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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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Gómez M, Martínez D, Páez-Triana L, Luna N, Ramírez A, Medina J, Cruz-Saavedra L, Hernández C, Castañeda S, Bohórquez Melo R, Suarez LA, Palma-Cuero M, Murcia LM, González Páez L, Estrada Bustos L, Medina MA, Ariza Campo K, Padilla HD, Zamora Flórez A, De las Salas JL, Muñoz M, Ramírez JD. Influence of dengue virus serotypes on the abundance of Aedes aegypti insect-specific viruses (ISVs). J Virol 2024; 98:e0150723. [PMID: 38095414 PMCID: PMC10804971 DOI: 10.1128/jvi.01507-23] [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: 09/26/2023] [Accepted: 11/13/2023] [Indexed: 01/24/2024] Open
Abstract
A comprehensive understanding of the virome in mosquito vectors is crucial for assessing the potential transmission of viral agents, designing effective vector control strategies, and advancing our knowledge of insect-specific viruses (ISVs). In this study, we utilized Oxford Nanopore Technologies metagenomics to characterize the virome of Aedes aegypti mosquitoes collected in various regions of Colombia, a country hyperendemic for dengue virus (DENV). Analyses were conducted on groups of insects with previous natural DENV infection (DENV-1 and DENV-2 serotypes), as well as mosquito samples that tested negative for virus infection (DENV-negative). Our findings indicate that the Ae. aegypti virome exhibits a similar viral composition at the ISV family and species levels in both DENV-positive and DENV-negative samples across all study sites. However, differences were observed in the relative abundance of viral families such as Phenuiviridae, Partitiviridae, Flaviviridae, Rhabdoviridae, Picornaviridae, Bromoviridae, and Virgaviridae, depending on the serotype of DENV-1 and DENV-2. In addition, ISVs are frequently found in the core virome of Ae. aegypti, such as Phasi Charoen-like phasivirus (PCLV), which was the most prevalent and showed variable abundance in relation to the presence of specific DENV serotypes. Phylogenetic analyses of the L, M, and S segments of the PCLV genome are associated with sequences from different regions of the world but show close clustering with sequences from Brazil and Guadeloupe, indicating a shared evolutionary relationship. The profiling of the Ae. aegypti virome in Colombia presented here improves our understanding of viral diversity within mosquito vectors and provides information that opens the way to possible connections between ISVs and arboviruses. Future studies aimed at deepening our understanding of the mechanisms underlying the interactions between ISVs and DENV serotypes in Ae. aegypti could provide valuable information for the design of effective vector-borne viral disease control and prevention strategies.IMPORTANCEIn this study, we employed a metagenomic approach to characterize the virome of Aedes aegypti mosquitoes, with and without natural DENV infection, in several regions of Colombia. Our findings indicate that the mosquito virome is predominantly composed of insect-specific viruses (ISVs) and that infection with different DENV serotypes (DENV-1 and DENV-2) could lead to alterations in the relative abundance of viral families and species constituting the core virome in Aedes spp. The study also sheds light on the identification of the genome and evolutionary relationships of the Phasi Charoen-like phasivirus in Ae. aegypti in Colombia, a widespread ISV in areas with high DENV incidence.
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Affiliation(s)
- Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
- Grupo de Investigación en Ciencias Básicas (NÚCLEO), Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - David Martínez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Luisa Páez-Triana
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Nicolás Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Angie Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Julián Medina
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Carolina Hernández
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Ramiro Bohórquez Melo
- Grupo de Estudios en Salud Pública de la Amazonía, Laboratorio de Salud Pública de Amazonas, Leticia, Colombia
| | - Luis Alejandro Suarez
- Grupo de Estudios en Salud Pública de la Amazonía, Laboratorio de Salud Pública de Amazonas, Leticia, Colombia
| | - Mónica Palma-Cuero
- Grupo de Estudios en Salud Pública de la Amazonía, Laboratorio de Salud Pública de Amazonas, Leticia, Colombia
| | - Luz Mila Murcia
- Grupo de Estudios en Salud Pública de la Amazonía, Laboratorio de Salud Pública de Amazonas, Leticia, Colombia
| | | | | | | | | | | | | | | | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
- Department of Pathology, Molecular and Cell-Based Medicine, Molecular Microbiology Laboratory, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Litov AG, Belova OA, Kholodilov IS, Kalyanova AS, Gadzhikurbanov MN, Rogova AA, Gmyl LV, Karganova GG. Viromes of Tabanids from Russia. Viruses 2023; 15:2368. [PMID: 38140608 PMCID: PMC10748123 DOI: 10.3390/v15122368] [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: 10/30/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Advances in sequencing technologies and bioinformatics have greatly enhanced our knowledge of virus biodiversity. Currently, the viromes of hematophagous invertebrates, such as mosquitoes and ixodid ticks, are being actively studied. Tabanidae (Diptera) are a widespread family, with members mostly known for their persistent hematophagous behavior. They transmit viral, bacterial, and other pathogens, both biologically and mechanically. However, tabanid viromes remain severely understudied. In this study, we used high-throughput sequencing to describe the viromes of several species in the Hybomitra, Tabanus, Chrysops, and Haematopota genera, which were collected in two distant parts of Russia: the Primorye Territory and Ryazan Region. We assembled fourteen full coding genomes of novel viruses, four partial coding genomes, as well as several fragmented viral sequences, which presumably belong to another twelve new viruses. All the discovered viruses were tested for their ability to replicate in mammalian porcine embryo kidney (PEK), tick HAE/CTVM8, and mosquito C6/36 cell lines. In total, 16 viruses were detected in at least one cell culture after three passages (for PEK and C6/36) or 3 weeks of persistence in HAE/CTVM8. However, in the majority of cases, qPCR showed a decline in virus load over time.
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Affiliation(s)
- Alexander G. Litov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Anna S. Kalyanova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Magomed N. Gadzhikurbanov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasia A. Rogova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
- Institute for Translational Medicine and Biotechnology, Sechenov University, 119991 Moscow, Russia
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Mohamed Ali S, Rakotonirina A, Heng K, Jacquemet E, Volant S, Temmam S, Boyer S, Eloit M. Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia. Viruses 2023; 15:1831. [PMID: 37766237 PMCID: PMC10535147 DOI: 10.3390/v15091831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae, along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown.
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Affiliation(s)
- Souand Mohamed Ali
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Antsa Rakotonirina
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Kimly Heng
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Elise Jacquemet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Sebastien Boyer
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
- Ecology and Emergence of Arthropod-Borne Diseases, Institut Pasteur, 75015 Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 94704 Maisons-Alfort, France
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Hegde S, Rauch HE, Hughes GL, Shariat N. Identification and characterization of two CRISPR/Cas systems associated with the mosquito microbiome. Access Microbiol 2023; 5:acmi000599.v4. [PMID: 37691844 PMCID: PMC10484321 DOI: 10.1099/acmi.0.000599.v4] [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: 03/28/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host-microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two novel clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems in Serratia sp. Ag1, which was isolated from the gut of an Anopheles gambiae mosquito. Two distinct CRISPR/Cas systems were identified in Serratia Ag1, CRISPR1 and CRISPR2. Based on cas gene composition, CRISPR1 is classified as a type I-E CRISPR/Cas system and has a single array, CRISPR1. CRISPR2 is a type I-F system with two arrays, CRISPR2.1 and CRISPR2.2. RT-PCR analyses show that all cas genes from both systems are expressed during logarithmic growth in culture media. The direct repeat sequences of CRISPRs 2.1 and 2.2 are identical and found in the arrays of other Serratia spp., including S. marcescens and S. fonticola , whereas CRISPR1 is not. We searched for potential spacer targets and revealed an interesting difference between the two systems: only 9 % of CRISPR1 (type I-E) targets are in phage sequences and 91 % are in plasmid sequences. Conversely, ~66 % of CRISPR2 (type I-F) targets are found within phage genomes. Our results highlight the presence of CRISPR loci in gut-associated bacteria of mosquitoes and indicate interplay between symbionts and invasive mobile genetic elements over evolutionary time.
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Affiliation(s)
- Shivanand Hegde
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Centre for Neglected Tropical Disease, Liverpool, UK
- Present address: School of Life Sciences, University of Keele, Newcastle, UK
| | - Hallie E. Rauch
- Department of Biology, Gettysburg College, Gettysburg, PA, USA
| | - Grant L. Hughes
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Centre for Neglected Tropical Disease, Liverpool, UK
| | - Nikki Shariat
- Department of Population Health, University of Georgia, Athens, GA, USA
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Xu Y, Xu J, Liu T, Liu P, Chen XG. Metagenomic analysis reveals the virome profiles of Aedes albopictus in Guangzhou, China. Front Cell Infect Microbiol 2023; 13:1133120. [PMID: 37333852 PMCID: PMC10272843 DOI: 10.3389/fcimb.2023.1133120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Aedes albopictus is an aggressive invasive mosquito species widely distributed around the world, and it is also a known vector of arboviruses. Virus metagenomics and RNA interference (RNAi) are important in studying the biology and antiviral defense of Ae. albopictus. However, the virome and potential transmission of plant viruses by Ae. albopictus remain understudied. Methods Mosquito samples of Ae. albopictus were collected from Guangzhou, China, and small RNA sequencing was performed. Raw data were filtered, and virus-associated contigs were generated using VirusDetect. The small RNA profiles were analyzed, and maximum-likelihood phylogenetic trees were constructed. Results The small RNA sequencing of pooled Ae. albopictus revealed the presence of five known viruses, including Wenzhou sobemo-like virus 4, mosquito nodavirus, Aedes flavivirus, Hubei chryso-like virus 1, and Tobacco rattle virus RNA1. Additionally, 21 new viruses that had not been previously reported were identified. The mapping of reads and contig assembly provided insights into the viral diversity and genomic characteristics of these viruses. Field survey confirmed the detection of the identified viruses in Ae. albopictus collected from Guangzhou. Discussion The comprehensive analysis of the virus metagenomics of Ae. albopictus in this study sheds light on the diversity and prevalence of viruses in mosquito populations. The presence of known and novel viruses highlights the need for continued surveillance and investigation into their potential impact on public health. The findings also emphasize the importance of understanding the virome and potential transmission of plant viruses by Ae. albopictus. Conclusion This study provides valuable insights into the virome of Ae. albopictus and its potential role as a vector for both known and novel viruses. Further research is needed to expand the sample size, explore additional viruses, and investigate the implications for public health.
