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da Silva AF, Machado LC, da Silva LMI, Dezordi FZ, Wallau GL. Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil. J Virol 2024; 98:e0008324. [PMID: 38995042 PMCID: PMC11334435 DOI: 10.1128/jvi.00083-24] [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: 01/12/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments. IMPORTANCE Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.
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Affiliation(s)
- Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Laís Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | | | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Department of Arbovirology and Entomology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
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2
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Herrera G, Castañeda S, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile. Microbiol Res 2024; 285:127739. [PMID: 38763016 DOI: 10.1016/j.micres.2024.127739] [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: 12/19/2023] [Revised: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Clostridioides difficile may have a negative impact on gut microbiota composition in terms of diversity and abundance, thereby triggering functional changes supported by the differential presence of genes involved in significant metabolic pathways, such as short-chain fatty acids (SCFA). This work has evaluated shotgun metagenomics data regarding 48 samples from four groups classified according to diarrhea acquisition site (community- and healthcare facility-onset) and positive or negative Clostridioides difficile infection (CDI) result. The metagenomic-assembled genomes (MAGs) obtained from each sample were taxonomically assigned for preliminary comparative analysis concerning differences in composition among groups. The predicted genes involved in metabolism, transport, and signaling remained constant in microbiota members; characteristic patterns were observed in MAGs and genes involved in SCFA butyrate and acetate metabolic pathways for each study group. A decrease in genera and species, as well as relative MAG abundance with the presence of the acetate metabolism-related gene, was evident in the HCFO/- group. Increased antibiotic resistance markers (ARM) were observed in MAGs along with the genes involved in acetate metabolism. The results highlight the need to explore the role of acetate in greater depth as a potential protector of the imbalances produced by CDI, as occurs in other inflammatory intestinal diseases.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia; Semillero de Investigación en Bioinformática - GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia; Grupo de Fundamentos y Enseñanza de la Física y las Sistemas Dinámicas, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E Pérez-Jaramillo
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia; Semillero de Investigación en Bioinformática - GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia; Health Sciences Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Instituto de Biotecnología-UN (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia.
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De Coninck L, Soto A, Wang L, De Wolf K, Smitz N, Deblauwe I, Mbigha Donfack KC, Müller R, Delang L, Matthijnssens J. Lack of abundant core virome in Culex mosquitoes from a temperate climate region despite a mosquito species-specific virome. mSystems 2024; 9:e0001224. [PMID: 38742876 PMCID: PMC11237611 DOI: 10.1128/msystems.00012-24] [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: 01/04/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
In arthropod-associated microbial communities, insect-specific viruses (ISVs) are prevalent yet understudied due to limited infectivity outside their natural hosts. However, ISVs might play a crucial role in regulating mosquito populations and influencing arthropod-borne virus transmission. Some studies have indicated a core virome in mosquitoes consisting of mostly ISVs. Employing single mosquito metagenomics, we comprehensively profiled the virome of native and invasive mosquito species in Belgium. This approach allowed for accurate host species determination, prevalence assessment of viruses and Wolbachia, and the identification of novel viruses. Contrary to our expectations, no abundant core virome was observed in Culex mosquitoes from Belgium. In that regard, we caution against rigidly defining mosquito core viromes and encourage nuanced interpretations of other studies. Nonetheless, our study identified 45 viruses of which 28 were novel, enriching our understanding of the mosquito virome and ISVs. We showed that the mosquito virome in this study is species-specific and less dependent on the location where mosquitoes from the same species reside. In addition, because Wolbachia has previously been observed to influence arbovirus transmission, we report the prevalence of Wolbachia in Belgian mosquitoes and the detection of several Wolbachia mobile genetic elements. The observed prevalence ranged from 83% to 92% in members from the Culex pipiens complex.IMPORTANCECulex pipiens mosquitoes are important vectors for arboviruses like West Nile virus and Usutu virus. Virome studies on individual Culex pipiens, and on individual mosquitoes in general, have been lacking. To mitigate this, we sequenced the virome of 190 individual Culex and 8 individual Aedes japonicus mosquitoes. We report the lack of a core virome in these mosquitoes from Belgium and caution the interpretation of other studies in this light. The discovery of new viruses in this study will aid our comprehension of insect-specific viruses and the mosquito virome in general in relation to mosquito physiology and mosquito population dynamics.
