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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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Potter-Birriel JM, Pollio AR, Knott BD, Chunashvili T, Fung CK, Conte MA, Reinbold-Wasson DD, Hang J. Metagenomics analysis reveals presence of the Merida-like virus in Georgia. Front Microbiol 2023; 14:1258810. [PMID: 37901812 PMCID: PMC10602647 DOI: 10.3389/fmicb.2023.1258810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
Arbovirus surveillance is fundamental for the discovery of novel viruses and prevention of febrile vector-borne illnesses. Vector-borne pathogens can rapidly expand and adapt in new geographic and environmental conditions. In this study, metagenomic surveillance was conducted to identify novel viruses in the Country of Georgia. A total of 521 mosquitoes were captured near a military training facility and pooled from species Culex pipiens (Linnaeus) (87%) and Aedes albopictus (Skuse) (13%). We decided to further analyze the Culex pipiens mosquitoes, due to the more extensive number of samples collected. Our approach was to utilize an unbiased total RNA-seq for pathogen discovery in order to explore the mosquito virome. The viral reads from this analysis were mostly aligned to Insect-specific viruses from two main families, the Iflaviridae; a positive-stranded RNA virus and the Rhabdoviridae; a negative- and single-stranded RNA virus. Our pathogen discovery analysis revealed viral reads aligning to the Merida-like virus Turkey (MERDLVT) strain among the Rhabdoviridae. To further validate this result, we conducted a BLAST sequence comparison analysis of our samples with the MERDLVT strain. Our positive samples aligned to the MERDLVT strain with 96-100% sequence identity and 99.7-100% sequence coverage. A bootstrapped maximum-likelihood phylogenetic tree was used to evaluate the evolutionary relationships among these positive pooled specimens with the (MERDLVT) strain. The Georgia samples clustered most closely with two strains from Turkey, the Merida-like virus KE-2017a isolate 139-1-21 and the Merida-like virus Turkey isolate P431. Collectively, these results show the presence of the MERDLVT strain in Georgia.
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Affiliation(s)
| | - Adam R. Pollio
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Brian D. Knott
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Christian K. Fung
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Matthew A. Conte
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Drew D. Reinbold-Wasson
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
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3
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Ternovoi VA, Shvalov AN, Kartashov MY, Ponomareva EP, Tupota NL, Khoroshavin YA, Bayandin RB, Gladysheva AV, Mikryukova TP, Tregubchak TV, Loktev VB. The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia. Viruses 2023; 15:1896. [PMID: 37766302 PMCID: PMC10537626 DOI: 10.3390/v15091896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters.
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Affiliation(s)
- Vladimir A. Ternovoi
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Alexander N. Shvalov
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Mikhail Yu. Kartashov
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Eugenia P. Ponomareva
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Natalia L. Tupota
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Yuri A. Khoroshavin
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Roman B. Bayandin
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Anastasia V. Gladysheva
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Tamara P. Mikryukova
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Tatyana V. Tregubchak
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Valery B. Loktev
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
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Faizah AN, Kobayashi D, Matsumura R, Watanabe M, Higa Y, Sawabe K, Isawa H. Blood meal source identification and RNA virome determination in Japanese encephalitis virus vectors collected in Ishikawa Prefecture, Japan, show distinct avian/mammalian host preference. JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:620-628. [PMID: 37027507 DOI: 10.1093/jme/tjad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 05/13/2023]
Abstract
In Asia, Culex mosquitoes are of particular interest because of their role in maintaining endemic mosquito-borne viral diseases, including the Japanese encephalitis virus (JEV). Nonetheless, host-feeding preferences, along with naturally infecting RNA viruses in certain Culex species, remain understudied. In this study, selected blood-fed mosquitoes were processed for avian and mammalian blood meal source identification. Concurrently, cell culture propagation and high-throughput sequencing (HTS) approaches were used to determine the RNA virome of Culex mosquitoes collected in Ishikawa Prefecture, Japan. The identification of blood meal sources from wild-caught Culex spp. revealed that Culex (Culex) tritaeniorhynchus Giles, 1901, has a robust preference toward wild boar (62%, 26/42), followed by heron (21%, 9/42). The other two species, Culex (Oculeomyia) bitaeniorhynchus Giles, 1901, and Culex (Culex) orientalis Edwards, 1921, showed a distinct preference for avian species, including migratory birds. From the HTS results, 34 virus sequences were detected, four of which were newly identified virus sequences of unclassified Aspiviridae, Qinviridae, Iflaviridae, and Picornaviridae. The absence of observable cytopathic effects in mammalian cells and phylogenetic analysis suggested that all identified virus sequences were insect-specific. Further investigations involving other mosquito populations collected in different areas are warranted to explore previously unknown vertebrate hosts that may be linked to JEV dispersal in nature.