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Affiliation(s)
- Ye Xu
- Department of Pathogen Biology, Institute of Tropical Medicine, School of Public Health, Southern Medical University, Guangzhou, China
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jiabao Xu
- Department of Pathogen Biology, Institute of Tropical Medicine, School of Public Health, Southern Medical University, Guangzhou, China
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Tong Liu
- Department of Pathogen Biology, Institute of Tropical Medicine, School of Public Health, Southern Medical University, Guangzhou, China
| | - Peiwen Liu
- Department of Pathogen Biology, Institute of Tropical Medicine, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xiao-Guang Chen
- Department of Pathogen Biology, Institute of Tropical Medicine, School of Public Health, Southern Medical University, Guangzhou, China
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8
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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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Gómez M, Martinez D, Muñoz M, Ramírez JD. Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission? Parasit Vectors 2022; 15:287. [PMID: 35945559 PMCID: PMC9364528 DOI: 10.1186/s13071-022-05401-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023] Open
Abstract
Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.
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Affiliation(s)
- Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - David Martinez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), 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, USA.
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10
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Djihinto OY, Medjigbodo AA, Gangbadja ARA, Saizonou HM, Lagnika HO, Nanmede D, Djossou L, Bohounton R, Sovegnon PM, Fanou MJ, Agonhossou R, Akoton R, Mousse W, Djogbénou LS. Malaria-Transmitting Vectors Microbiota: Overview and Interactions With Anopheles Mosquito Biology. Front Microbiol 2022; 13:891573. [PMID: 35668761 PMCID: PMC9164165 DOI: 10.3389/fmicb.2022.891573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Malaria remains a vector-borne infectious disease that is still a major public health concern worldwide, especially in tropical regions. Malaria is caused by a protozoan parasite of the genus Plasmodium and transmitted through the bite of infected female Anopheles mosquitoes. The control interventions targeting mosquito vectors have achieved significant success during the last two decades and rely mainly on the use of chemical insecticides through the insecticide-treated nets (ITNs) and indoor residual spraying (IRS). Unfortunately, resistance to conventional insecticides currently being used in public health is spreading in the natural mosquito populations, hampering the long-term success of the current vector control strategies. Thus, to achieve the goal of malaria elimination, it appears necessary to improve vector control approaches through the development of novel environment-friendly tools. Mosquito microbiota has by now given rise to the expansion of innovative control tools, such as the use of endosymbionts to target insect vectors, known as "symbiotic control." In this review, we will present the viral, fungal and bacterial diversity of Anopheles mosquitoes, including the bacteriophages. This review discusses the likely interactions between the vector microbiota and its fitness and resistance to insecticides.
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Affiliation(s)
- Oswald Y. Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Adandé A. Medjigbodo
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Albert R. A. Gangbadja
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Helga M. Saizonou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Hamirath O. Lagnika
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Dyane Nanmede
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Laurette Djossou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Roméo Bohounton
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Pierre Marie Sovegnon
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Marie-Joel Fanou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Romuald Agonhossou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Romaric Akoton
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Wassiyath Mousse
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Luc S. Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
- Regional Institute of Public Health, University of Abomey-Calavi, Ouidah, Benin
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11
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Krokovsky L, Paiva MHS, Guedes DRD, Barbosa RMR, de Oliveira ALS, Anastácio DB, Pontes CR, Ayres CFJ. Arbovirus Surveillance in Field-Collected Mosquitoes From Pernambuco-Brazil, During the Triple Dengue, Zika and Chikungunya Outbreak of 2015-2017. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.875031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The (re) emergence of arboviruses around the world is a public health concern once severe outbreaks are usually associated with these infections. The co-circulation of Dengue (DENV), Zika (ZIKV) and Chikungunya (CHIKV) viruses in the past few years has caused a unique epidemic situation in Brazil. The northeast region of the country was the most affected by clinical complications from such arboviruses’ infections, including neurological disorders caused by ZIKV. In this particular region, Aedes mosquitoes are the main vectors of DENV, ZIKV and CHIKV, with Culex quinquefasciatus also considered as a potential vector of ZIKV. Therefore, virological surveillance in mosquitoes contributes to understanding the epidemiological profile of these diseases. Here, we report the circulation of DENV, ZIKV and CHIKV in Aedes spp. and Cx. quinquefasciatus female mosquitoes collected in areas with a high arbovirus circulation in humans in the Metropolitan Region of Recife, Pernambuco, Brazil, during the triple-epidemics of 2015-17. All the field-caught mosquitoes were sent to the laboratory for arbovirus screening after RNA extraction and RT-PCR/RT-qPCR. A total of 6,227 females were evaluated and, as a result, DENV, ZIKV and CHIKV were identified in Ae. aegypti, Ae. taeniorhynchus and Cx. quinquefasciatus mosquito pools. In addition, DENV and ZIKV were isolated in C6/36 cells. In conclusion, it is important to highlight that arbovirus surveillance performed in mosquitoes from DENV-ZIKV-CHIKV hotspots areas can serve as an early-warning system to target vector control actions more efficiently in each studied area.
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12
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Hussain AG, Wennmann JT, Goergen G, Bryon A, Ros VI. Viruses of the Fall Armyworm Spodoptera frugiperda: A Review with Prospects for Biological Control. Viruses 2021; 13:v13112220. [PMID: 34835026 PMCID: PMC8625175 DOI: 10.3390/v13112220] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/17/2022] Open
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is a native pest species in the Western hemisphere. Since it was first reported in Africa in 2016, FAW has spread throughout the African continent and is now also present in several countries in Asia as well as Australia. The invasion of FAW in these areas has led to a high yield reduction in crops, leading to huge economic losses. FAW management options in the newly invaded areas are limited and mainly rely on the use of synthetic pesticides. Since there is a risk of resistance development against pesticides in addition to the negative environmental and human health impacts, other effective, sustainable, and cost-efficient control alternatives are desired. Insect pathogenic viruses fulfil these criteria as they are usually effective and highly host-specific with no significant harmful effect on beneficial insects and non-target organisms. In this review, we discuss all viruses known from FAW and their potential to be used for biological control. We specifically focus on baculoviruses and describe the recent advancements in the use of baculoviruses for biological control in the native geographic origin of FAW, and their potential use in the newly invaded areas. Finally, we identify current knowledge gaps and suggest new avenues for productive research on the use of viruses as a biopesticide against FAW.
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Affiliation(s)
- Ahmed G. Hussain
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.G.H.); (A.B.)
| | - Jörg T. Wennmann
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany;
| | - Georg Goergen
- International Institute of Tropical Agriculture (IITA), Biological Control Centre for Africa, Cotonou 08 BP 0932, Benin;
| | - Astrid Bryon
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.G.H.); (A.B.)
| | - Vera I.D. Ros
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.G.H.); (A.B.)
- Correspondence:
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13
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Virome in adult Aedes albopictus captured during different seasons in Guangzhou City, China. Parasit Vectors 2021; 14:415. [PMID: 34407871 PMCID: PMC8371599 DOI: 10.1186/s13071-021-04922-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/03/2021] [Indexed: 01/09/2023] Open
Abstract
Background The mosquito Aedes albopictus is an important vector for many pathogens. Understanding the virome in Ae. albopictus is critical for assessing the risk of disease transmission, implementation of vector control measures, and health system strengthening. Methods In this study, viral metagenomic and PCR methods were used to reveal the virome in adult Ae. albopictus captured in different areas and during different seasons in Guangzhou, China. Results The viral composition of adult Ae. albopictus varied mainly between seasons. Over 50 viral families were found, which were specific to vertebrates, invertebrates, plants, fungi, bacteria, and protozoa. In rural areas, Siphoviridae (6.5%) was the most common viral family harbored by mosquitoes captured during winter and spring, while Luteoviridae (1.1%) was the most common viral family harbored by mosquitoes captured during summer and autumn. Myoviridae (7.0% and 1.3%) was the most common viral family in mosquitoes captured in urban areas during all seasons. Hepatitis B virus (HBV) was detected by PCR in a female mosquito pool. The first near full-length HBV genome from Ae. albopictus was amplified, which showed a high level of similarity with human HBV genotype B sequences. Human parechovirus (HPeV) was detected in male and female mosquito pools, and the sequences were clustered with HPeV 1 and 3 sequences. Conclusions Large numbers of viral species were found in adult Ae. albopictus, including viruses from vertebrates, insects, and plants. The viral composition in Ae. albopictus mainly varied between seasons. Herein, we are the first to report the detection of HPeV and HBV in mosquitoes. This study not only provides valuable information for the control and prevention of mosquito-borne diseases, but it also demonstrates the feasibility of xenosurveillance. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04922-z.
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14
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He W, Gao Y, Wen Y, Ke X, Ou Z, Li Y, He H, Chen Q. Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats. Front Microbiol 2021; 12:653873. [PMID: 34177835 PMCID: PMC8221242 DOI: 10.3389/fmicb.2021.653873] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Hepatitis is a major global health concern. However, the etiology of 10-20% hepatitis cases remains unclear. Some hepatitis-associated viruses, like the hepatitis E virus, are zoonotic pathogens. Rats, shrews, and bats are reservoirs for many zoonotic pathogens. Therefore, understanding the virome in the liver of these animals is important for the investigation of the etiologies of hepatitis and monitoring the emerging zoonotic viruses. In this study, viral metagenomics and PCR methods were used to investigate viral communities in rats, mice, house shrews, and bats livers. Viral metagenomic analysis showed a diverse set of sequences in liver samples, comprising: sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses. Using PCR methods, we first detected hepatovirus sequences in Hipposideros larvatus (3.85%). We also reported the first detection of Zika virus-related sequences in rats and house shrews. Sequences related to influenza A virus and herpesviruses were detected in liver. Higher detection rates of pegivirus sequences were found in liver tissue and serum samples from rats (7.85% and 15.79%, respectively) than from house shrews. Torque teno virus sequences had higher detection rates in the serum samples of rats and house shrews (52.72% and 5.26%, respectively) than in the liver. Near-full length genomes of pegivirus and torque teno virus were amplified. This study is the first to compare the viral communities in the liver of bats, rats, mice, and house shrews. Its findings expand our understanding of the virome in the liver of these animals and provide an insight into hepatitis-related viruses.
