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Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, Mahar JE, Holmes EC. Australian terrestrial environments harbour extensive RNA virus diversity. Virology 2024; 593:110007. [PMID: 38346363 DOI: 10.1016/j.virol.2024.110007] [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: 10/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, such as the Nodamuvirales and Ghabrivirales, the novel viruses identified here comprised entirely new clades. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Sobelivirales and Ghabrivirales. Viral read abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.
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Affiliation(s)
- Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alex B McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liana E Pozza
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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2
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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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3
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Lamichhane B, Brockway C, Evasco K, Nicholson J, Neville PJ, Levy A, Smith D, Imrie A. Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia. Pathogens 2024; 13:107. [PMID: 38392845 PMCID: PMC10892203 DOI: 10.3390/pathogens13020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.
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Affiliation(s)
- Binit Lamichhane
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA 6009, Australia;
| | - Craig Brockway
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Kimberly Evasco
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Jay Nicholson
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Peter J. Neville
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Avram Levy
- PathWest Laboratory Medicine, Nedlands, WA 6009, Australia; (A.L.); (D.S.)
| | - David Smith
- PathWest Laboratory Medicine, Nedlands, WA 6009, Australia; (A.L.); (D.S.)
- UWA Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Allison Imrie
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA 6009, Australia;
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Thamamongood T, Jengarn J, Muangsanit P, Petpiroon N, Srisutthisamphan K, Attasombat K, Wongwanakul R, Aueviriyavit S, Laohathai S, Jongkaewwattana A, Teeravechyan S. Pseudotyped zoonotic thogotoviruses exhibit broad entry range in mammalian cells. Virology 2024; 589:109914. [PMID: 37931589 DOI: 10.1016/j.virol.2023.109914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/10/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Viruses in the thogotovirus genus of the family Orthomyxoviridae are much less well-understood than influenza viruses despite documented zoonotic transmission and association with human disease. This study therefore developed a cell-cell fusion assay and three pseudotyping tools and used them to assess envelope function and cell tropism. Envelope glycoproteins of Dhori (DHOV), Thogoto (THOV), Bourbon, and Sinu viruses were all revealed to exhibit pH-dependent triggering of membrane fusion. Lentivirus vectors were robustly pseudotyped with these glycoproteins while influenza virus vectors showed pseudotyping compatibility, albeit at lower efficiencies. Replication-competent vesicular stomatitis virus expressing DHOV or THOV glycoproteins were also successfully generated. These pseudotyped viruses mediated entry into a wide range of mammalian cell lines, including human primary cells. The promiscuousness of these viruses suggests the use of a relatively ubiquitous receptor and their entry into numerous mammalian cells emphasize their high potential as veterinary and zoonotic diseases.
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Affiliation(s)
- Thiprampai Thamamongood
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Juggragarn Jengarn
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Papon Muangsanit
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Nalinrat Petpiroon
- Nano Safety and Bioactivity Research Team, National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kanjana Srisutthisamphan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Khemphitcha Attasombat
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Ratjika Wongwanakul
- Nano Safety and Bioactivity Research Team, National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Sasitorn Aueviriyavit
- Nano Safety and Bioactivity Research Team, National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Sira Laohathai
- Cardiothoracic Surgery Unit, Department of Surgery, Faculty of Medicine, Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Samaporn Teeravechyan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
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Michie A, Ernst T, Pyke AT, Nicholson J, Mackenzie JS, Smith DW, Imrie A. Genomic Analysis of Sindbis Virus Reveals Uncharacterized Diversity within the Australasian Region, and Support for Revised SINV Taxonomy. Viruses 2023; 16:7. [PMID: 38275942 PMCID: PMC10820390 DOI: 10.3390/v16010007] [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: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Sindbis virus (SINV) is a widely dispersed mosquito-borne alphavirus. Reports of Sindbis disease are largely restricted to northern Europe and South Africa. SINV is frequently sampled in Australian mosquito-based arbovirus surveillance programs, but human disease has rarely been reported. Molecular epidemiological studies have characterized six SINV genotypes (G1-G6) based on E2 gene phylogenies, mostly comprising viruses derived from the African-European zoogeographical region and with limited representation of Australasian SINV. In this study, we conducted whole genome sequencing of 66 SINV isolates sampled between 1960 and 2014 from countries of the Australasian region: Australia, Malaysia, and Papua New Guinea. G2 viruses were the most frequently and widely sampled, with three distinct sub-lineages defined. No new G6 SINV were identified, confirming geographic restriction of these viruses to south-western Australia. Comparison with global SINV characterized large-scale nucleotide and amino acid sequence divergence between African-European G1 viruses and viruses that circulate in Australasia (G2 and G3) of up to 26.83% and 14.55%, respectively, divergence that is sufficient for G2/G3 species demarcation. We propose G2 and G3 are collectively a single distinct alphavirus species that we name Argyle virus, supported by the inapparent or mild disease phenotype and the higher evolutionary rate compared with G1. Similarly, we propose G6, with 24.7% and 12.61% nucleotide and amino acid sequence divergence, is a distinct alphavirus species that we name Thomson's Lake virus.
