratory using an artificial membrane feeding system. Ticks collected from the region without evidence of TBEV circulation had lower infection rates for TBEV-NL as compared to TBEV-Neudoerfl. Vice versa, ticks collected from the TBEV-NL endemic region had higher infection rates for TBEV-NL compared to TBEV-Neudoerfl. In addition, LIV infection rates were much lower in Dutch ticks compared to TBEV, which may explain why LIV is not present in the Netherlands. Our findings show that ticks from two distinct geographical populations differ in their susceptibility to TBEV strains, which could be the result of differences in the genetic background of the tick populations.
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Affiliation(s)
- Julian W. Bakker
- Laboratory of Entomology, Wageningen University & Research, Wageningen, Netherlands
| | - Helen J. Esser
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, Netherlands
| | - Hein Sprong
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Gert-Jan Godeke
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Tabitha E. Hoornweg
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Willem F. de Boer
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, Netherlands
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Martyn C, Hayes BM, Lauko D, Midthun E, Castaneda G, Bosco-Lauth A, Salkeld DJ, Kistler A, Pollard KS, Chou S. Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements. mSystems 2024; 9:e0032124. [PMID: 38742892 DOI: 10.1128/msystems.00321-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks. IMPORTANCE Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.
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Affiliation(s)
- Calla Martyn
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
- Gladstone Institute of Data Science & Biotechnology, San Francisco, California, USA
| | - Beth M Hayes
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
- One Health Institute, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Domokos Lauko
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
| | - Edward Midthun
- Department of Biomedical Sciences, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Gloria Castaneda
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
| | - Angela Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Daniel J Salkeld
- Department of Biology, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science & Biotechnology, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
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3
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Pei T, Zhang M, Gao Z, Li L, Bing Z, Meng J, Nwanade CF, Yuan C, Yu Z, Liu J. Molecular characterization and induced changes of histone acetyltransferases in the tick Haemaphysalis longicornis in response to cold stress. Parasit Vectors 2024; 17:218. [PMID: 38735919 PMCID: PMC11089763 DOI: 10.1186/s13071-024-06288-4] [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: 02/02/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Epigenetic modifications of histones play important roles in the response of eukaryotic organisms to environmental stress. However, many histone acetyltransferases (HATs), which are responsible for histone acetylation, and their roles in mediating the tick response to cold stress have yet to be identified. In the present study, HATs were molecularly characterized and their associations with the cold response of the tick Haemaphysalis longicornis explored. METHODS HATs were characterized by using polymerase chain reaction (PCR) based on published genome sequences, followed by multiple bioinformatic analyses. The differential expression of genes in H. longicornis under different cold treatment conditions was evaluated using reverse transcription quantitative PCR (RT-qPCR). RNA interference was used to explore the association of HATs with the cold response of H. longicornis. RESULTS Two HAT genes were identified in H. longicornis (Hl), a GCN5-related N-acetyltransferase (henceforth HlGNAT) and a type B histone acetyltransferase (henceforth HlHAT-B), which are respectively 960 base pairs (bp) and 1239 bp in length. Bioinformatics analysis revealed that HlGNAT and HlHAT-B are unstable hydrophilic proteins characterized by the presence of the acetyltransferase 16 domain and Hat1_N domain, respectively. RT-qPCR revealed that the expression of HlGNAT and HlHAT-B decreased after 3 days of cold treatment, but gradually increased with a longer period of cold treatment. The mortality rate following knockdown of HlGNAT or HlHAT-B by RNA interference, which was confirmed by RT-qPCR, significantly increased (P < 0.05) when H. longicornis was treated at the lowest lethal temperature (- 14 °C) for 2 h. CONCLUSIONS The findings demonstrate that HATs may play a crucial role in the cold response of H. longicornis. Thus further research is warranted to explore the mechanisms underlying the epigenetic regulation of the cold response in ticks.
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Affiliation(s)
- Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Miao Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ziwen Gao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Lu Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ziyan Bing
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Jianglei Meng
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chuks Fidel Nwanade
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chaohui Yuan
- The Professional and Technical Center of Hebei Administration for Market Regulation, Shijiazhuang, 050024, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
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4
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Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M. Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity. Nat Ecol Evol 2024; 8:947-959. [PMID: 38519631 DOI: 10.1038/s41559-024-02365-0] [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: 08/28/2023] [Accepted: 02/11/2024] [Indexed: 03/25/2024]
Abstract
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.