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Affiliation(s)
- Wenqiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuhan Gao
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuqi Wen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Xuemei Ke
- Xiamen Center for Disease Control and Prevention, Xiamen, China
| | - Zejin Ou
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yongzhi Li
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Huan He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
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15
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Batson J, Dudas G, Haas-Stapleton E, Kistler AL, Li LM, Logan P, Ratnasiri K, Retallack H. Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay. eLife 2021; 10:e68353. [PMID: 33904402 PMCID: PMC8110308 DOI: 10.7554/elife.68353] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Mosquitoes are major infectious disease-carrying vectors. Assessment of current and future risks associated with the mosquito population requires knowledge of the full repertoire of pathogens they carry, including novel viruses, as well as their blood meal sources. Unbiased metatranscriptomic sequencing of individual mosquitoes offers a straightforward, rapid, and quantitative means to acquire this information. Here, we profile 148 diverse wild-caught mosquitoes collected in California and detect sequences from eukaryotes, prokaryotes, 24 known and 46 novel viral species. Importantly, sequencing individuals greatly enhanced the value of the biological information obtained. It allowed us to (a) speciate host mosquito, (b) compute the prevalence of each microbe and recognize a high frequency of viral co-infections, (c) associate animal pathogens with specific blood meal sources, and (d) apply simple co-occurrence methods to recover previously undetected components of highly prevalent segmented viruses. In the context of emerging diseases, where knowledge about vectors, pathogens, and reservoirs is lacking, the approaches described here can provide actionable information for public health surveillance and intervention decisions.
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Affiliation(s)
| | - Gytis Dudas
- Gothenburg Global Biodiversity CentreGothenburgSweden
| | | | | | - Lucy M Li
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | - Kalani Ratnasiri
- Program in Immunology, Stanford University School of MedicineStanfordUnited States
| | - Hanna Retallack
- Department of Biochemistry and Biophysics, University of California San FranciscoSan FranciscoUnited States
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16
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Nebbak A, Monteil-Bouchard S, Berenger JM, Almeras L, Parola P, Desnues C. Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France. Viruses 2021; 13:v13050768. [PMID: 33925487 PMCID: PMC8145591 DOI: 10.3390/v13050768] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 12/28/2022] Open
Abstract
Some mosquito species have significant public health importance given their ability to transmit major diseases to humans and animals, making them the deadliest animals in the world. Among these, the Aedes (Ae.) genus is a vector of several viruses such as Dengue, Chikungunya, and Zika viruses that can cause serious pathologies in humans. Since 2004, Ae. albopictus has been encountered in the South of France, and autochthonous cases of Dengue, Chikungunya, and Zika diseases have recently been reported, further highlighting the need for a comprehensive survey of the mosquitoes and their associated viruses in this area. Using high throughput sequencing (HTS) techniques, we report an analysis of the DNA and RNA viral communities of three mosquito species Ae. albopictus, Culex (Cx.) pipiens, and Culiseta (Cs.) longiareolata vectors of human infectious diseases in a small sub-urban city in the South of France. Results revealed the presence of a significant diversity of viruses known to infect bacteria, plants, insects, and mammals. Several novel viruses were detected, including novel members of the Rhabdoviridae, Totiviridae, Iflaviviridae, Circoviridae, and Sobemoviridae families. No sequence related to major zoonotic viruses transmitted by mosquitoes was detected. The use of HTS on arthropod vector populations is a promising strategy for monitoring the emergence and circulation of zoonoses and epizooties. This study is a contribution to the knowledge of the mosquito microbiome.
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Affiliation(s)
- Amira Nebbak
- IHU-Méditerranée Infection, 13005 Marseille, France; (A.N.); (J.-M.B.); (L.A.); (P.P.)
- Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs Infections Tropicales et Méditerranéennes (VITROME), 13005 Marseille, France
- Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), BP 384, Zone Industrielle, Bou-Ismail RP 42004, Tipaza, Algeria
| | - Sonia Monteil-Bouchard
- Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI) UM 63, 13005 Marseille, France;
- Aix-Marseille Université, Université de Toulon, Centre National pour la Recherche Scientifique (CNRS), Intitut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France
| | - Jean-Michel Berenger
- IHU-Méditerranée Infection, 13005 Marseille, France; (A.N.); (J.-M.B.); (L.A.); (P.P.)
- Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs Infections Tropicales et Méditerranéennes (VITROME), 13005 Marseille, France
| | - Lionel Almeras
- IHU-Méditerranée Infection, 13005 Marseille, France; (A.N.); (J.-M.B.); (L.A.); (P.P.)
- Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs Infections Tropicales et Méditerranéennes (VITROME), 13005 Marseille, France
- Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
| | - Philippe Parola
- IHU-Méditerranée Infection, 13005 Marseille, France; (A.N.); (J.-M.B.); (L.A.); (P.P.)
- Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs Infections Tropicales et Méditerranéennes (VITROME), 13005 Marseille, France
| | - Christelle Desnues
- Aix Marseille Université, Intitut de Recherche pour le Développement (IRD), Assistance Publique-Hopitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI) UM 63, 13005 Marseille, France;
- Aix-Marseille Université, Université de Toulon, Centre National pour la Recherche Scientifique (CNRS), Intitut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France
- Correspondence:
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17
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He X, Yin Q, Zhou L, Meng L, Hu W, Li F, Li Y, Han K, Zhang S, Fu S, Zhang X, Wang J, Xu S, Zhang Y, He Y, Dong M, Shen X, Zhang Z, Nie K, Liang G, Ma X, Wang H. Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region, China. PLoS Negl Trop Dis 2021; 15:e0009381. [PMID: 33901182 PMCID: PMC8101993 DOI: 10.1371/journal.pntd.0009381] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 05/06/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently. METHODS Mosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes. RESULTS A total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes. CONCLUSION Viral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.
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Affiliation(s)
- Xiaozhou He
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Qikai Yin
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Liwei Zhou
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, People’s Republic of China
| | - Lei Meng
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, People’s Republic of China
| | - Weijun Hu
- Shaanxi Provincial Center for Disease Control and Prevention, Xi’an, People’s Republic of China
| | - Fan Li
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Kun Han
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, People’s Republic of China
| | - Shaobai Zhang
- Shaanxi Provincial Center for Disease Control and Prevention, Xi’an, People’s Republic of China
| | - Shihong Fu
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiaoshu Zhang
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, People’s Republic of China
| | - Ji Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Songtao Xu
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yi Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ying He
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Maoxing Dong
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, People’s Republic of China
| | - Xinxin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zheng Zhang
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, People’s Republic of China
| | - Kai Nie
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Guodong Liang
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- * E-mail: (XJM); (HYW)
| | - Huanyu Wang
- Chinese Center for Disease Control and Prevention -Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- * E-mail: (XJM); (HYW)
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Abstract
Culex modestus mosquitoes are considered potential transmission vectors of West Nile virus and Usutu virus. Their presence has been reported across several European countries, including one larva detected in Belgium in 2018. In this study, mosquitoes were collected in the city of Leuven and surrounding areas in the summers of 2019 and 2020. Species identification was performed based on morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene. The 107 mosquitoes collected in 2019 belonged to eight mosquito species, Culex pipiens (24.3%), Cx. modestus (48.6%), Cx. torrentium (0.9%), Culiseta annulata (0.9%), Culiseta morsitans (0.9%), Aedes sticticus (14.0%), Aedes cinereus (9.3%), and Anopheles plumbeus (0.9%), suggesting the presence of an established Cx. modestus population in Belgium. The collection of Cx. modestus mosquitoes at the same locations in 2020 confirmed their establishment in the region. Haplotype network analysis of the COI sequences for Cx. modestus showed that the Belgian population is rather diverse, suggesting that it may have been established in Belgium for some time. The Belgian Cx. modestus population was most closely related to populations from the United Kingdom and Germany. Characterization of the virome of the collected mosquitoes resulted in the identification of at least 33 eukaryotic viral species. Nine (nearly) complete genomes belonging to 6 viral species were identified, all of which were closely related to known viruses. In conclusion, here, we report the presence of Cx. modestus in the surrounding areas of Leuven, Belgium. As this species is considered to be a vector of several arboviruses, the implementation of vector surveillance programs to monitor this species is recommended. IMPORTANCECulex modestus mosquitoes are considered to be a potential “bridge” vector, being able to transmit pathogens between birds as well as from birds to mammals, including humans. In Belgium, this mosquito species was considered absent until the finding of one larva in 2018 and subsequent evidence of a large population in 2019 to 2020 described here. We collected mosquitoes in the summers of 2019 and 2020 in the city of Leuven and surrounding areas. The mosquito species was identified by morphological and molecular methods, demonstrating the presence of Cx. modestus in this region. The ability of mosquitoes to transmit pathogens can depend on several factors, one of them being their natural virus composition. Therefore, we identified the mosquito-specific viruses harbored by Belgian mosquitoes. As Cx. modestus is able to transmit viruses such as West Nile virus and Usutu virus, the establishment of this mosquito species may increase the risk of virus transmission in the region. It is thus advisable to implement mosquito surveillance programs to monitor this species.
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Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Sci Rep 2021; 11:6921. [PMID: 33767340 PMCID: PMC7994813 DOI: 10.1038/s41598-021-86427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.