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Affiliation(s)
- Astri Nur Faizah
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ryo Matsumura
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Mamoru Watanabe
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yukiko Higa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Palatini U, Alfano N, Carballar RL, Chen XG, Delatte H, Bonizzoni M. Virome and nrEVEome diversity of Aedes albopictus mosquitoes from La Reunion Island and China. Virol J 2022; 19:190. [DOI: 10.1186/s12985-022-01918-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Aedes albopictus is a public health threat for its worldwide spread and ability to transmit arboviruses. Understanding mechanisms of mosquito immunity can provide new tools to control arbovirus spread. The genomes of Aedes mosquitoes contain hundreds of nonretroviral endogenous viral elements (nrEVEs), which are enriched in piRNA clusters and produce piRNAs, with the potential to target cognate viruses. Recently, one nrEVE was shown to limit cognate viral infection through nrEVE-derived piRNAs. These findings suggest that nrEVEs constitute an archive of past viral infection and that the landscape of viral integrations may be variable across populations depending on their viral exposure.
Methods
We used bioinformatics and molecular approaches to identify known and novel (i.e. absent in the reference genome) viral integrations in the genome of wild collected Aedes albopictus mosquitoes and characterize their virome.
Results
We showed that the landscape of viral integrations is dynamic with seven novel viral integrations being characterized, but does not correlate with the virome, which includes both viral species known and unknown to infect mosquitoes. However, the small RNA coverage profile of nrEVEs and the viral genomic contigs we identified confirmed an interaction among these elements and the piRNA and siRNA pathways in mosquitoes.
Conclusions
Mosquitoes nrEVEs have been recently described as a new form of heritable, sequence-specific mechanism of antiviral immunity. Our results contribute to understanding the dynamic distribution of nrEVEs in the genomes of wild Ae. albopictus and their interaction with mosquito viruses.
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Lee CC, Hsu HW, Lin CY, Gustafson N, Matsuura K, Lee CY, Yang CCS. First Polycipivirus and Unmapped RNA Virus Diversity in the Yellow Crazy Ant, Anoplolepis gracilipes. Viruses 2022; 14:v14102161. [PMID: 36298716 PMCID: PMC9612232 DOI: 10.3390/v14102161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/01/2022] Open
Abstract
The yellow crazy ant, Anoplolepis gracilipes is a widespread invasive ant that poses significant threats to local biodiversity. Yet, compared to other global invasive ant species such as the red imported fire ant (Solenopsis invicta) or the Argentine ant (Linepithema humile), little is known about the diversity of RNA viruses in the yellow crazy ant. In the current study, we generated a transcriptomic database for A. gracilipes using a high throughput sequencing approach to identify new RNA viruses and characterize their genomes. Four virus species assigned to Dicistroviridae, two to Iflaviridae, one to Polycipiviridae, and two unclassified Riboviria viruses were identified. Detailed genomic characterization was carried out on the polycipivirus and revealed that this virus comprises 11,644 nucleotides with six open reading frames. Phylogenetic analysis and pairwise amino acid identity comparison classified this virus into the genus Sopolycivirus under Polycipiviridae, which is tentatively named "Anoplolepis gracilipes virus 3 (AgrV-3)". Evolutionary analysis showed that AgrV-3 possesses a high level of genetic diversity and elevated mutation rate, combined with the common presence of multiple viral strains within single worker individuals, suggesting AgrV-3 likely evolves following the quasispecies model. A subsequent field survey placed the viral pathogen "hotspot" of A. gracilipes in the Southeast Asian region, a pattern consistent with the region being recognized as part of the ant's native range. Lastly, infection of multiple virus species seems prevalent across field colonies and may have been linked to the ant's social organization.
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Affiliation(s)
- Chih-Chi Lee
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 6068502, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto 6110011, Japan
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Hung-Wei Hsu
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 6068502, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto 6110011, Japan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Yi Lin
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto 6110011, Japan
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA
| | - Nicolas Gustafson
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 6068502, Japan
| | - Chow-Yang Lee
- Department of Entomology, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Chin-Cheng Scotty Yang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Correspondence: ; Tel.: +1-540-231-3052
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Pollio AR, Jiang J, Lee SS, Gandhi JS, Knott BD, Chunashvili T, Conte MA, Walls SD, Hulseberg CE, Farris CM, Reinbold-Wasson DD, Hang J. Discovery of Rickettsia spp. in mosquitoes collected in Georgia by metagenomics analysis and molecular characterization. Front Microbiol 2022; 13:961090. [PMID: 36160204 PMCID: PMC9493313 DOI: 10.3389/fmicb.2022.961090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Arthropods have a broad and expanding worldwide presence and can transmit a variety of viral, bacterial, and parasite pathogens. A number of Rickettsia and Orientia species associated with ticks, fleas, lice, and mites have been detected in, or isolated from, patients with febrile illness and/or animal reservoirs throughout the world. Mosquitoes are not currently considered vectors for Rickettsia spp. pathogens to humans or to animals. In this study, we conducted a random metagenome next-generation sequencing (NGS) of 475 pools of Aedes, Culex, and Culiseta species of mosquitoes collected in Georgia from 2018 to 2019, identifying rickettsial gene sequences in 33 pools of mosquitoes. We further confirmed the findings of the Rickettsia by genus-specific quantitative PCR (qPCR) and multi-locus sequence typing (MLST). The NGS and MLST results indicate that Rickettsia spp. are closely related to Rickettsia bellii, which is not known to be pathogenic in humans. The results, together with other reports of Rickettsia spp. in mosquitoes and the susceptibility and transmissibility experiments, suggest that mosquitoes may play a role in the transmission cycle of Rickettsia spp.