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Affiliation(s)
- Yuan-Fei Pan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Hailong Zhao
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Pei-Bo Shi
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, China
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guangpeng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Bing Zhang
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Zirui Ren
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Shiqin Peng
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Geng-Yan Luo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shi-Jia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin Hou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Min-Wu Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jian-Bin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin-Xin Chen
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chun-Hui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shi-Qiang Mei
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yu-Qi Liao
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jing-Xia Cheng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - Chaolemen
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir, China
| | - Yu-Hui Wu
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir, China
| | - Jian-Bo Wang
- Hulunbuir Center for Disease Control and Prevention, Hulunbuir, China
| | - Tongqing An
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyi Huang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Jin
- BGI Research, Shenzhen, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Bo Li
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory for Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China.
| | - Daxi Wang
- BGI Research, Shenzhen, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China.
| | - Junhua Li
- BGI Research, Shenzhen, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China.
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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5
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Wang Y, Lin X, Li C, Liu G, Wang S, Chen M, Wei X, Wen H, Tao Z, Xu Y. Metagenomic sequencing reveals viral diversity of mosquitoes from Shandong Province, China. Microbiol Spectr 2024; 12:e0393223. [PMID: 38466099 PMCID: PMC10986517 DOI: 10.1128/spectrum.03932-23] [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: 12/13/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
Mosquitoes carry a large number of known and unknown viruses, some of which could cause serious diseases in humans or animals. Metagenomic sequencing for mosquito viromes is crucial for understanding the evolutionary history of viruses and preventing emerging mosquito-borne diseases. We collected 1,598 mosquitoes belonging to four species from five counties in Shandong Province, China in 2021. They were grouped by species and sampling locations and subjected to metagenomic next-generation sequencing for the analysis of the viromes. A total of 233,317,352 sequencing reads were classified into 30 viral families and an unclassified group. Comparative analysis showed that mosquitoes in Shandong Province generally possessed host-specific virome. We detected mosquito-borne viruses including Japanese encephalitis virus, Getah virus, and Kadipiro virus in Culex tritaeniorhynchus and Anopheles sinensis samples. Phylogenetic analysis showed that these pathogenic viruses may have existed in mosquitoes in Shandong Province for a long time. Meanwhile, we identified 22 novel viruses belonging to seven families and the genus Negevirus. Our study comprehensively described the viromes of several common mosquito species in Shandong Province, China, and demonstrated the major role of host species in shaping mosquito viromes. Furthermore, the metagenomic data provided valuable epidemiological information on multiple mosquito-borne viruses, highlighting the potential risk of infection transmission. IMPORTANCE Mosquitoes are known as the source of various pathogens for humans and animals. Culex tritaeniorhynchus, Armigeres subalbatus, and Anopheles sinensis have been found to transmit the Getah virus, which has recently caused increasing infections in China. Cx. tritaeniorhynchus and Culex pipiens are the main vectors of Japanese encephalitis virus and have caused epidemics of Japanese encephalitis in China in past decades. These mosquitoes are widely present in Shandong Province, China, leading to a great threat to public health and the breeding industry. This study provided a comprehensive insight into the viromes of several common mosquito species in Shandong Province, China. The metagenomic sequencing data revealed the risks of multiple pathogenic mosquito-borne viruses, including Japanese encephalitis virus, Getah virus, and Kadipiro virus, which are of great importance for preventing emerging viral epidemics.
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Affiliation(s)
- Yuhao Wang
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaojuan Lin
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Chao Li
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Guifang Liu
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Suting Wang
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Meng Chen
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Xuemin Wei
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Hongling Wen
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zexin Tao
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Yifei Xu
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu, China
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6
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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 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.
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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.
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7
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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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8
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Ni XB, Pei Y, Ye YT, Shum MHH, Cui XM, Wu YQ, Pierce MP, Zhao L, Wang GP, Wei JT, Fan JL, Wang Q, Smith DK, Sun Y, Du LF, Zhang J, Jiang JF, He PJ, Chen X, Wei H, Zhao NQ, Cao WC, Lam TTY, Jia N. Ecoclimate drivers shape virome diversity in a globally invasive tick species. THE ISME JOURNAL 2024; 18:wrae087. [PMID: 38747389 PMCID: PMC11187987 DOI: 10.1093/ismejo/wrae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Spillovers of viruses from animals to humans occur more frequently under warmer conditions, particularly arboviruses. The invasive tick species Haemaphysalis longicornis, the Asian longhorned tick, poses a significant public health threat due to its global expansion and its potential to carry a wide range of pathogens. We analyzed meta-transcriptomic data from 3595 adult H. longicornis ticks collected between 2016 and 2019 in 22 provinces across China encompassing diverse ecological conditions. Generalized additive modeling revealed that climate factors exerted a stronger influence on the virome of H. longicornis than other ecological factors, such as ecotypes, distance to coastline, animal host, tick gender, and antiviral immunity. To understand how climate changes drive the tick virome, we performed a mechanistic investigation using causality inference with emphasis on the significance of this process for public health. Our findings demonstrated that higher temperatures and lower relative humidity/precipitation contribute to variations in animal host diversity, leading to increased diversity of the tick virome, particularly the evenness of vertebrate-associated viruses. These findings may explain the evolution of tick-borne viruses into generalists across multiple hosts, thereby increasing the probability of spillover events involving tick-borne pathogens. Deep learning projections have indicated that the diversity of the H. longicornis virome is expected to increase in 81.9% of regions under the SSP8.5 scenario from 2019 to 2030. Extension of surveillance should be implemented to avert the spread of tick-borne diseases.