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20
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Hameed M, Wahaab A, Shan T, Wang X, Khan S, Di D, Xiqian L, Zhang JJ, Anwar MN, Nawaz M, Li B, Liu K, Shao D, Qiu Y, Wei J, Ma Z. A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan-Myanmar Border of China. Front Microbiol 2021; 11:591478. [PMID: 33628201 PMCID: PMC7898981 DOI: 10.3389/fmicb.2020.591478] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Metagenomic analysis of mosquito-borne and mosquito-specific viruses is useful to understand the viral diversity and for the surveillance of pathogens of medical and veterinary importance. Yunnan province is located at the southwest of China and has rich abundance of mosquitoes. Arbovirus surveillance is not conducted regularly in this province particularly at animal farms, which have public health as well as veterinary importance. Here, we have analyzed 10 pools of mosquitoes belonging to Culex tritaeniorhyncus, Aedes aegypti, Anopheles sinensis, and Armigeres subalbatus species, collected from different animal farms located at Yunnan province of China by using metagenomic next-generation sequencing technique. The generated viral metagenomic data reveal that the viral community matched by the reads was highly diverse and varied in abundance among animal farms, which contained more than 19 viral taxonomic families, specific to vertebrates, invertebrates, fungi, plants, protozoa, and bacteria. Additionally, a large number of viral reads were related to viruses that are non-classified. The viral reads related to animal viruses included parvoviruses, anelloviruses, circoviruses, flaviviruses, rhabdoviruses, and seadornaviruses, which might be taken by mosquitoes from viremic animal hosts during blood feeding. Notably, the presence of viral reads matched with Japanese encephalitis virus, Getah virus, and porcine parvoviruses in mosquitoes collected from different geographic sites suggested a potential circulation of these viruses in their vertebrate hosts. Overall, this study provides a comprehensive knowledge of diverse viral populations present at animal farms of Yunnan province of China, which might be a potential source of diseases for humans and domestic animals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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21
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Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes. mSystems 2020; 5:5/5/e00640-20. [PMID: 32994288 PMCID: PMC7527137 DOI: 10.1128/msystems.00640-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aedes mosquitoes can efficiently transmit many pathogenic arboviruses, placing a great burden on public health worldwide. In addition, they also carry a number of insect-specific viruses (ISVs), and it was recently suggested that some of these ISVs might form a stable species-specific "core virome" in mosquito populations. However, little is known about such a core virome in laboratory colonies and if it is present across different developmental stages. In this study, we compared the viromes in eggs, larvae, pupae, and adults of Aedes albopictus mosquitoes collected from a lab colony and compared each to the virome of different developmental stages collected in the field. The virome in lab-derived A. albopictus was very stable across all stages, consistent with a vertical transmission route of these viruses, and formed a possible "vertically transmitted core virome." The different stages of field-collected A. albopictus mosquitoes also contained this stable vertically transmitted core virome, as well as another set of viruses (e.g., viruses distantly related to Guadeloupe mosquito virus, Hubei virga-like virus 2, and Sarawak virus) shared by mosquitoes across different stages, which might represent an "environment-derived core virome." To further study this core set of ISVs, we screened 48 publicly available SRA viral metagenomic data sets of mosquitoes belonging to the genus Aedes, showing that some of the identified ISVs were identified in the majority of SRAs and providing further evidence supporting the core-virome concept.IMPORTANCE Our study revealed that the virome was very stable across all developmental stages of both lab-derived and field-collected Aedes albopictus The data representing the core virome in lab A. albopictus proved the vertical transmission route of these viruses, forming a "vertically transmitted core virome." Field mosquitoes also contained this stable vertically transmitted core virome as well as additional viruses, which probably represented "environment-derived core virome" and which therefore were less stable over time and geography. By further screening publicly available SRA viral metagenomic data sets from mosquitoes belonging to the genus Aedes, some of the identified core ISVs were shown to be present in the majority of SRAs, such as Phasi Charoen-like phasivirus and Guadeloupe mosquito virus. How these core ISVs influence the biology of the mosquito host and arbovirus infection and evolution deserves to be further explored.
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22
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St.Hilaire M, Austin S, Landis RC, Steininger C. Highly Sensitive Virome Characterization of Aedes aegypti and Culex pipiens Complex from Central Europe and the Caribbean Reveals Potential for Interspecies Viral Transmission. Pathogens 2020; 9:E686. [PMID: 32839419 PMCID: PMC7559857 DOI: 10.3390/pathogens9090686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022] Open
Abstract
Mosquitoes are the most important vectors for arthropod-borne viral diseases. Mixed viral infections of mosquitoes allow genetic recombination or reassortment of diverse viruses, turning mosquitoes into potential virologic mixing bowls. In this study, we field-collected mosquitoes of different species (Aedes aegypti and Culex pipiens complex), from different geographic locations and environments (central Europe and the Caribbean) for highly sensitive next-generation sequencing-based virome characterization. We found a rich virus community associated with a great diversity of host species. Among those, we detected a large diversity of novel virus sequences that we could predominately assign to circular Rep-encoding single-stranded (CRESS) DNA viruses, including the full-length genome of a yet undescribed Gemykrogvirus species. Moreover, we report for the first time the detection of a potentially zoonotic CRESS-DNA virus (Cyclovirus VN) in mosquito vectors. This study expands the knowledge on virus diversity in medically important mosquito vectors, especially for CRESS-DNA viruses that have previously been shown to easily recombine and jump the species barrier.
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Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
| | - Nicolas Rascovan
- Department of Genomes & Genetics, Institut Pasteur, 75015 Paris, France;
| | - Anna Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, 8036 Graz, Austria;
| | - Carina Zittra
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (C.Z.); (H.-P.F.)
- Unit Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, 1010 Vienna, Austria
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (C.Z.); (H.-P.F.)
| | - Thea Scantlebury-Manning
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados; (T.S.-M.); (S.A.)
| | - Marquita Gittens-St.Hilaire
- Faculty of Medical Sciences, University of the West Indies, Queen Elizabeth Hospital, St. Michael BB14004, Barbados;
| | - Shane Austin
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados; (T.S.-M.); (S.A.)
| | - Robert Clive Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown BB11115, Barbados;
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
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Birnberg L, Temmam S, Aranda C, Correa-Fiz F, Talavera S, Bigot T, Eloit M, Busquets N. Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes. Viruses 2020; 12:E274. [PMID: 32121402 PMCID: PMC7150749 DOI: 10.3390/v12030274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 01/10/2023] Open
Abstract
Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public and animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% of the recognized EIDs. To assess new alternatives for arthropod-borne viral diseases surveillance, and for the detection of new viruses, honey-baited Flinders Technology Associates (FTA) cards were used as sugar bait in mosquito traps during entomological surveys at the Llobregat River Delta (Catalonia, Spain). Next generation sequencing (NGS) metagenomics analysis was applied on honey-baited FTA cards, which had been exposed to field-captured mosquitoes to characterize their associated virome. Arthropod- and plant-infecting viruses governed the virome profile on FTA cards. Twelve near-complete viral genomes were successfully obtained, suggesting good quality preservation of viral RNAs. Mosquito pools linked to the FTA cards were screened for the detection of mosquito-associated viruses by specific RT-PCRs to confirm the presence of these viruses. The circulation of viruses related to Alphamesonivirus, Quaranjavirus and unclassified Bunyavirales was detected in mosquitoes, and phylogenetic analyses revealed their similarities to viruses previously reported in other continents. To the best our knowledge, our findings constitute the first distribution record of these viruses in European mosquitoes and the first hint of insect-specific viruses in mosquitoes' saliva in field conditions, demonstrating the feasibility of this approach to monitor the transmissible fraction of the mosquitoes' virome. In conclusion, this pilot viromics study on honey-baited FTA cards was shown to be a valid approach for the detection of viruses circulating in mosquitoes, thereby setting up an alternative tool for arbovirus surveillance and control programs.
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Affiliation(s)
- Lotty Birnberg
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
| | - Sarah Temmam
- Institut Pasteur, Pathogen Discovery Laboratory, 75015 Paris, France; (S.T.); (T.B.); (M.E.)
| | - Carles Aranda
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
- Servei de Control de Mosquits del Consell Comarcal del Baix Llobregat, 08820 Barcelona, Spain
| | - Florencia Correa-Fiz
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
| | - Sandra Talavera
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
| | - Thomas Bigot
- Institut Pasteur, Pathogen Discovery Laboratory, 75015 Paris, France; (S.T.); (T.B.); (M.E.)
- Institut Pasteur – Bioinformatics and Biostatistics Hub—Computational Biology department, Institut Pasteur, USR 3756 CNRS—75015 Paris, France
| | - Marc Eloit
- Institut Pasteur, Pathogen Discovery Laboratory, 75015 Paris, France; (S.T.); (T.B.); (M.E.)
- National Veterinary School of Alfort, Paris-Est University, 94704 CEDEX, Maisons-Alfort, France
| | - Núria Busquets
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
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24
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Deciphering the Virome of Culex vishnui Subgroup Mosquitoes, the Major Vectors of Japanese Encephalitis, in Japan. Viruses 2020; 12:v12030264. [PMID: 32121094 PMCID: PMC7150981 DOI: 10.3390/v12030264] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
Japanese encephalitis (JE) remains a public health concern in several countries, and the Culex mosquito plays a central role in its transmission cycle. Culex mosquitoes harbor a wide range of viruses, including insect-specific viruses (ISVs), and can transmit a variety of arthropod-borne viruses (arboviruses) that cause human and animal diseases. The current trend of studies displays enhanced efforts to characterize the mosquito virome through bulk RNA sequencing due to possible arbovirus-ISV interactions; however, the extent of viral diversity in the mosquito taxon is still poorly understood, particularly in some disease vectors. In this study, arboviral screening and RNA virome analysis of Culex tritaeniorhynchus and C. pseudovishnui, which are part of the Culex vishnui subgroup mosquitoes, were performed. Results from these two mosquito species, known as the major vectors of JE virus (JEV) in Asia, collected in three prefectures in Japan were also compared with the sympatric species C. inatomii. A total of 27 viruses, including JEV, were detected from these Culex mosquitoes. Molecular and phylogenetic analyses of the detected viruses classified 15 of the 27 viruses as novel species, notably belonging to the Flaviviridae, Rhabdoviridae, Totiviridae, and Iflaviridae families. The successful isolation of JEV genotype I confirmed its continuous presence in Japan, suggesting the need for periodic surveillance. Aside from JEV, this study has also reported the diversity of the RNA virome of disease vectors and broadened the knowledge on mosquito virome profiles containing both arbovirus and ISV. Mosquito taxon seemed to contribute largely to the virome structure (e.g., virome composition, diversity, and abundance) as opposed to the geographical location of the mosquito species. This study therefore offers notable insights into the ecology and evolution of each identified virus and viral family. To the authors' knowledge, this is the first study to characterize the viromes of the major JE vectors in Japan.