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Affiliation(s)
- Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Alina Soto
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Mosquito Virology Team, Leuven, Belgium
| | - Lanjiao Wang
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Mosquito Virology Team, Leuven, Belgium
| | - Katrien De Wolf
- Department Biomedical Sciences, The Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Ghent, Belgium
| | - Nathalie Smitz
- Department of Biology, Royal Museum for Central Africa (Barcoding Facility for Organisms and Tissues of Policy Concern), Tervuren, Belgium
| | - Isra Deblauwe
- Department Biomedical Sciences, The Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Karelle Celes Mbigha Donfack
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ruth Müller
- Department Biomedical Sciences, The Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Delang
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Mosquito Virology Team, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
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Dos Santos ER, de Camargo BR, da Silva LA, Laumann RA, Ribeiro BM, Ardisson-Araújo DMP. The multispecies stinkbug iflavirus Halyomorpha halys virus detected in the multispecies stinkbug egg parasitoid microwasp, Telenomus podisi (Ashmead) (Hymenoptera: Platygastridae). Braz J Microbiol 2024; 55:1913-1921. [PMID: 38615311 PMCID: PMC11153462 DOI: 10.1007/s42770-024-01340-y] [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: 01/12/2024] [Accepted: 03/27/2024] [Indexed: 04/15/2024] Open
Abstract
Wasps are important parasitoids of stinkbugs and frequently exposed to various types of microorganisms through environmental contact and fecal-oral transmission route. Many parasitize stinkbug eggs and are commercially used in the field to control insect population. The parasitoid T. podisi is known for its high parasitism capacity and ability to target multiple species of stinkbugs. In this study we asked whether T. podisi exposed to eggs infected by a multispecies asymptomatic stinkbug virus, the Halyomorpha halys virus (HhV) would get infected. HhV is a geographically distributed multispecies iflavirus previously found to infect four stinkbug hosts, including three Brazilian species, Chinavia ubica, Euschistus heros and Diceraeus melacanthus, and T. posidi can parasitize all of them. As results, RT-PCR screening revealed positive samples for the HhV genome in two out of four tested pools of T. podisi, whereas the antigenome, indicative of replicative activity, was not detected. The wasps were raised in E. heros eggs that presented both the genome and the antigenome forms of the HhV genome. Subsequent RNA-deep sequencing of HhV positive T. podisi RNA pools yielded a complete genome of HhV with high coverage. Phylogenetic analysis positioned the isolate HhV-Tp (isolate Telenomus podisi) alongside with the stinkbug HhV. Analysis of transcriptomes from several hymenopteran species revealed HhV-Tp reads in four species. However, the transmission mechanism and the ecological significance of HhV remain elusive, warranting further studies to illuminate both the transmission process and its capacity for environmental propagation using T. podisi as a potential vector.
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Affiliation(s)
- Ethiane Rozo Dos Santos
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Brenda Rabelo de Camargo
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Leonardo Assis da Silva
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Raul Alberto Laumann
- Laboratory of Chemical Ecology, EMBRAPA Genetic Resources and Biotechnology, Brasília, DF, 70770-900, Brazil
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - Daniel M P Ardisson-Araújo
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
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5
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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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Morel C, Gil P, Exbrayat A, Loire E, Charriat F, Prepoint B, Condachou C, Gimonneau G, Fall AG, Biteye B, Seck MT, Eloit M, Gutierrez S. Host influence on the eukaryotic virome of sympatric mosquitoes and abundance of diverse viruses with a broad host range. PLoS One 2024; 19:e0300915. [PMID: 38687731 PMCID: PMC11060559 DOI: 10.1371/journal.pone.0300915] [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: 11/13/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024] Open
Abstract
Mosquitoes harbor a large diversity of eukaryotic viruses. Those viromes probably influence mosquito physiology and the transmission of human pathogens. Nevertheless, their ecology remains largely unstudied. Here, we address two key questions in virome ecology. First, we assessed the influence of mosquito species on virome taxonomic diversity and relative abundance. Contrary to most previous studies, the potential effect of the habitat was explicitly included. Thousands of individuals of Culex poicilipes and Culex tritaeniorhynchus, two vectors of viral diseases, were concomitantly sampled in three habitats over two years. A total of 95 viral taxa from 25 families were identified with meta-transcriptomics, with 75% of taxa shared by both mosquitoes. Viromes significantly differed by mosquito species but not by habitat. Differences were largely due to changes in relative abundance of shared taxa. Then, we studied the diversity of viruses with a broad host range. We searched for viral taxa shared by the two Culex species and Aedes vexans, another disease vector, present in one of the habitats. Twenty-six out of the 163 viral taxa were found in the three mosquitoes. These taxa encompassed 14 families. A database analysis supported broad host ranges for many of those viruses, as well as a widespread geographical distribution. Thus, the viromes of mosquitoes from the same genera mainly differed in the relative abundance of shared taxa, whereas differences in viral diversity dominated between mosquito genera. Whether this new model of virome diversity and structure applies to other mosquito communities remains to be determined.