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Affiliation(s)
- Xue-Bing Ni
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Yao Pei
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Yong-Tao Ye
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, People’s Republic of China
| | - Yu-Qian Wu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Mac P Pierce
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Lin Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan 250012, Shandong, People’s Republic of China
| | - Gong-Pei Wang
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Jia-Te Wei
- Beijing Friendship Hospital, Capital Medical University, Beijing 100083, People’s Republic of China
| | - Jing-Li Fan
- Center for Sustainable Development and Energy Policy Research (SDEP), School of Energy and Mining Engineering, China University of Mining and Technology, Beijing 100083, People’s Republic of China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
| | - Li-Feng Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
| | - Jie Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, People’s Republic of China
| | - Pei-Jun He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- School of Public Health and Health Management, Gannan Medical University, Ganzhou 341000, People’s Republic of China
| | - Xin Chen
- School of Public Health and Health Management, Gannan Medical University, Ganzhou 341000, People’s Republic of China
| | - Hua Wei
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan 250012, Shandong, People’s Republic of China
| | - Ning-Qi Zhao
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, People’s Republic of China
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan 250012, Shandong, People’s Republic of China
- The representative of Tick Genome and Microbiome Consortium (TIGMIC)
| | - 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, Hong Kong SAR, People’s Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong SAR, People’s Republic of China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou 515063, Guangdong, People’s Republic of China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen 518045, Guangdong, People’s Republic of China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People’s Republic of China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, People’s Republic of China
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9
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Wang H, Chao S, Yan Q, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Yang B, He J, Zhang S, Zhang L, Simmonds P, Feng G. Genetic diversity of RNA viruses infecting invertebrate pests of rice. SCIENCE CHINA. LIFE SCIENCES 2024; 67:175-187. [PMID: 37946067 DOI: 10.1007/s11427-023-2398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 11/12/2023]
Abstract
Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.
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Affiliation(s)
- Haoran Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shufen Chao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Qing Yan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya, 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Baojun Yang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Jiachun He
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310012, China
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Guozhong Feng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China.
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10
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Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
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Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
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11
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Wang R, Liu S, Sun H, Xu C, Wen Y, Wu X, Zhang W, Nie K, Li F, Fu S, Yin Q, He Y, Xu S, Liang G, Deng L, Wei Q, Wang H. Metatranscriptomics Reveals the RNA Virome of Ixodes Persulcatus in the China-North Korea Border, 2017. Viruses 2023; 16:62. [PMID: 38257762 PMCID: PMC10819109 DOI: 10.3390/v16010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
In recent years, numerous viruses have been identified from ticks, and some have been linked to clinical cases of emerging tick-borne diseases. Chinese northeast frontier is tick infested. However, there is a notable lack of systematic monitoring efforts to assess the viral composition in the area, leaving the ecological landscape of viruses carried by ticks not clear enough. Between April and June 2017, 7101 ticks were collected to perform virus surveillance on the China-North Korea border, specifically in Tonghua, Baishan, and Yanbian. A total of 2127 Ixodes persulcatus were identified. Further investigation revealed the diversity of tick-borne viruses by transcriptome sequencing of Ixodes persulcatus. All ticks tested negative for tick-borne encephalitis virus. Transcriptome sequencing expanded 121 genomic sequence data of 12 different virus species from Ixodes persulcatus. Notably, a new segmented flavivirus, named Baishan Forest Tick Virus, were identified, closely related to Alongshan virus and Harz mountain virus. Therefore, this new virus may pose a potential threat to humans. Furthermore, the study revealed the existence of seven emerging tick-borne viruses dating back to 2017. These previously identified viruses included Mudanjiang phlebovirus, Onega tick phlebovirus, Sara tick phlebovirus, Yichun mivirus, and three unnamed viruses (one belonging to the Peribunyaviridae family and the other two belonging to the Phenuiviridae family). The existence of these emerging tick-borne viruses in tick samples collected in 2017 suggests that their history may extend further than previously recognized. This study provides invaluable insights into the virome of Ixodes persulcatus in the China-North Korea border region, enhancing our ongoing efforts to manage the risks associated with tick-borne viruses.