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Bourgarel M, Noël V, Pfukenyi D, Michaux J, André A, Becquart P, Cerqueira F, Barrachina C, Boué V, Talignani L, Matope G, Missé D, Morand S, Liégeois F. Next-Generation Sequencing on Insectivorous Bat Guano: An Accurate Tool to Identify Arthropod Viruses of Potential Agricultural Concern. Viruses 2019; 11:v11121102. [PMID: 31795197 PMCID: PMC6950063 DOI: 10.3390/v11121102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/12/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Viruses belonging to the Dicistroviridae family have attracted a great deal of attention from scientists owing to their negative impact on agricultural economics, as well as their recent identification as potential aetiological agents of febrile illness in human patients. On the other hand, some Dicistroviruses are also studied for their potential biopesticide properties. To date, Dicistrovirus characterized in African mainland remain scarce. By using High-Throughput Sequencing technology on insectivorous bat faeces (Hipposideros Caffer) sampled in a cave used by humans to collect bat guano (bat manure) as fertilizer in Zimbabwe, we characterized the full-length sequences of three Dicistrovirus belonging to the Cripavirus and Aparavirus genus: Big Sioux River Virus-Like (BSRV-Like), Acute Bee Paralysis Virus (ABPV), and Aphid Lethal Paralysis Virus (ALPV). Phylogenetic analyses of ORF-1 and ORF-2 genes showed a complex evolutionary history between BSRV and close viruses, as well as for the Aparavirus genus. Herewith, we provide the first evidence of the presence of Dicistrovirus in Zimbabwe and highlight the need to further document the impact of such viruses on crops, as well as in beekeeping activities in Zimbabwe which represent a crucial source of income for Zimbabwean people.
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Affiliation(s)
- Mathieu Bourgarel
- Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France; (M.B.); (S.M.)
- Centre International de Recherche Agronomique pour le Développement (CIRAD), Research Platform-Production and Conservation in Partership, Unité Mixe de Recherche ASTRE, Harare, Zimbabwe
| | - Valérie Noël
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Davies Pfukenyi
- Faculty of Veterinary Science, University of Zimbabwe, P.O. Box MP167, Mt. Pleasant Harare P.O. Box MP167, Zimbabwe; (D.P.); (G.M.)
| | - Johan Michaux
- Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France; (M.B.); (S.M.)
- Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium; (J.M.); (A.A.)
| | - Adrien André
- Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium; (J.M.); (A.A.)
| | - Pierre Becquart
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Frédérique Cerqueira
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, Centre National de Recherche Scientifique (CNRS), Ecole Pratique des Hautes Etude (EPHE)s, Institut de Recherche pour le Développement (IRD), 34398 Montpellier, France;
| | - Célia Barrachina
- Montpellier GenomiX (MGX), Biocampus Montpellier, Centre National de Recherche Scientifique (CNRS), Intitut National de la Santé et de la Recherche Médicale (INSERM), Univ Montpellier, 34094 Montpellier, France;
| | - Vanina Boué
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Loïc Talignani
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Gift Matope
- Faculty of Veterinary Science, University of Zimbabwe, P.O. Box MP167, Mt. Pleasant Harare P.O. Box MP167, Zimbabwe; (D.P.); (G.M.)
| | - Dorothée Missé
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Serge Morand
- Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France; (M.B.); (S.M.)
- Institut des Sciences de l’Evolution de Montpellier (ISEM) Univ. Montpellier, Centre National de Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Centre International de Recherche Agronomique pour le Développement (CIRAD), 34000 Montpellier, France
| | - Florian Liégeois
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
- Correspondence:
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Hameed M, Liu K, Anwar MN, Wahaab A, Li C, Di D, Wang X, Khan S, Xu J, Li B, Nawaz M, Shao D, Qiu Y, Wei J, Ma Z. A viral metagenomic analysis reveals rich viral abundance and diversity in mosquitoes from pig farms. Transbound Emerg Dis 2019; 67:328-343. [PMID: 31512812 DOI: 10.1111/tbed.13355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 08/02/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022]
Abstract
Mosquitoes harbour a diversity of viruses and are responsible for several mosquito-borne viral diseases of humans and animals, thereby leading to major public health concerns, and significant economic losses across the globe. Viral metagenomics offers a great opportunity for bulk analysis of viral genomes retrieved directly from environmental samples. In this study, we performed a viral metagenomic analysis of five pools of mosquitoes belonging to Aedes, Anopheles and Culex species, collected from different pig farms in the vicinity of Shanghai, China, to explore the viral community carried by mosquitoes. The resulting metagenomic data revealed that viral community in the mosquitoes was highly diverse and varied in abundance among pig farms, which comprised of more than 48 viral taxonomic families, specific to vertebrates, invertebrates, plants, fungi, bacteria and protozoa. In addition, a considerable number of viral reads were related to viruses that are not classified by host. The read sequences related to animal viruses included parvoviruses, anelloviruses, circoviruses, flavivirus, rhabdovirus and seadornaviruses, which might be taken up by mosquitoes from viremic animal hosts during blood feeding. Notably, sample G1 contained the most abundant sequence related to Banna virus, which is of public health interest because it causes encephalitis in humans. Furthermore, non-classified viruses also shared considerable virus sequences in all the samples, presumably belonging to unexplored virus category. Overall, the present study provides a comprehensive knowledge of diverse viral populations carried by mosquitoes at pig farms, which is a potential source of diseases for mammals including humans and animals. These viral metagenomic data are valuable for assessment of emerging and re-emerging viral epidemics.
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Affiliation(s)
- Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Chenxi Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Di Di
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Xin Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Sawar Khan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Jinpeng Xu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Mohsin Nawaz
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
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Scolari F, Casiraghi M, Bonizzoni M. Aedes spp. and Their Microbiota: A Review. Front Microbiol 2019; 10:2036. [PMID: 31551973 PMCID: PMC6738348 DOI: 10.3389/fmicb.2019.02036] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Aedes spp. are a major public health concern due to their ability to be efficient vectors of dengue, Chikungunya, Zika, and other arboviruses. With limited vaccines available and no effective therapeutic treatments against arboviruses, the control of Aedes spp. populations is currently the only strategy to prevent disease transmission. Host-associated microbes (i.e., microbiota) recently emerged as a promising field to be explored for novel environmentally friendly vector control strategies. In particular, gut microbiota is revealing its impact on multiple aspects of Aedes spp. biology, including vector competence, thus being a promising target for manipulation. Here we describe the technological advances, which are currently expanding our understanding of microbiota composition, abundance, variability, and function in the two main arboviral vectors, the mosquitoes Aedes aegypti and Aedes albopictus. Aedes spp. microbiota is described in light of its tight connections with the environment, with which mosquitoes interact during their various developmental stages. Unraveling the dynamic interactions among the ecology of the habitat, the mosquito and the microbiota have the potential to uncover novel physiological interdependencies and provide a novel perspective for mosquito control.
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Affiliation(s)
- Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Maurizio Casiraghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Shi C, Beller L, Deboutte W, Yinda KC, Delang L, Vega-Rúa A, Failloux AB, Matthijnssens J. Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics. MICROBIOME 2019; 7:121. [PMID: 31462331 PMCID: PMC6714450 DOI: 10.1186/s40168-019-0734-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/13/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies generally performed metagenomics sequencing on pools of mosquitoes, without assessment of the viral diversity in individual mosquitoes. To address this issue, we applied our optimized viral metagenomics protocol (NetoVIR) to compare the virome of single and pooled Aedes aegypti and Culex quinquefasciatus mosquitoes collected from different locations in Guadeloupe, in 2016 and 2017. RESULTS The total read number and viral reads proportion of samples containing a single mosquito have no significant difference compared with those of pools containing five mosquitoes, which proved the feasibility of using single mosquito for viral metagenomics. A comparative analysis of the virome revealed a higher abundance and more diverse eukaryotic virome in Aedes aegypti, whereas Culex quinquefasciatus harbors a richer and more diverse phageome. The majority of the identified eukaryotic viruses were mosquito-species specific. We further characterized the genomes of 11 novel eukaryotic viruses. Furthermore, qRT-PCR analyses of the six most abundant eukaryotic viruses indicated that the majority of individual mosquitoes were infected by several of the selected viruses with viral genome copies per mosquito ranging from 267 to 1.01 × 108 (median 7.5 × 106) for Ae. aegypti and 192 to 8.69 × 106 (median 4.87 × 104) for Cx. quinquefasciatus. Additionally, in Cx. quinquefasciatus, a number of phage contigs co-occurred with several marker genes of Wolbachia sp. strain wPip. CONCLUSIONS We firstly demonstrate the feasibility to use single mosquito for viral metagenomics, which can provide much more precise virome profiles of mosquito populations. Interspecific comparisons show striking differences in abundance and diversity between the viromes of Ae. aegypti and Cx. quinquefasciatus. Those two mosquito species seem to have their own relatively stable "core eukaryotic virome", which might have important implications for the competence to transmit important medically relevant arboviruses. The presence of Wolbachia in Cx. quinquefasciatus might explain (1) the lower overall viral load compared to Ae. aegypti, (2) the identification of multiple unknown phage contigs, and (3) the difference in competence for important human pathogens. How these viruses, phages, and bacteria influence the physiology and vector competence of mosquito hosts warrants further research.
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Affiliation(s)
- Chenyan Shi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Leen Beller
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Kwe Claude Yinda
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT USA
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Anubis Vega-Rúa
- Institut Pasteur of Guadeloupe, Laboratory of Vector Control Research, Unit Transmission, Reservoirs and Pathogen Diversity, Les Abymes, Guadeloupe
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Jelle Matthijnssens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
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Vogel E, Santos D, Mingels L, Verdonckt TW, Broeck JV. RNA Interference in Insects: Protecting Beneficials and Controlling Pests. Front Physiol 2019; 9:1912. [PMID: 30687124 PMCID: PMC6336832 DOI: 10.3389/fphys.2018.01912] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/18/2018] [Indexed: 01/01/2023] Open
Abstract
Insects constitute the largest and most diverse group of animals on Earth with an equally diverse virome. The main antiviral immune system of these animals is the post-transcriptional gene-silencing mechanism known as RNA(i) interference. Furthermore, this process can be artificially triggered via delivery of gene-specific double-stranded RNA molecules, leading to specific endogenous gene silencing. This is called RNAi technology and has important applications in several fields. In this paper, we review RNAi mechanisms in insects as well as the potential of RNAi technology to contribute to species-specific insecticidal strategies. Regarding this aspect, we cover the range of strategies considered and investigated so far, as well as their limitations and the most promising approaches to overcome them. Additionally, we discuss patterns of viral infection, specifically persistent and acute insect viral infections. In the latter case, we focus on infections affecting economically relevant species. Within this scope, we review the use of insect-specific viruses as bio-insecticides. Last, we discuss RNAi-based strategies to protect beneficial insects from harmful viral infections and their potential practical application. As a whole, this manuscript stresses the impact of insect viruses and RNAi technology in human life, highlighting clear lines of investigation within an exciting and promising field of research.