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Affiliation(s)
- Côme Morel
- ASTRE, Cirad, INRAe, Univ Montpellier, Montpellier, France
| | - Patricia Gil
- ASTRE, Cirad, INRAe, Univ Montpellier, Montpellier, France
| | | | - Etienne Loire
- ASTRE, Cirad, INRAe, Univ Montpellier, Montpellier, France
| | | | | | | | - Geoffrey Gimonneau
- ASTRE, Cirad, INRAe, Univ Montpellier, Montpellier, France
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires (ISRA), Dakar-Hann, Senegal
| | - Assane Gueye Fall
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires (ISRA), Dakar-Hann, Senegal
| | - Biram Biteye
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires (ISRA), Dakar-Hann, Senegal
| | - Momar Talla Seck
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires (ISRA), Dakar-Hann, Senegal
| | - Marc Eloit
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
- Institut Pasteur, Université Paris Cité, The WOAH (OIE) Collaborating Center for The Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, Maisons-Alfort, France
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Da Silva AG, Bach E, Ellwanger JH, Chies JAB. Tips and tools to obtain and assess mosquito viromes. Arch Microbiol 2024; 206:132. [PMID: 38436750 DOI: 10.1007/s00203-023-03813-4] [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: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 03/05/2024]
Abstract
Due to their vectorial capacity, mosquitoes (Diptera: Culicidae) receive special attention from health authorities and entomologists. These cosmopolitan insects are responsible for the transmission of many viral diseases, such as dengue and yellow fever, causing huge impacts on human health and justifying the intensification of research focused on mosquito-borne diseases. In this context, the study of the virome of mosquitoes can contribute to anticipate the emergence and/or the reemergence of infectious diseases. The assessment of mosquito viromes also contributes to the surveillance of a wide variety of viruses found in these insects, allowing the early detection of pathogens with public health importance. However, the study of mosquito viromes can be challenging due to the number and complexities of steps involved in this type of research. Therefore, this article aims to describe, in a straightforward and simplified way, the steps necessary for obtention and assessment of mosquito viromes. In brief, this article explores: the capture and preservation of specimens; sampling strategies; treatment of samples before DNA/RNA extraction; extraction methodologies; enrichment and purification processes; sequencing choices; and bioinformatics analysis.
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Affiliation(s)
- Amanda Gonzalez Da Silva
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Evelise Bach
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Joel Henrique Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil.
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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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Jeffries CL, Tantely LM, Kadriaj P, Blagrove MSC, Lytra I, Orsborne J, Al-Amin HM, Mohammed AR, Alam MS, Girod R, Afrane YA, Bino S, Robert V, Boyer S, Baylis M, Velo E, Hughes GL, Walker T. Mitochondrial and microbial diversity of the invasive mosquito vector species Culex tritaeniorhynchus across its extensive inter-continental geographic range. Wellcome Open Res 2024; 9:18. [PMID: 38800519 PMCID: PMC11128058 DOI: 10.12688/wellcomeopenres.20761.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2023] [Indexed: 05/29/2024] Open
Abstract
Background Culex (Cx.) tritaeniorhynchus is an invasive mosquito species with an extensive and expanding inter-continental distribution, currently reported across Asia, Africa, the Middle East, Europe and now Australia. It is an important vector of medical and veterinary pathogens which cause significant morbidity and mortality in human and animal populations. Across regions endemic for Japanese encephalitis virus (JEV), Cx. tritaeniorhynchus is considered the major vector and has also been shown to contribute to the transmission of several other zoonotic arboviruses including Rift Valley fever virus (RVFV) and West Nile virus (WNV). Methods In this study, we used laboratory vector competence experiments to determine if Cx. tritaeniorhynchus from a Southern European population were competent JEV vectors. We also obtained samples from multiple geographically dispersed Cx. tritaeniorhynchus populations from countries within Europe, Africa, Eurasia and Asia to perform phylogenetic analysis to measure the level of mitochondrial divergence using the cytochrome oxidase subunit 1 ( CO1) gene. We also undertook bacterial 16S rRNA gene amplicon sequencing to determine microbial diversity and used multi-locus sequence typing (MLST) to determine any evidence for the presence of strains of the naturally occurring endosymbiotic bacterium Wolbachia. Results Cx. tritaeniorhynchus from a Greek population were shown be be competent vectors of JEV with high levels of virus present in saliva. We found a signficant level of mitochondrial genetic diversity using the mosquito CO1 gene between geographically dispersed populations. Furthermore, we report diverse microbiomes identified by 16S rRNA gene amplicon sequencing within and between geographical populations. Evidence for the detection of the endosymbiotic bacteria Wolbachia was confirmed using Wolbachia-specific PCR and MLST. Conclusions This study enhances our understanding of the diversity of Cx. tritaeniorhynchus and the associated microbiome across its inter-continental range and highlights the need for greater surveillance of this invasive vector species in Europe.