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Affiliation(s)
- Alice Michie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
| | - Timo Ernst
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
| | - Alyssa T. Pyke
- Department of Health, Public Health Virology Laboratory, Forensic and Scientific Services, Queensland Government, Coopers Plains, QLD 4108, Australia;
| | - Jay Nicholson
- Environmental Health Directorate, Department of Health, Perth, WA 6000, Australia;
| | - John S. Mackenzie
- PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia; (J.S.M.); (D.W.S.)
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
- Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - David W. Smith
- PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia; (J.S.M.); (D.W.S.)
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
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6
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Bendl E, Fuchs J, Kochs G. Bourbon virus, a newly discovered zoonotic thogotovirus. J Gen Virol 2023; 104. [PMID: 37643129 DOI: 10.1099/jgv.0.001887] [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: 08/31/2023] Open
Abstract
The recent discovery of Bourbon virus (BRBV) put a new focus on the genus of thogotoviruses as zoonotic, tick-transmitted pathogens within the orthomyxovirus family. Since 2014, BRBV has been linked to several human cases in the Midwest United States with severe acute febrile illness and a history of tick bites. The detection of the virus in the Lone Star tick, Amblyomma americanum, and a high sero-prevalence in wild animals suggest widespread circulation of BRBV. Phylogenetic analysis of the viral RNA genome classified BRBV into the subgroup of Dhori-like thogotoviruses. Strikingly, BRBV is apathogenic in mice, contrasting not only with the fatal disease in affected patients but also with the severe disease in mice caused by other members of the thogotovirus genus. To gain insights into this intriguing discrepancy, we will review the molecular biology and pathology of BRBV and its unique position within the thogotovirus genus. Lastly, we will discuss the zoonotic threat posed by this newly discovered pathogen.
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Affiliation(s)
- Elias Bendl
- Institute of Virology, Medical Center and Faculty of Medicine, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Jonas Fuchs
- Institute of Virology, Medical Center and Faculty of Medicine, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center and Faculty of Medicine, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
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7
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Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC. Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics. PLoS Pathog 2023; 19:e1011588. [PMID: 37651317 PMCID: PMC10470969 DOI: 10.1371/journal.ppat.1011588] [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] [Indexed: 09/02/2023] Open
Abstract
Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.