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Affiliation(s)
- Elise Vogel
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Lina Mingels
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Thomas-Wolf Verdonckt
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
| | - Jozef Vanden Broeck
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium
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Nascimento J, Sampaio VS, Karl S, Kuehn A, Almeida A, Vitor-Silva S, de Melo GC, Baia da Silva DC, C. P. Lopes S, Fé NF, Lima JBP, Guerra MGB, Pimenta PFP, Bassat Q, Mueller I, Lacerda MVG, Monteiro WM. Use of anthropophilic culicid-based xenosurveillance as a proxy for Plasmodium vivax malaria burden and transmission hotspots identification. PLoS Negl Trop Dis 2018; 12:e0006909. [PMID: 30418971 PMCID: PMC6258424 DOI: 10.1371/journal.pntd.0006909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/26/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
Vector-borne diseases account for more than 17% of all infectious diseases, causing more than one million deaths annually. Malaria remains one of the most important public health problems worldwide. These vectors are bloodsucking insects, which can transmit disease-producing microorganisms during a blood meal. The contact of culicids with human populations living in malaria-endemic areas suggests that the identification of Plasmodium genetic material in the blood present in the gut of these mosquitoes may be possible. The process of assessing the blood meal for the presence of pathogens is termed 'xenosurveillance'. In view of this, the present work investigated the relationship between the frequency with which Plasmodium DNA is found in culicids and the frequency with which individuals are found to be carrying malaria parasites. A cross-sectional study was performed in a peri-urban area of Manaus, in the Western Brazilian Amazon, by simultaneously collecting human blood samples and trapping culicids from households. A total of 875 individuals were included in the study and a total of 13,374mosquito specimens were captured. Malaria prevalence in the study area was 7.7%. The frequency of households with at least one culicid specimen carrying Plasmodium DNA was 6.4%. Plasmodium infection incidence was significantly related to whether any Plasmodium positive blood-fed culicid was found in the same household [IRR 3.49 (CI95% 1.38-8.84); p = 0.008] and for indoor-collected culicids [IRR 4.07 (CI95%1.25-13.24); p = 0.020]. Furthermore, the number of infected people in the house at the time of mosquito collection was related to whether there were any positive blood-fed culicid mosquitoes in that household for collection methods combined [IRR 4.48 (CI95%2.22-9.05); p<0.001] or only for indoor-collected culicids [IRR 4.88 (CI95%2.01-11.82); p<0.001]. Our results suggest that xenosurveillance can be used in endemic tropical regions in order to estimate the malaria burden and identify transmission foci in areas where Plasmodium vivax is predominant.
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Affiliation(s)
- Joabi Nascimento
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Vanderson S. Sampaio
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Stephan Karl
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Entomology Section, Vector-borne Diseases Unit, Papua New Guinea Institute of Medical Research, Papua, New Guinea
- Department of Medical Biology, University of Melbourne, Australia
| | - Andrea Kuehn
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Anne Almeida
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Sheila Vitor-Silva
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Gisely Cardoso de Melo
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Djane C. Baia da Silva
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
| | | | - Nelson F. Fé
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
| | - José B. Pereira Lima
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Maria G. Barbosa Guerra
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Paulo F. P. Pimenta
- Laboratório de Entomologia Médica, Centro de Pesquisas René Rachou (Fiocruz), Belo Horizonte, MG, Brazil
| | - Quique Bassat
- ISGlobal, Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain
| | - Ivo Mueller
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Australia
- Parasites & Hosts Unit, Institut Pasteur, Paris, France
| | - Marcus V. G. Lacerda
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, AM, Brazil
| | - Wuelton M. Monteiro
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
- * E-mail:
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31
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Xiao P, Han J, Zhang Y, Li C, Guo X, Wen S, Tian M, Li Y, Wang M, Liu H, Ren J, Zhou H, Lu H, Jin N. Metagenomic Analysis of Flaviviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes From Dengue and Zika Viruses. Front Cell Infect Microbiol 2018; 8:359. [PMID: 30406038 PMCID: PMC6207848 DOI: 10.3389/fcimb.2018.00359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
More than 6,000 mosquitoes of six species from six sites were collected and tested for their virome using metagenomics sequencing and bioinformatic analysis. The identified viral sequences belonged to more than 50 viral families. The results were verified by PCR of selected viruses in all mosquitoes, followed by phylogenetic analysis. In the present study, we identified the partial dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) sequences in mosquitoes. Metagenomic analysis and the PCR amplification revealed three DENV sequences, one of which encodes a partial envelope protein. Two ZIKV sequences both encoding partial nonstructural protein 3 and one JEV sequence encoding the complete envelope protein were identified. There was variability in the viral titers of the newly isolated virus JEV-China/YN2016-1 of different passage viruses. The newly identified Zika virus gene from ZIKV-China/YN2016-1 was an Asian genotype and shared the highest nucleotide sequence identity (97.1%) with a ZIKV sequence from Thailand isolated in 2004. Phylogenetic analysis of ZIKV-China/YN2016-1 and ZIKV-China/YN2016-2 with known Flavivirus genes indicated that ZIKV has propagated in Yunnan province, China.
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Affiliation(s)
- Pengpeng Xiao
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jicheng Han
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Chenghui Li
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Shubo Wen
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Mingyao Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yiquan Li
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Maopeng Wang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hao Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jingqiang Ren
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Division of Economic Animal Epidemic, Institute of Special Economic Animal and Plant Sciences, Changchun, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ningyi Jin
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
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Xiao P, Li C, Zhang Y, Han J, Guo X, Xie L, Tian M, Li Y, Wang M, Liu H, Ren J, Zhou H, Lu H, Jin N. Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses. Front Cell Infect Microbiol 2018; 8:364. [PMID: 30406041 PMCID: PMC6202873 DOI: 10.3389/fcimb.2018.00364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022] Open
Abstract
We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.
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Affiliation(s)
- Pengpeng Xiao
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China.,Institute of Virology, Wenzhou University, Wenzhou, China
| | - Chenghui Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Jicheng Han
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Lv Xie
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Mingyao Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yiquan Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Maopeng Wang
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hao Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jingqiang Ren
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Division of Economic Animal Epidemic, Institute of Special Economic Animal and Plant Sciences, Changchun, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ningyi Jin
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
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Xia H, Liu H, Zhao L, Atoni E, Wang Y, Yuan Z. First Isolation and Characterization of a Group C Banna Virus (BAV) from Anopheles sinensis Mosquitoes in Hubei, China. Viruses 2018; 10:v10100555. [PMID: 30314338 PMCID: PMC6213526 DOI: 10.3390/v10100555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022] Open
Abstract
Banna virus (BAV) is considered to be an emerging human pathogen that is transmitted by blood-sucking insects. BAV was isolated from various species of mosquitoes, midges, and livestock. It is widely distributed geographically, since it was identified in China, Vietnam, and Indonesia. Previously reported evolution studies of BAV indicated that BAV can be divided into two groups, including isolates from China and Vietnam clustered in group A, and Indonesian isolates in group B. In this study, we report the isolation of a new strain of BAV named HB14-71-01 from Anopheles sinensis mosquitoes from Hubei, China. An in vitro comparison study of the HB14-71-01 isolate and the group A BAV revealed differences based on observed cytopathic effect, plaque size, and viral growth rates. Additionally, the phylogenetic analysis indicated that the Hubei isolate belongs to a novel genotype of BAV and emerged nearly 105 years ago (95% highest posterior density (HPD): 35–434), unlike the two previously reported genotypes A and B. Our findings extend the knowledge about the genomic diversity and potential vectors/hosts of BAVs and will improve understanding of the relationships between genetic variation and pathogenicity.
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Affiliation(s)
- Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Hong Liu
- School of Life Sciences, Shandong University of Technology, Zibo 255000, China.
| | - Lu Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Evans Atoni
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Yujuan Wang
- Henan Province OriginBio Biotechnology Co., Ltd., Zhengzhou 450000, China.
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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Fujita R, Kato F, Kobayashi D, Murota K, Takasaki T, Tajima S, Lim CK, Saijo M, Isawa H, Sawabe K. Persistent viruses in mosquito cultured cell line suppress multiplication of flaviviruses. Heliyon 2018; 4:e00736. [PMID: 30167494 PMCID: PMC6107885 DOI: 10.1016/j.heliyon.2018.e00736] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/25/2018] [Accepted: 08/08/2018] [Indexed: 11/16/2022] Open
Abstract
In the growth kinetics analysis of flaviviruses in Aedes albopictus C6/36 cell lines obtained from the Japanese Collection of Research Bioresources (JCRB) Cell Bank and the European Collection of Authenticated Cell Culture (ECACC), these two cells line showed different viral susceptibility for Zika virus (ZIKV), Dengue virus (DENV), and Japanese encephalitis virus (JEV). Next-generation sequencing (NGS) analysis revealed that the C6/36 JCRB strain was persistently infected with two viruses without showing any cytopathic effects. The complete sequence analysis demonstrated that the one virus was Menghai rhabdovirus (MERV), which has been found from Aedes albopictus mosquito. The other virus was a novel virus, designated as Shinobi tetravirus (SHTV). Interestingly, the viral susceptibility of these two strains was almost even for Sindbis virus and Getah virus. We cloned SHTV and MERV from JCRB C6/36 cell line and then re-infected them into another C6/36 cell line, resulting in the reproduction of persistent infection with each virus. ZIKV growth was suppressed in SHTV and/or MERV re-infected C6/36 cells also. To our knowledge, this is the first demonstration that persistent infection with rhabdovirus and/or permutotetravirus suppressed flavivirus replication in mosquito cells.