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Affiliation(s)
- Claire L. Jeffries
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Luciano M Tantely
- Unite d'entomologie medicale, Institute Pasteur de Madagascar, Antanarivo, Madagascar
| | - Perparim Kadriaj
- Vector Control Unit, Control of Infectious Diseases Department, Institute of Public Health, Tirana, Albania
| | - Marcus S C Blagrove
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England, UK
- Health Protection Research Unit on Emerging and Zoonotic Infections, University of Liverpool, Liverpool, England, UK
| | - Ioanna Lytra
- Department of Entomology and Agricultural Zoology, Benaki Phytopathological Institute, Athens, Greece
| | - James Orsborne
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Hasan Mohammad Al-Amin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
- Berghofer Medical Research Institute, Queensland Institute of Medical Research, Brisbane, Australia
| | - Abdul Rahim Mohammed
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Greater Accra Region, Ghana
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Romain Girod
- Unite d'entomologie medicale, Institute Pasteur de Madagascar, Antanarivo, Madagascar
| | - Yaw A Afrane
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Greater Accra Region, Ghana
| | - Silvia Bino
- Vector Control Unit, Control of Infectious Diseases Department, Institute of Public Health, Tirana, Albania
| | - Vincent Robert
- MIVEGEC, CNRS, Institute of Research for Development (IRD), University of Montpellier, Montpellier, France
| | - Sebastien Boyer
- Unite d'entomologie medicale, Institute Pasteur de Madagascar, Antanarivo, Madagascar
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Matthew Baylis
- Health Protection Research Unit on Emerging and Zoonotic Infections, University of Liverpool, Liverpool, England, UK
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England, UK
| | - Enkelejda Velo
- Vector Control Unit, Control of Infectious Diseases Department, Institute of Public Health, Tirana, Albania
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, University of Liverpool, Liverpool, England, UK
| | - Thomas Walker
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- School of Life Sciences, University of Warwick, Coventry, England, UK
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10
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Hermanns K, Marklewitz M, Zirkel F, Kopp A, Kramer-Schadt S, Junglen S. Mosquito community composition shapes virus prevalence patterns along anthropogenic disturbance gradients. eLife 2023; 12:e66550. [PMID: 37702388 PMCID: PMC10547478 DOI: 10.7554/elife.66550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/12/2023] [Indexed: 09/14/2023] Open
Abstract
Previously unknown pathogens often emerge from primary ecosystems, but there is little knowledge on the mechanisms of emergence. Most studies analyzing the influence of land-use change on pathogen emergence focus on a single host-pathogen system and often observe contradictory effects. Here, we studied virus diversity and prevalence patterns in natural and disturbed ecosystems using a multi-host and multi-taxa approach. Mosquitoes sampled along a disturbance gradient in Côte d'Ivoire were tested by generic RT-PCR assays established for all major arbovirus and insect-specific virus taxa including novel viruses previously discovered in these samples based on cell culture isolates enabling an unbiased and comprehensive approach. The taxonomic composition of detected viruses was characterized and viral infection rates according to habitat and host were analyzed. We detected 331 viral sequences pertaining to 34 novel and 15 previously identified viruses of the families Flavi-, Rhabdo-, Reo-, Toga-, Mesoni- and Iflaviridae and the order Bunyavirales. Highest host and virus diversity was observed in pristine and intermediately disturbed habitats. The majority of the 49 viruses was detected with low prevalence. However, nine viruses were found frequently across different habitats of which five viruses increased in prevalence towards disturbed habitats, in congruence with the dilution effect hypothesis. These viruses were mainly associated with one specific mosquito species (Culex nebulosus), which increased in relative abundance from pristine (3%) to disturbed habitats (38%). Interestingly, the observed increased prevalence of these five viruses in disturbed habitats was not caused by higher host infection rates but by increased host abundance, an effect tentatively named abundance effect. Our data show that host species composition is critical for virus abundance. Environmental changes that lead to an uneven host community composition and to more individuals of a single species are a key driver of virus emergence.
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Affiliation(s)
- Kyra Hermanns
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
| | - Marco Marklewitz
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical CentreBerlinGermany
| | - Anne Kopp
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
| | - Stephanie Kramer-Schadt
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife ResearchBerlinGermany
- Institute of Ecology, Technische Universität BerlinBerlinGermany
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
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11
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Gil P, Exbrayat A, Loire E, Rakotoarivony I, Charriat F, Morel C, Baldet T, Boisseau M, Marie A, Frances B, L’Ambert G, Bessat M, Otify Y, Goffredo M, Mancini G, Busquets N, Birnberg L, Talavera S, Aranda C, Ayari E, Mejri S, Sghaier S, Bennouna A, El Rhaffouli H, Balenghien T, Chlyeh G, Fassi Fihri O, Reveillaud J, Simonin Y, Eloit M, Gutierrez S. Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens. Virus Evol 2023; 9:vead054. [PMID: 37719779 PMCID: PMC10504824 DOI: 10.1093/ve/vead054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/22/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Our knowledge of the diversity of eukaryotic viruses has recently undergone a massive expansion. This diversity could influence host physiology through yet unknown phenomena of potential interest to the fields of health and food production. However, the assembly processes of this diversity remain elusive in the eukaryotic viromes of terrestrial animals. This situation hinders hypothesis-driven tests of virome influence on host physiology. Here, we compare taxonomic diversity between different spatial scales in the eukaryotic virome of the mosquito Culex pipiens. This mosquito is a vector of human pathogens worldwide. The experimental design involved sampling in five countries in Africa and Europe around the Mediterranean Sea and large mosquito numbers to ensure a thorough exploration of virus diversity. A group of viruses was found in all countries. This core group represented a relatively large and diverse fraction of the virome. However, certain core viruses were not shared by all host individuals in a given country, and their infection rates fluctuated between countries and years. Moreover, the distribution of coinfections in individual mosquitoes suggested random co-occurrence of those core viruses. Our results also suggested differences in viromes depending on geography, with viromes tending to cluster depending on the continent. Thus, our results unveil that the overlap in taxonomic diversity can decrease with spatial scale in the eukaryotic virome of C. pipiens. Furthermore, our results show that integrating contrasted spatial scales allows us to identify assembly patterns in the mosquito virome. Such patterns can guide future studies of virome influence on mosquito physiology.