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Affiliation(s)
- Brandon D Hollingsworth
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Nathan D Grubaugh
- Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale University, New Haven, Connecticut, United States of America
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Courtney C Murdock
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
- Northeast Regional Center for Excellence in Vector-borne Diseases, Cornell University, Ithaca, New York, United States of America
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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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9
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Tangudu CS, Hargett AM, Laredo-Tiscareño SV, Smith RC, Blitvich BJ. Isolation of a novel rhabdovirus and detection of multiple novel viral sequences in Culex species mosquitoes in the United States. Arch Virol 2022; 167:2577-2590. [PMID: 36056958 DOI: 10.1007/s00705-022-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
To increase our understanding of the diversity of the mosquito virome, 6956 mosquitoes of five species (Culex erraticus, Culex pipiens, Culex restuans, Culex tarsalis, and Culex territans) collected in Iowa in the United States in 2017 and 2020 were assayed for novel viruses by performing polyethylene glycol precipitation, virus isolation in cell culture, and unbiased high-throughput sequencing. A novel virus, provisionally named "Walnut Creek virus", was isolated from Cx. tarsalis, and its genomic sequence and organization are characteristic of viruses in the genus Hapavirus (family Rhabdoviridae). Replication of Walnut Creek virus occurred in avian, mammalian, and mosquito, but not tick, cell lines. A novel virus was also isolated from Cx. restuans, and partial genome sequencing revealed that it is distantly related to an unclassified virus of the genus Phytoreovirus (family Sedoreoviridae). Two recognized viruses were also isolated: Culex Y virus (family Birnaviridae) and Houston virus (family Mesoniviridae). We also identified sequences of eight novel viruses from six families (Amalgaviridae, Birnaviridae, Partitiviridae, Sedoreoviridae, Tombusviridae, and Totiviridae), two viruses that do not belong to any established families, and many previously recognized viruses. In summary, we provide evidence of multiple novel and recognized viruses in Culex spp. mosquitoes in the United States.
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Affiliation(s)
- Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Alissa M Hargett
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - S Viridiana Laredo-Tiscareño
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ryan C Smith
- Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.
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10
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Konstantinidis K, Dovrolis N, Kouvela A, Kassela K, Rosa Freitas MG, Nearchou A, de Courcy Williams M, Veletza S, Karakasiliotis I. Defining Virus-Carrier Networks that Shape the Composition of the Mosquito Core Virome of a Local Ecosystem. Virus Evol 2022; 8:veac036. [PMID: 35505691 PMCID: PMC9055857 DOI: 10.1093/ve/veac036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Mosquitoes are the most important vectors of emerging infectious diseases. During the past decade, our understanding of the diversity of viruses they carry has greatly expanded. Most of these viruses are considered mosquito-specific, but there is increasing evidence that these viruses may affect the vector competence of mosquitoes. Metagenomics approaches have focused on specific mosquito species for the identification of what is called the core virome. Despite the fact that, in most ecosystems, multiple species may participate in virus emergence and circulation, there is a lack of understanding of the virus-carrier/host network for both vector-borne and mosquito-specific viruses. Here, we studied the core virome of mosquitoes in a diverse local ecosystem that had 24 different mosquito species. The analysis of the viromes of these 24 mosquito species resulted in the identification of 34 viruses, which included 15 novel viruses, as determined according to the species demarcation criteria of the respective virus families. Most of the mosquito species had never been analysed previously, and a comparison of the individual viromes of the 24 mosquito species revealed novel relationships among mosquito species and virus families. Groups of related viruses and mosquito species from multiple genera formed a complex web in the local ecosystem. Furthermore, analyses of the virome of mixed-species pools of mosquitoes from representative traps of the local ecosystem showed almost complete overlap with the individual-species viromes identified in the study. Quantitative analysis of viruses’ relative abundance revealed a linear relationship to the abundance of the respective carrier/host mosquito species, supporting the theory of a stable core virome in the most abundant species of the local ecosystem. Finally, our study highlights the importance of using a holistic approach to investigating mosquito viromes relationships in rich and diverse ecosystems.