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Affiliation(s)
- Ryosuke Fujita
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
- Isotope Imaging Laboratory, Creative Research Institution, Hokkaido University, Sapporo, Japan
- Department of Research Promotion, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Fumihiro Kato
- Department of Research Promotion, Japan Agency for Medical Research and Development, Tokyo, Japan
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Katsunori Murota
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Research Promotion, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Tomohiko Takasaki
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Tajima
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chang-Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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Xia H, Wang Y, Shi C, Atoni E, Zhao L, Yuan Z. Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China. Virol Sin 2018; 33:59-66. [PMID: 29500689 DOI: 10.1007/s12250-018-0015-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/12/2018] [Indexed: 11/28/2022] Open
Abstract
Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An. sinensis, Ar. subalbatus, Cx. quinquefasciatus, and Cx. tritaeniorhynchus, respectively, with the highest prevalence of virus-associated reads being observed in Cx. quinquefasciatus. The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families, together with an unclassified group of viruses. Anelloviridae, Circoviridae, Genomoviridae, Iridoviridae, Mesoniviridae, Microviridae, Myoviridae, Parvoviridae, Phenuiviridae, and Podoviridae were the top ten significantly different viral families among the four species. Further analysis reveals that the virome is species-specific in four mosquito samples, and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes. This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.
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Affiliation(s)
- Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yujuan Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenyan Shi
- Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, KU Leuven - University of Leuven, 3000, Louvain, Belgium
| | - Evans Atoni
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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Xia H, Wang Y, Atoni E, Zhang B, Yuan Z. Mosquito-Associated Viruses in China. Virol Sin 2018; 33:5-20. [PMID: 29532388 PMCID: PMC5866263 DOI: 10.1007/s12250-018-0002-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/05/2017] [Indexed: 10/30/2022] Open
Abstract
Mosquitoes are classified into approximately 3500 species and further grouped into 41 genera. Epidemiologically, they are considered to be among the most important disease vectors in the world and they can harbor a wide variety of viruses. Several mosquito viruses are considered to be of significant medical importance and can cause serious public health issues throughout the world. Such viruses are Japanese encephalitis virus (JEV), dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV). Others are the newly recognized mosquito viruses such as Banna virus (BAV) and Yunnan orbivirus (YNOV) with unclear medical significance. The remaining mosquito viruses are those that naturally infect mosquitoes but do not appear to infect humans or other vertebrates. With the continuous development and improvement of mosquito and mosquito-associated virus surveillance systems in China, many novel mosquito-associated viruses have been discovered in recent years. This review aims to systematically outline the history, characteristics, distribution, and/or current epidemic status of mosquito-associated viruses in China.
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Affiliation(s)
- Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yujuan Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Evans Atoni
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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37
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Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China. Viruses 2018; 10:v10010030. [PMID: 29329230 PMCID: PMC5795443 DOI: 10.3390/v10010030] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/03/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Many blood-feeding arthropods are known vectors of viruses that are a source of unprecedented global health concern. Mosquitoes are an integral part of these arthropod vectors. Advancements in next-generation sequencing and bioinformatics has expanded our knowledge on the richness of viruses harbored by arthropods. In the present study, we applied a metagenomic approach to determine the intercontinental virome diversity of Culex quinquefasciatus and Culex tritaeniorhynchus in Kwale, Kenya and provinces of Hubei and Yunnan in China. Our results showed that viromes from the three locations were strikingly diverse and comprised 30 virus families specific to vertebrates, invertebrates, plants, and protozoa as well as unclassified group of viruses. Though sampled at different times, both Kwale and Hubei mosquito viromes were dominated by vertebrate viruses, in contrast to the Yunnan mosquito virome, which was dominated by insect-specific viruses. However, each virome was unique in terms of virus proportions partly influenced by type of ingested meals (blood, nectar, plant sap, environment substrates). The dominant vertebrate virus family in the Kwale virome was Papillomaviridae (57%) while in Hubei it was Herpesviridae (30%) and the Yunnan virome was dominated by an unclassified viruses group (27%). Given that insect-specific viruses occur naturally in their hosts, they should be the basis for defining the viromes. Hence, the dominant insect-specific viruses in Kwale, Hubei, and Yunnan were Baculoviridae, Nimaviridae and Iflaviridae, respectively. Our study is preliminary but contributes to growing and much needed knowledge, as mosquito viromes could be manipulated to prevent and control pathogenic arboviruses.
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38
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Varghese FS, van Rij RP. Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches. Methods Mol Biol 2018; 1746:197-213. [PMID: 29492897 DOI: 10.1007/978-1-4939-7683-6_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Insects are the most abundant and diverse group of animals on earth, but our knowledge of their viruses is biased toward insect-borne viruses that cause disease in plants, animals, or humans. Recent metagenomic studies and systematic surveys of viruses in wild-caught insects have identified an unanticipated large repertoire of novel viruses and viral sequences. These include new members of existing clades, new clades, and even entirely new virus families. These studies greatly expand the known virosphere in insects, provide opportunities to study virus-host interactions, and generate new insights into virus evolution. In this chapter, we discuss the methods used to identify novel viruses in insects and highlight some notable surprises arising from these studies.
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Affiliation(s)
- Finny S Varghese
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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39
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de Souza WM, Fumagalli MJ, de Araujo J, Sabino-Santos G, Maia FGM, Romeiro MF, Modha S, Nardi MS, Queiroz LH, Durigon EL, Nunes MRT, Murcia PR, Figueiredo LTM. Discovery of novel anelloviruses in small mammals expands the host range and diversity of the Anelloviridae. Virology 2017; 514:9-17. [PMID: 29128758 DOI: 10.1016/j.virol.2017.11.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/26/2017] [Accepted: 11/01/2017] [Indexed: 10/18/2022]
Abstract
The Anelloviridae comprises single-stranded DNA viruses currently grouped in sixty-eight species classified in twelve genera. They have been found in many vertebrate hosts including primates. In this study, we describe the application of the high-throughput sequencing to examine the frequency and diversity of anelloviruses in rodents, bats and opossums captured in São Paulo State, Brazil. We report a total of twenty-six anelloviruses with sixteen nearly complete genomes and ten partial genomes, which include eleven potential novel species identified in rodents (Cricetidae), bats (Molossidae and Phyllostomidae), and opossums (Didelphidae). We also propose the inclusion of two potential new genera within the Anelloviridae family, provisionally named Omegatorquevirus and Sigmatorquevirus, including six and three novel species of anelloviruses, respectively. In summary, this study expands the diversity and the host range of the known anelloviruses.
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Affiliation(s)
- William Marciel de Souza
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.
| | - Marcílio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jansen de Araujo
- Laboratory Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gilberto Sabino-Santos
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe Gonçalves Motta Maia
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marilia Farignoli Romeiro
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Marcello Schiavo Nardi
- Divisão Técnica de Medicina Veterinária e Manejo da Fauna Silvestre, Prefeitura de São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Laboratory Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Márcio Roberto Teixeira Nunes
- Center for Technological Innovations, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Wamonje FO, Michuki GN, Braidwood LA, Njuguna JN, Musembi Mutuku J, Djikeng A, Harvey JJW, Carr JP. Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus. Virol J 2017; 14:188. [PMID: 28969654 PMCID: PMC5625602 DOI: 10.1186/s12985-017-0854-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/20/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. RESULTS Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination, with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus. CONCLUSIONS The discovery of ALPV and RhPV in aphids and maize further demonstrates the broad occurrence of these dicistroviruses. Dicistroviruses are remarkable in that they use plants as reservoirs that facilitate infection of their insect replicative hosts, such as aphids. This is the first report of these viruses being isolated from either organism. The BSRV-like sequences represent a potentially novel dicistrovirus infecting A. fabae.
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Affiliation(s)
- Francis O Wamonje
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - George N Michuki
- International Livestock Research Institute, 30709 Naivasha Road, Nairobi, Kenya
- Present Address: The Africa Genomics Center and Consultancy, Nairobi, Kenya
| | - Luke A Braidwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Joyce N Njuguna
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, 30709-00100, Kenya
| | - J Musembi Mutuku
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, 30709-00100, Kenya
| | - Appolinaire Djikeng
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, 30709-00100, Kenya
- Present Address: Centre for Tropical Livestock Genetics and Health, The Roslin Institute & Royal (Dick) School of Veterinary Studies, Easter Bush, Edinburgh, Midlothian, EH25 9RG, UK
| | - Jagger J W Harvey
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, 30709-00100, Kenya
- Present Address: The Feed the Future Innovation Lab for the Reduction of Post-Harvest Loss, Kansas State University, Manhattan, KS, 66506, USA
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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Sadeghi M, Popov V, Guzman H, Phan TG, Vasilakis N, Tesh R, Delwart E. Genomes of viral isolates derived from different mosquitos species. Virus Res 2017; 242:49-57. [PMID: 28855097 DOI: 10.1016/j.virusres.2017.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/10/2017] [Accepted: 08/23/2017] [Indexed: 10/19/2022]
Abstract
Eleven viral isolates derived mostly in albopictus C6/36 cells from mosquito pools collected in Southeast Asia and the Americas between 1966 and 2014 contained particles with electron microscopy morphology typical of reoviruses. Metagenomics analysis yielded the near complete genomes of three novel reoviruses, Big Cypress orbivirus, Ninarumi virus, and High Island virus and a new tetravirus, Sarawak virus. Strains of previously characterized Sathuvarachi, Yunnan, Banna and Parry's Lagoon viruses (Reoviridae), Bontang virus (Mesoniviridae), and Culex theileri flavivirus (Flaviviridae) were also characterized. The availability of these mosquito virus genomes will facilitate their detection by metagenomics or PCR to better determine their geographic range, extent of host tropism, and possible association with arthropod or vertebrate disease.
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Affiliation(s)
- Mohammadreza Sadeghi
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA; Department of Virology, University of Helsinki, Helsinki, Finland
| | - Vsevolod Popov
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Hilda Guzman
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Robert Tesh
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
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42
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Yang X, Xu P, Graham RI, Yuan H, Wu K. Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm. J Vis Exp 2017:55534. [PMID: 28448051 PMCID: PMC5564690 DOI: 10.3791/55534] [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: 10/31/2022] Open
Abstract
Many novel viruses have been discovered in animal hosts using next-generation sequencing technologies. Previously, we reported a mutualistic virus, Helicoverpa armigera densovirus (HaDV2), in a lepidopteran species, the cotton bollworm, Helicoverpa armigera (Hubner). Here, we describe the protocols that are currently used to study the effect of HaDV2 on its host. First, we establish a HaDV2-free cotton bollworm colony from a single breeding pair. Then, we orally inoculate some neonate larval offspring with HaDV2-containing filtered liquid to produce two colonies with the same genetic background: one HaDV2-infected, the other uninfected. A protocol to compare life table parameters (e.g., larval, pupal, and adult periods and fecundity) between the HaDV2-infected and -uninfected individuals is also presented, as are the protocols for determining the host-tissue distribution and transmission efficiency of HaDV2. These protocols would also be suitable for investigating the effects of other orally transmitted viruses on their insect hosts, lepidopteran hosts in particular.