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Affiliation(s)
- Patricia Gil
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Antoni Exbrayat
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Etienne Loire
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Ignace Rakotoarivony
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Florian Charriat
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Côme Morel
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Thierry Baldet
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Michel Boisseau
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | | | | | | | - Mohamed Bessat
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 5410012, Egypt
| | - Yehia Otify
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 5410012, Egypt
| | - Maria Goffredo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Teramo 64100, Italy
| | - Giuseppe Mancini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Teramo 64100, Italy
| | - Núria Busquets
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
| | - Lotty Birnberg
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
| | - Sandra Talavera
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
| | - Carles Aranda
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
- Servei de Control de Mosquits del Consell Comarcal del Baix Llobregat, Barcelona 08980, Spain
| | - Emna Ayari
- Institut de la Recherche Vétérinaire de Tunisie - Université Tunis El Manar, Tunis 1068, Tunisia
| | - Selma Mejri
- Institut de la Recherche Vétérinaire de Tunisie - Université Tunis El Manar, Tunis 1068, Tunisia
| | - Soufien Sghaier
- Institut de la Recherche Vétérinaire de Tunisie - Université Tunis El Manar, Tunis 1068, Tunisia
| | - Amal Bennouna
- Department of Animal Pathology and Public Health, Hassan II Agronomy & Veterinary Institute, Rabat BP 6202, Morocco
| | | | - Thomas Balenghien
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
- Department of Animal Pathology and Public Health, Hassan II Agronomy & Veterinary Institute, Rabat BP 6202, Morocco
| | - Ghita Chlyeh
- Département de Production, Protection et Biotechnologies Végétales, Unité de Zoologie, Institute of Agronomy and Veterinary Medicine Hassan II, Rabat BP 6202, Morocco
| | - Ouafaa Fassi Fihri
- Department of Animal Pathology and Public Health, Hassan II Agronomy & Veterinary Institute, Rabat BP 6202, Morocco
| | - Julie Reveillaud
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Yannick Simonin
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
- Pathogenesis and Control of Chronic Infections, University of Montpellier, INSERM, EFS, Montpellier 34394, France
| | - Marc Eloit
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris 75015, France
- Institut Pasteur, The OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Paris 75724, France
- École nationale vétérinaire d’Alfort, Maisons-Alfort 94700, France
| | - Serafin Gutierrez
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
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12
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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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13
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Chang T, Hunt BPV, Hirai J, Suttle CA. Divergent RNA viruses infecting sea lice, major ectoparasites of fish. PLoS Pathog 2023; 19:e1011386. [PMID: 37347729 DOI: 10.1371/journal.ppat.1011386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/25/2023] [Indexed: 06/24/2023] Open
Abstract
Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order Mononegavirales, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (Lepeophtheirus salmonis, Caligus clemensi, and Caligus rogercresseyi) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in C. rogercresseyi. Our analyses showed that most of the viruses found in C. rogercresseyi occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms.
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Affiliation(s)
- Tianyi Chang
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Brian P V Hunt
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
- Hakai Institute, Campbell River, Canada
| | - Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
- Hakai Institute, Campbell River, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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14
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Liu Q, Cui F, Liu X, Fu Y, Fang W, Kang X, Lu H, Li S, Liu B, Guo W, Xia Q, Kang L, Jiang F. Association of virome dynamics with mosquito species and environmental factors. MICROBIOME 2023; 11:101. [PMID: 37158937 PMCID: PMC10165777 DOI: 10.1186/s40168-023-01556-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND The pathogenic viruses transmitted by mosquitoes cause a variety of animal and human diseases and public health concerns. Virome surveillance is important for the discovery, and control of mosquito-borne pathogenic viruses, as well as early warning systems. Virome composition in mosquitoes is affected by mosquito species, food source, and geographic region. However, the complex associations of virome composition remain largely unknown. RESULTS Here, we profiled the high-depth RNA viromes of 15 species of field-caught adult mosquitoes, especially from Culex, Aedes, Anopheles, and Armigeres in Hainan Island from 2018 to 2020. We detected 57 known and 39 novel viruses belonging to 15 families. We established the associations of the RNA viruses with mosquito species and their foods, indicating the importance of feeding acquisition of RNA viruses in determining virome composition. A large fraction of RNA viruses were persistent in the same mosquito species across the 3 years and different locations, showing the species-specific stability of viromes in Hainan Island. In contrast, the virome compositions of single mosquito species in different geographic regions worldwide are visibly distinct. This is consistent with the differences in food sources of mosquitoes distributed broadly across continents. CONCLUSIONS Thus, species-specific viromes in a relatively small area are limited by viral interspecific competition and food sources, whereas the viromes of mosquito species in large geographic regions may be governed by ecological interactions between mosquitoes and local environmental factors. Video Abstract.
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Affiliation(s)
- Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yumei Fu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- NHC Key Laboratory of Tropical Disease Control, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Wenjing Fang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xun Kang
- NHC Key Laboratory of Tropical Disease Control, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Hong Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Siping Li
- NHC Key Laboratory of Tropical Disease Control, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Biao Liu
- NHC Key Laboratory of Tropical Disease Control, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qianfeng Xia
- NHC Key Laboratory of Tropical Disease Control, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China.