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Affiliation(s)
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Adamantia Kouvela
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Katerina Kassela
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Goreti Rosa Freitas
- Laboratório de Mosquitoes Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andreas Nearchou
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Stavroula Veletza
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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11
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Konstantinidis K, Bampali M, de Courcy Williams M, Dovrolis N, Gatzidou E, Papazilakis P, Nearchou A, Veletza S, Karakasiliotis I. Dissecting the Species-Specific Virome in Culicoides of Thrace. Front Microbiol 2022; 13:802577. [PMID: 35330767 PMCID: PMC8940260 DOI: 10.3389/fmicb.2022.802577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 12/14/2022] Open
Abstract
Biting midges (Culicoides) are vectors of arboviruses of both veterinary and medical importance. The surge of emerging and reemerging vector-borne diseases and their expansion in geographical areas affected by climate change has increased the importance of understanding their capacity to contribute to novel and emerging infectious diseases. The study of Culicoides virome is the first step in the assessment of this potential. In this study, we analyzed the RNA virome of 10 Culicoides species within the geographical area of Thrace in the southeastern part of Europe, a crossing point between Asia and Europe and important path of various arboviruses, utilizing the Ion Torrent next-generation sequencing (NGS) platform and a custom bioinformatics pipeline based on TRINITY assembler and alignment algorithms. The analysis of the RNA virome of 10 Culicoides species resulted in the identification of the genomic signatures of 14 novel RNA viruses, including three fully assembled viruses and four segmented viruses with at least one segment fully assembled, most of which were significantly divergent from previously identified related viruses from the Solemoviridae, Phasmaviridae, Phenuiviridae, Reoviridae, Chuviridae, Partitiviridae, Orthomyxoviridae, Rhabdoviridae, and Flaviviridae families. Each Culicoides species carried a species-specific set of viruses, some of which are related to viruses from other insect vectors in the same area, contributing to the idea of a virus-carrier web within the ecosystem. The identified viruses not only expand our current knowledge on the virome of Culicoides but also set the basis of the genetic diversity of such viruses in the area of southeastern Europe. Furthermore, our study highlights that such metagenomic approaches should include as many species as possible of the local virus-carrier web that interact and share the virome of a geographical area.
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Affiliation(s)
| | - Maria Bampali
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Nikolas Dovrolis
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Elisavet Gatzidou
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | | | - Stavroula Veletza
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
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12
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Feng G, Zhang J, Zhang Y, Li C, Zhang D, Li Y, Zhou H, Li N, Xiao P. Metagenomic Analysis of Togaviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes from Chikungunya and Ross River Viruses. Front Cell Infect Microbiol 2022; 12:849662. [PMID: 35223559 PMCID: PMC8878809 DOI: 10.3389/fcimb.2022.849662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
We collected 5,500 mosquitoes belonging to six species in three locations in China. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The affluent viral sequences that were detected and annotated belong to 22 viral taxonomic families. Then, PCR was performed to confirm the results, followed by phylogenetic analysis. Herein, part of mosquito virome was identified, including chikungunya virus (CHIKV), Getah virus (GETV), and Ross river virus (RRV). After metagenomic analysis, seven CHIKV sequences were verified by PCR amplification, among which CHIKV-China/YN2018-1 had the highest homology with the CHIKV isolated in Senegal, 1983, with a nucleotide (nt) identity of at least 81%, belonging to genotype West Africa viral genes. Five GETV sequences were identified, which had a high homology with the GETV sequences isolated from Equus caballus in Japan, 1978, with a (nt) identity of at least 97%. The newly isolated virus CHIKV-China/YN2018-1 became more infectious after passage of the BHK-21 cell line to the Vero cell line. The newly identified RRV gene had the highest homology with the 2006 RRV isolate from Australia, with a (nt) identity of at least 94%. In addition, numerous known and unknown viruses have also been detected in mosquitoes from Yunnan province, China, and propagation tests will be carried out.
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Affiliation(s)
- Guanrong Feng
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Jinyong Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Chenghui Li
- College of Agriculture, Yanbian University, Yanji, China
| | - Duo Zhang
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
| | - Yiquan Li
- Academician Workstation of Jilin Province, Changchun University of Chinese Medicine, Changchun, China
| | | | - Nan Li
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
- *Correspondence: Nan Li, ; Pengpeng Xiao,
| | - Pengpeng Xiao
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, China
- *Correspondence: Nan Li, ; Pengpeng Xiao,
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