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Affiliation(s)
- Xianming Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences
| | | | - He Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences;
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43
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Ergünay K, Brinkmann A, Litzba N, Günay F, Kar S, Öter K, Örsten S, Sarıkaya Y, Alten B, Nitsche A, Linton YM. A novel rhabdovirus, related to Merida virus, in field-collected mosquitoes from Anatolia and Thrace. Arch Virol 2017; 162:1903-1911. [PMID: 28283817 DOI: 10.1007/s00705-017-3314-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/21/2017] [Indexed: 01/26/2023]
Abstract
Next-generation sequencing technologies have significantly facilitated the discovery of novel viruses, and metagenomic surveillance of arthropods has enabled exploration of the diversity of novel or known viral agents. We have identified a novel rhabdovirus that is genetically related to the recently described Merida virus via next-generation sequencing in a mosquito pool from Thrace. The complete viral genome contains 11,798 nucleotides with 83% genome-wide nucleotide sequence similarity to Merida virus. Five major putative open reading frames that follow the canonical rhabdovirus genome organization were identified. A total of 1380 mosquitoes comprising 13 species, collected from Thrace and the Mediterranean and Aegean regions of Anatolia were screened for the novel virus using primers based on the N and L genes of the prototype genome. Eight positive pools (6.2%) exclusively comprised Culex pipiens sensu lato specimens originating from all study regions. Infections were observed in pools with female as well as male or mixed-sex individuals. The overall and Cx. pipiens-specific minimal infection rates were calculated to be 5.7 and 14.8, respectively. Sequencing of the PCR products revealed marked diversity within a portion of the N gene, with up to 4% divergence and distinct amino acid substitutions that were unrelated to the collection site. Phylogenetic analysis of the complete and partial viral polymerase (L gene) amino acid sequences placed the novel virus and Merida virus in a distinct group, indicating that these strains are closely related. The strain is tentatively named "Merida-like virus Turkey". Studies are underway to isolate and further explore the host range and distribution of this new strain.
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Affiliation(s)
- Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Morphology Building 3rd Floor, Sihhiye, 06100, Ankara, Turkey. .,Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany.
| | - Annika Brinkmann
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Nadine Litzba
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Filiz Günay
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Sırrı Kar
- Department of Biology, Faculty of Arts and Sciences, Namık Kemal University, Tekirdağ, Turkey
| | - Kerem Öter
- Department of Parasitology, Faculty of Veterinary Medicine, Istanbul University, Istanbul, Turkey
| | - Serra Örsten
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Morphology Building 3rd Floor, Sihhiye, 06100, Ankara, Turkey
| | - Yasemen Sarıkaya
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Bülent Alten
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Andreas Nitsche
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA.,Department of Entomology, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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44
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Assessing the feasibility of fly based surveillance of wildlife infectious diseases. Sci Rep 2016; 6:37952. [PMID: 27901062 PMCID: PMC5128827 DOI: 10.1038/srep37952] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022] Open
Abstract
Monitoring wildlife infectious agents requires acquiring samples suitable for analyses, which is often logistically demanding. A possible alternative to invasive or non-invasive sampling of wild-living vertebrates is the use of vertebrate material contained in invertebrates feeding on them, their feces, or their remains. Carrion flies have been shown to contain vertebrate DNA; here we investigate whether they might also be suitable for wildlife pathogen detection. We collected 498 flies in Taï National Park, Côte d’Ivoire, a tropical rainforest and examined them for adenoviruses (family Adenoviridae), whose DNA is frequently shed in feces of local mammals. Adenoviral DNA was detected in 6/142 mammal-positive flies. Phylogenetic analyses revealed that five of these sequences were closely related to sequences obtained from local non-human primates, while the sixth sequence was closely related to a murine adenovirus. Next-generation sequencing-based DNA-profiling of the meals of the respective flies identified putative hosts that were a good fit to those suggested by adenoviral sequence affinities. We conclude that, while characterizing the genetic diversity of wildlife infectious agents through fly-based monitoring may not be cost-efficient, this method could probably be used to detect the genetic material of wildlife infectious agents causing wildlife mass mortality in pristine areas.
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Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance. Int J Mol Sci 2016; 17:ijms17101743. [PMID: 27775568 PMCID: PMC5085771 DOI: 10.3390/ijms17101743] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 11/17/2022] Open
Abstract
Surveillance and monitoring of viral pathogens circulating in humans and wildlife, together with the identification of emerging infectious diseases (EIDs), are critical for the prediction of future disease outbreaks and epidemics at an early stage. It is advisable to sample a broad range of vertebrates and invertebrates at different temporospatial levels on a regular basis to detect possible candidate viruses at their natural source. However, virus surveillance systems can be expensive, costly in terms of finances and resources and inadequate for sampling sufficient numbers of different host species over space and time. Recent publications have presented the concept of a new virus surveillance system, coining the terms "flying biological syringes", "xenosurveillance" and "vector-enabled metagenomics". According to these novel and promising surveillance approaches, viral metagenomics on engorged mosquitoes might reflect the viral diversity of numerous mammals, birds and humans, combined in the mosquitoes' blood meal during feeding on the host. In this review article, we summarize the literature on vector-enabled metagenomics (VEM) techniques and its application in disease surveillance in humans. Furthermore, we highlight the combination of VEM and "invertebrate-derived DNA" (iDNA) analysis to identify the host DNA within the mosquito midgut.
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46
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Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique. PLoS One 2016; 11:e0162751. [PMID: 27682810 PMCID: PMC5040392 DOI: 10.1371/journal.pone.0162751] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/26/2016] [Indexed: 11/19/2022] Open
Abstract
Mosquitoes carry a wide variety of viruses that can cause vector-borne infectious diseases and affect both human and veterinary public health. Although Mozambique can be considered a hot spot for emerging infectious diseases due to factors such as a rich vector population and a close vector/human/wildlife interface, the viral flora in mosquitoes have not previously been investigated. In this study, viral metagenomics was employed to analyze the viral communities in Culex and Mansonia mosquitoes in the Zambezia province of Mozambique. Among the 1.7 and 2.6 million sequences produced from the Culex and Mansonia samples, respectively, 3269 and 983 reads were classified as viral sequences. Viruses belonging to the Flaviviridae, Rhabdoviridae and Iflaviridae families were detected, and different unclassified single- and double-stranded RNA viruses were also identified. A near complete genome of a flavivirus, tentatively named Cuacua virus, was obtained from the Mansonia mosquitoes. Phylogenetic analysis of this flavivirus, using the NS5 amino acid sequence, showed that it grouped with 'insect-specific' viruses and was most closely related to Nakiwogo virus previously identified in Uganda. Both mosquito genera had viral sequences related to Rhabdoviruses, and these were most closely related to Culex tritaeniorhynchus rhabdovirus (CTRV). The results from this study suggest that several viruses specific for insects belonging to, for example, the Flaviviridae and Rhabdoviridae families, as well as a number of unclassified RNA viruses, are present in mosquitoes in Mozambique.
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47
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Phan TG, Messacar K, Dominguez SR, da Costa AC, Deng X, Delwart E. A new densovirus in cerebrospinal fluid from a case of anti-NMDA-receptor encephalitis. Arch Virol 2016; 161:3231-5. [PMID: 27522586 DOI: 10.1007/s00705-016-3002-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/26/2016] [Indexed: 01/16/2023]
Abstract
We characterized the genome of a densovirus, tentatively called human CSF-associated densovirus 1 (HuCSFDV1), in cerebrospinal fluid (CSF) from a human case of encephalitis with antibodies against the N-methyl D-aspartate receptor. The presence of the viral genome in CSF was independently confirmed. This virus, which is proposed to be a member of a new species in the genus Iteradensovirus of the subfamily Densovirinae, showed the typical two ORFs encoding nonstructural and structural proteins with low-level identities of 22 and 16 % to the closest known densovirus relative. No other eukaryotic viral sequences were detected using deep sequencing. The replication and pathogenicity in humans of this virus, which belongs to a viral subfamily whose members are only known to replicate in invertebrates, remain to be demonstrated. Alternative explanations for the detection of densovirus DNA in CSF are discussed.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Kevin Messacar
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel R Dominguez
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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48
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Charles J, Firth AE, Loroño-Pino MA, Garcia-Rejon JE, Farfan-Ale JA, Lipkin WI, Blitvich BJ, Briese T. Merida virus, a putative novel rhabdovirus discovered in Culex and Ochlerotatus spp. mosquitoes in the Yucatan Peninsula of Mexico. J Gen Virol 2016; 97:977-987. [PMID: 26868915 DOI: 10.1099/jgv.0.000424] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequences corresponding to a putative, novel rhabdovirus [designated Merida virus (MERDV)] were initially detected in a pool of Culex quinquefasciatus collected in the Yucatan Peninsula of Mexico. The entire genome was sequenced, revealing 11 798 nt and five major ORFs, which encode the nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). The deduced amino acid sequences of the N, G and L proteins have no more than 24, 38 and 43 % identity, respectively, to the corresponding sequences of all other known rhabdoviruses, whereas those of the P and M proteins have no significant identity with any sequences in GenBank and their identity is only suggested based on their genome position. Using specific reverse transcription-PCR assays established from the genome sequence, 27 571 C. quinquefasciatus which had been sorted in 728 pools were screened to assess the prevalence of MERDV in nature and 25 pools were found positive. The minimal infection rate (calculated as the number of positive mosquito pools per 1000 mosquitoes tested) was 0.9, and similar for both females and males. Screening another 140 pools of 5484 mosquitoes belonging to four other genera identified positive pools of Ochlerotatus spp. mosquitoes, indicating that the host range is not restricted to C. quinquefasciatus. Attempts to isolate MERDV in C6/36 and Vero cells were unsuccessful. In summary, we provide evidence that a previously undescribed rhabdovirus occurs in mosquitoes in Mexico.
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Affiliation(s)
- Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria A Loroño-Pino
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Julian E Garcia-Rejon
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Jose A Farfan-Ale
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
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