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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15
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Li C, Liu S, Zhou H, Zhu W, Cui M, Li J, Wang J, Liu J, Zhu J, Li W, Bi Y, Carr MJ, Holmes EC, Shi W. Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome. Microbiol Spectr 2023; 11:e0465522. [PMID: 36786616 PMCID: PMC10101097 DOI: 10.1128/spectrum.04655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Mosquitoes are important vector hosts for numerous viral pathogens and harbor a large number of mosquito-specific viruses as well as human-infecting viruses. Previous studies have mainly focused on the discovery of mosquito viruses, and our understanding of major ecological factors associated with virome structure in mosquitoes remains limited. We utilized metatranscriptomic sequencing to characterize the viromes of five mosquito species sampled across eight locations in Yunnan Province, China. This revealed the presence of 52 viral species, of which 19 were novel, belonging to 15 viral families/clades. Of particular note was Culex hepacivirus 1, clustering within the avian clade of hepaciviruses. Notably, both the viromic diversity and abundance of Aedes genus mosquitoes were significantly higher than those of the Culex genus, while Aedes albopictus mosquitoes harbored a higher diversity than Aedes aegypti mosquitoes. Our findings thus point to discernible differences in viromic structure between mosquito genera and even between mosquito species within the same genus. Importantly, such differences were not attributable to differences in sampling between geographical location. Our study also revealed the ubiquitous presence of the endosymbiont bacterium Wolbachia, with the genetic diversity and abundance also varying between mosquito species. In conclusion, our results suggested that the mosquito host species play an important role in shaping the virome's structure. IMPORTANCE This study revealed the huge capability of mosquitoes in harboring a rich diversity of RNA viruses, although relevant studies have characterized the intensively unparalleled diversity of RNA viruses previously. Furthermore, our findings showed discernible differences not only in viromic structure between mosquito genera and even between mosquito species within the same genus but also in the genetic diversity and abundance of Wolbachia between different mosquito populations. These findings emphasize the importance of host genetic background in shaping the virome composition of mosquitoes.
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Affiliation(s)
- Cixiu Li
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Shuqi Liu
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Hong Zhou
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Wei Zhu
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Mingxue Cui
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Juan Li
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Jiao Wang
- Mengla County Center for Disease Control and Prevention, Mengla, China
| | - Jiangyun Liu
- Mengla County Center for Disease Control and Prevention, Mengla, China
| | - Jin Zhu
- Xishuangbanna Prefecture Center for Disease Control and Prevention, Jinghong, China
| | - Weiping Li
- Xishuangbanna Prefecture Center for Disease Control and Prevention, Jinghong, China
| | - Yuhai Bi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Michael J. Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
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16
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Yang X, Qin S, Liu X, Zhang N, Chen J, Jin M, Liu F, Wang Y, Guo J, Shi H, Wang C, Chen Y. Meta-Viromic Sequencing Reveals Virome Characteristics of Mosquitoes and Culicoides on Zhoushan Island, China. Microbiol Spectr 2023; 11:e0268822. [PMID: 36651764 PMCID: PMC9927462 DOI: 10.1128/spectrum.02688-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mosquitoes and biting Culicoides species are arbovirus vectors. Effective virome profile surveillance is essential for the prevention and control of insect-borne diseases. From June to September 2021, we collected eight species of female mosquito and Culicoides on Zhoushan Island, China, and used meta-viromic sequencing to analyze their virome compositions and characteristics. The classified virus reads were distributed in 191 genera in 66 families. The virus sequences in mosquitoes with the largest proportions were Iflaviridae (30.03%), Phasmaviridae (23.09%), Xinmoviridae (21.82%), Flaviviridae (13.44%), and Rhabdoviridae (8.40%). Single-strand RNA+ viruses formed the largest proportions of viruses in all samples. Blood meals indicated that blood-sucking mosquito hosts were mainly chicken, duck, pig, and human, broadly consistent with the habitats where the mosquitoes were collected. Novel viruses of the Orthobunyavirus, Narnavirus, and Iflavirus genera were found in Culicoides by de-novo assembly. The viruses with vertebrate hosts carried by mosquitoes and Culicoides also varied widely. The analysis of unclassified viruses and deep-learning analysis of the "dark matter" in the meta-viromic sequencing data revealed the presence of a large number of unknown viruses. IMPORTANCE The monitoring of the viromes of mosquitoes and Culicoides, widely distributed arbovirus transmission vectors, is crucial to evaluate the risk of infectious disease transmission. In this study, the compositions of the viromes of mosquitoes and Culicoides on Zhoushan Island varied widely and were related mainly to the host species, with different host species having different core viromes. and many unknown sequences in the Culicoides viromes remain to be annotated, suggesting the presence of a large number of unknown viruses.