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Affiliation(s)
- Ruichen Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Shenghui Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Hongliang Sun
- Changchun Institute of Biological Products Co., Ltd., Changchun 130012, China; (H.S.); (X.W.)
| | - Chongxiao Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Yanhan Wen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Xiwen Wu
- Changchun Institute of Biological Products Co., Ltd., Changchun 130012, China; (H.S.); (X.W.)
| | - Weijia Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Kai Nie
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Fan Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Shihong Fu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Qikai Yin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Ying He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Songtao Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Guodong Liang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
| | - Liquan Deng
- School of Public Health, Jilin University, Changchun 130021, China
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huanyu Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (R.W.); (S.L.); (C.X.); (Y.W.); (W.Z.); (K.N.); (F.L.); (S.F.); (Q.Y.); (Y.H.); (S.X.); (G.L.)
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12
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Zhang W, Li R, Li S, Li SY, Niu J, Wang JJ. RNA virus diversity in three parasitoid wasps of tephritid flies: insights from novel and known species. Microbiol Spectr 2023; 11:e0313923. [PMID: 37930041 PMCID: PMC10714968 DOI: 10.1128/spectrum.03139-23] [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] [Received: 08/20/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Parasitoid wasp populations have developed persistent beneficial symbiotic relationships with several viruses through repeated evolution. However, there have been limited reports on RNA viruses in parasitoid wasps of tephritid flies, a significant pest group affecting fruits and vegetables. This study explores the diversity of RNA viruses in three parasitoid wasps of tephritid flies and highlights the potential biological significance of specific viruses in Diachasmimorpha longicaudata. These findings have important implications for the development of sustainable pest management strategies and the enhancement of artificial rearing techniques for parasitoid wasps.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Rong Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Shuai Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Shao-Yang Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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13
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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.
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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
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14
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Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M. Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555221. [PMID: 37732272 PMCID: PMC10508733 DOI: 10.1101/2023.08.28.555221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.
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Affiliation(s)
- Yuan-fei Pan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Hailong Zhao
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Qin-yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Pei-bo Shi
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Jun-hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan 430024, China
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wei-hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Guangpeng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang 550004, China
| | - Bing Zhang
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, School of Basic Medical Sciences Xinjiang Medical University, Urumqi 830011, China
| | - Zirui Ren
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Shiqin Peng
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Geng-yan Luo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Shi-jia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Gen-yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin Hou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Min-wu Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jian-bin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin-xin Chen
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Chun-hui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Shi-qiang Mei
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Yu-qi Liao
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jing-xia Cheng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - Chaolemen
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir 021500, China
| | - Yu-hui Wu
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir 021500, China
| | - Jian-bo Wang
- Hulunbuir Center for Disease Control and Prevention, Hulunbuir 021008, China
| | - Tongqing An
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xinyi Huang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510000, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xin Jin
- BGI Research, Shenzhen 518083, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bo Li
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Daxi Wang
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Junhua Li
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Wei-chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
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15
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Liu H, Zhang Y, Liu Y, Xiao J, Huang Z, Li Y, Li H, Li P. Virome analysis of an ectomycorrhizal fungus Suillus luteus revealing potential evolutionary implications. Front Cell Infect Microbiol 2023; 13:1229859. [PMID: 37662006 PMCID: PMC10470027 DOI: 10.3389/fcimb.2023.1229859] [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: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Suillus luteus is a widespread edible ectomycorrhizal fungus that holds significant importance in both ecological and economic value. Mycoviruses are ubiquitous infectious agents hosted in different fungi, with some known to exert beneficial or detrimental effects on their hosts. However, mycoviruses hosted in ectomycorrhizal fungi remain poorly studied. To address this gap in knowledge, we employed next-generation sequencing (NGS) to investigate the virome of S. luteus. Using BLASTp analysis and phylogenetic tree construction, we identified 33 mycovirus species, with over half of them belonging to the phylum Lenarviricota, and 29 of these viruses were novel. These mycoviruses were further grouped into 11 lineages, with the discovery of a new negative-sense single-stranded RNA viral family in the order Bunyavirales. In addition, our findings suggest the occurrence of cross-species transmission (CST) between the fungus and ticks, shedding light on potential evolutionary events that have shaped the viral community in different hosts. This study is not only the first study to characterize mycoviruses in S. luteus but highlights the enormous diversity of mycoviruses and their implications for virus evolution.
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Affiliation(s)
| | | | | | | | | | | | - Huaping Li
- Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Pengfei Li
- Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
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