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Affiliation(s)
- Xiaojing Yang
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shiyu Qin
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xiong Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Na Zhang
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jiali Chen
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Meiling Jin
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Fangni Liu
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yong Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinpeng Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hua Shi
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Changjun Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yong Chen
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
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17
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Wu Q, Guo C, Li XK, Yi BY, Li QL, Guo ZM, Lu JH. A meta-transcriptomic study of mosquito virome and blood feeding patterns at the human-animal-environment interface in Guangdong Province, China. One Health 2023; 16:100493. [PMID: 36817976 PMCID: PMC9932184 DOI: 10.1016/j.onehlt.2023.100493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Mosquitoes are a formidable reservoir of viruses and important vectors of zoonotic pathogens. Blood-fed mosquitoes have been utilized to determine host infection status, overcoming the difficulties associated with sampling from human and animal populations. Comprehensive surveillance of potential pathogens at the interface of humans, animals, and the environment is currently an accredited method to provide an early warning of emerging or re-emerging infectious diseases and to proactively respond to them. Herein we performed comprehensive sampling of mosquitoes from seven habitats (residential areas, hospital, airplane, harbor, zoo, domestic sheds, and forest park) across five cities in Guangdong Province, China. Our aim was to characterize the viral communities and blood feeding patterns at the human-animal-environment interface and analyze the potential risk of cross-species transmission using meta-transcriptomic sequencing. 1898 female adult mosquitoes were collected, including 1062 Aedes and 836 Culex mosquitoes, of which approximately 12% (n = 226) were satiated with blood. Consequently, 101 putative viruses were identified, which included DNA and RNA viruses, and positive-stranded RNA viruses (+ssRNA) were the most abundant. According to viral diversity analysis, the composition of the viral structure was highly dependent on host species, and Culex mosquitoes showed richer viral diversity than Aedes mosquitoes. Although the virome of mosquitoes from different sampling habitats showed an overlap of 39.6%, multiple viruses were specific to certain habitats, particularly at the human-animal interface. Blood meal analysis found four mammals and one bird bloodmeal source, including humans, dogs, cats, poultry, and rats. Further, the blood feeding patterns of mosquitoes were found to be habitat dependent, and mosquitoes at the human-animal interface and from forests had a wider choice of hosts, including humans, domesticated animals, and wildlife, which in turn considerably increases the risk of spillover of potential zoonotic pathogens. To summarize, we are the first to investigate the virome of mosquitoes from multiple interfaces based on the One Health concept. The characteristics of viral community and blood feeding patterns of mosquitoes at the human-animal-environment interface were determined. Our findings should support surveillance activities to identify known and potential pathogens that are pathogenic to vertebrates.
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Affiliation(s)
- Qin Wu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York 10032, USA
| | - Xiao-kang Li
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Bo-Yang Yi
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qian-Lin Li
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhong-Min Guo
- Laboratory Animal Center, Sun Yat-Sen University, Guangzhou 510080, China,Corresponding author.
| | - Jia-Hai Lu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou 510080, China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou 571199, China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou 510080, China,Corresponding author at: School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China.
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18
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Kostygov AY, Malysheva MN, Ganyukova AI, Razygraev AV, Drachko DO, Yurchenko V, Agasoi VV, Frolov AO. The Roles of Mosquitoes in the Circulation of Monoxenous Trypanosomatids in Temperate Climates. Pathogens 2022; 11:1326. [PMID: 36422578 PMCID: PMC9695722 DOI: 10.3390/pathogens11111326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Monoxenous (insect-restricted) trypanosomatids are highly diverse and abundant in nature. While many papers focus on the taxonomy and distribution of these parasites, studies on their biology are still scarce. In particular, this concerns trypanosomatids inhabiting the ubiquitous mosquitoes. To shed light on the circulation of monoxenous trypanosomatids with the participation of mosquitoes, we performed a multifaceted study combining the examination of naturally- and experimentally-infected insects using light and electron microscopy and molecular identification of parasites. Our examination of overwintering mosquitoes (genera Culex and Culiseta) revealed that their guts contained living trypanosomatids, which can be spread during the next season. Experimental infections with Crithidia spp. demonstrated that imagines represent permissive hosts, while larvae are resistant to these parasites. We argue that for the parasites with wide specificity, mosquitoes act as facultative hosts. Other trypanosomatids may have specific adaptations for vertical transmission in these insects at the expense of their potential to infect a wider range of hosts and, consequently, abundance in nature.
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Affiliation(s)
- Alexei Y. Kostygov
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Marina N. Malysheva
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Anna I. Ganyukova
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Alexey V. Razygraev
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Daria O. Drachko
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic
| | - Vera V. Agasoi
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Alexander O. Frolov
- Zoological Institute of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
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19
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Ferchiou S, Caza F, de Boissel PGJ, Villemur R, St-Pierre Y. Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems. ISME COMMUNICATIONS 2022; 2:61. [PMID: 37938655 PMCID: PMC9723566 DOI: 10.1038/s43705-022-00145-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 10/04/2023]
Abstract
Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.
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Affiliation(s)
- Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | | | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
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20
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Transcriptomics Reveal Several Novel Viruses from Canegrubs (Coleoptera: Scarabaeidae) in Central Queensland, Australia. Viruses 2022; 14:v14030649. [PMID: 35337056 PMCID: PMC8949096 DOI: 10.3390/v14030649] [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: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 12/21/2022] Open
Abstract
Canegrubs (Coleoptera: Scarabaeidae) are major pests of sugarcane crops in Australia, but despite long-term and intensive research, no commercially viable biological control agents have been identified. We used the RNA-Seq approach to explore the viriomes of three different species of canegrubs from central Queensland, Australia to identify potential candidates for biological control. We identified six novel RNA viruses, characterized their genomes, and inferred their evolutionary relationships with other closely related viruses. These novel viruses showed similarity to other known members from picornaviruses, benyviruses, sobemoviruses, totiviruses, and reoviruses. The abundance of viral reads varied in these libraries; for example, Dermolepida albohirtum picorna-like virus (9696 nt) was built from 83,894 assembled reads while only 1350 reads mapped to Lepidiota negatoria beny-like virus (6371 nt). Future studies are essential to determine their natural incidence in different life stages of the host, biodiversity, geographical distributions, and potential as biological control agents for these important pests of sugarcane.
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21
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Eberhard FE, Klimpel S, Guarneri AA, Tobias NJ. Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus. MICROBIOME 2022; 10:45. [PMID: 35272716 PMCID: PMC8908696 DOI: 10.1186/s40168-022-01240-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND The causative agent of Chagas disease, Trypanosoma cruzi, and its nonpathogenic relative, Trypanosoma rangeli, are transmitted by haematophagous triatomines and undergo a crucial ontogenetic phase in the insect's intestine. In the process, the parasites interfere with the host immune system as well as the microbiome present in the digestive tract potentially establishing an environment advantageous for development. However, the coherent interactions between host, pathogen and microbiota have not yet been elucidated in detail. We applied a metagenome shotgun sequencing approach to study the alterations in the microbiota of Rhodnius prolixus, a major vector of Chagas disease, after exposure to T. cruzi and T. rangeli focusing also on the functional capacities present in the intestinal microbiome of the insect. RESULTS The intestinal microbiota of R. prolixus was dominated by the bacterial orders Enterobacterales, Corynebacteriales, Lactobacillales, Clostridiales and Chlamydiales, whereas the latter conceivably originated from the blood used for pathogen exposure. The anterior and posterior midgut samples of the exposed insects showed a reduced overall number of organisms compared to the control group. However, we also found enriched bacterial groups after exposure to T. cruzi as well as T rangeli. While the relative abundance of Enterobacterales and Corynebacteriales decreased considerably, the Lactobacillales, mainly composed of the genus Enterococcus, developed as the most abundant taxonomic group. This applies in particular to vectors challenged with T. rangeli and at early timepoints after exposure to vectors challenged with T. cruzi. Furthermore, we were able to reconstruct four metagenome-assembled genomes from the intestinal samples and elucidate their unique metabolic functionalities within the triatomine microbiome, including the genome of a recently described insect symbiont, Candidatus Symbiopectobacterium, and the secondary metabolites producing bacteria Kocuria spp. CONCLUSIONS Our results facilitate a deeper understanding of the processes that take place in the intestinal tract of triatomine vectors during colonisation by trypanosomal parasites and highlight the influential aspects of pathogen-microbiota interactions. In particular, the mostly unexplored metabolic capacities of the insect vector's microbiome are clearer, underlining its role in the transmission of Chagas disease. Video Abstract.
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Affiliation(s)
- Fanny E. Eberhard
- Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Biologicum Campus Riedberg, Max-von-Laue-Str. 13, 60439 Frankfurt/Main, Germany
| | - Sven Klimpel
- Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Biologicum Campus Riedberg, Max-von-Laue-Str. 13, 60439 Frankfurt/Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt/Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Alessandra A. Guarneri
- Vector Behaviour and Pathogen Interaction Group, Instituto René Rachou, Avenida Augusto de Lima,1715, Belo Horizonte, MG CEP 30190-009 Brazil
| | - Nicholas J. Tobias
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt/Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
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22
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da Silva AF, Dezordi FZ, Machado LC, de Oliveira RD, Qin S, Fan H, Zhang X, Tong Y, Silva MM, Loreto ELS, Wallau GL. Metatranscriptomic analysis identifies different viral-like sequences in two neotropical Mansoniini mosquito species. Virus Res 2021; 301:198455. [PMID: 34015364 DOI: 10.1016/j.virusres.2021.198455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 10/21/2022]
Abstract
Mosquitoes interact with a wide range of viruses including both arboviruses and insect-specific viruses. This study aimed to characterize the RNA viruses that are interacting with Mansonia wilsoni and Coquillettidia hermanoi mosquito species. The total RNA extracted from mosquito pools were sequenced on a Ion torrent platform. Viral contigs were identified against viral databases and their evolutionary relationship were reconstructed. We identified a total of 107 viral sequences, 11 of which were assigned as endogenous viral elements, and at least six known viral families were identified. Phylogenetic reconstructions were performed for 4 viral families. All Mansoniini viruses investigated through phylogenetic analysis are closely related to insect-specific viruses found in other mosquito species although with considerable divergence at the amino acid level, suggesting that we have detected new viral lineages. This study enhanced our understanding about the virome of two sylvatic Mansoniini mosquitoes.
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Affiliation(s)
- Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Programa de Pós-graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Núcleo de Bioinformática, Fundação Oswaldo Cruz, Departamento de Entomologia, Recife, Pernambuco, Brazil
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Programa de Pós-graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Núcleo de Bioinformática, Fundação Oswaldo Cruz, Departamento de Entomologia, Recife, Pernambuco, Brazil
| | - Laís Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Programa de Pós-graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Rodrigo Dias de Oliveira
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Hang Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Monica Medeiros Silva
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Programa de Pós-graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Núcleo de Bioinformática, Fundação Oswaldo Cruz, Departamento de Entomologia, Recife, Pernambuco, Brazil.
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