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Affiliation(s)
- Adam R. Pollio
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Ju Jiang
- Naval Medical Research Center, Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Sam S. Lee
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Jaykumar S. Gandhi
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Brian D. Knott
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Matthew A. Conte
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Shannon D. Walls
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Christine E. Hulseberg
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | | | - Drew D. Reinbold-Wasson
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
- *Correspondence: Jun Hang,
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Konstantinidis K, Bampali M, de Courcy Williams M, Dovrolis N, Gatzidou E, Papazilakis P, Nearchou A, Veletza S, Karakasiliotis I. Dissecting the Species-Specific Virome in Culicoides of Thrace. Front Microbiol 2022; 13:802577. [PMID: 35330767 PMCID: PMC8940260 DOI: 10.3389/fmicb.2022.802577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 12/14/2022] Open
Abstract
Biting midges (Culicoides) are vectors of arboviruses of both veterinary and medical importance. The surge of emerging and reemerging vector-borne diseases and their expansion in geographical areas affected by climate change has increased the importance of understanding their capacity to contribute to novel and emerging infectious diseases. The study of Culicoides virome is the first step in the assessment of this potential. In this study, we analyzed the RNA virome of 10 Culicoides species within the geographical area of Thrace in the southeastern part of Europe, a crossing point between Asia and Europe and important path of various arboviruses, utilizing the Ion Torrent next-generation sequencing (NGS) platform and a custom bioinformatics pipeline based on TRINITY assembler and alignment algorithms. The analysis of the RNA virome of 10 Culicoides species resulted in the identification of the genomic signatures of 14 novel RNA viruses, including three fully assembled viruses and four segmented viruses with at least one segment fully assembled, most of which were significantly divergent from previously identified related viruses from the Solemoviridae, Phasmaviridae, Phenuiviridae, Reoviridae, Chuviridae, Partitiviridae, Orthomyxoviridae, Rhabdoviridae, and Flaviviridae families. Each Culicoides species carried a species-specific set of viruses, some of which are related to viruses from other insect vectors in the same area, contributing to the idea of a virus-carrier web within the ecosystem. The identified viruses not only expand our current knowledge on the virome of Culicoides but also set the basis of the genetic diversity of such viruses in the area of southeastern Europe. Furthermore, our study highlights that such metagenomic approaches should include as many species as possible of the local virus-carrier web that interact and share the virome of a geographical area.
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Affiliation(s)
| | - Maria Bampali
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Nikolas Dovrolis
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Elisavet Gatzidou
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | | | - Stavroula Veletza
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
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9
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Transcriptomics Reveal Several Novel Viruses from Canegrubs (Coleoptera: Scarabaeidae) in Central Queensland, Australia. Viruses 2022; 14:v14030649. [PMID: 35337056 PMCID: PMC8949096 DOI: 10.3390/v14030649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 12/21/2022] Open
Abstract
Canegrubs (Coleoptera: Scarabaeidae) are major pests of sugarcane crops in Australia, but despite long-term and intensive research, no commercially viable biological control agents have been identified. We used the RNA-Seq approach to explore the viriomes of three different species of canegrubs from central Queensland, Australia to identify potential candidates for biological control. We identified six novel RNA viruses, characterized their genomes, and inferred their evolutionary relationships with other closely related viruses. These novel viruses showed similarity to other known members from picornaviruses, benyviruses, sobemoviruses, totiviruses, and reoviruses. The abundance of viral reads varied in these libraries; for example, Dermolepida albohirtum picorna-like virus (9696 nt) was built from 83,894 assembled reads while only 1350 reads mapped to Lepidiota negatoria beny-like virus (6371 nt). Future studies are essential to determine their natural incidence in different life stages of the host, biodiversity, geographical distributions, and potential as biological control agents for these important pests of sugarcane.
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Vargas-Espinosa JH, Aguirre-Obando OA. Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA. ZOOLOGIA 2022. [DOI: 10.1590/s1984-4689.v39.e21029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sanborn MA, Wuertz KM, Kim HC, Yang Y, Li T, Pollett SD, Jarman RG, Berry IM, Klein TA, Hang J. Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea. Mol Ecol 2021; 30:5470-5487. [PMID: 34418188 DOI: 10.1111/mec.16133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022]
Abstract
Recent outbreaks of emerging and re-emerging viruses have shown that timely detection of novel arboviruses with epidemic potential is essential to mitigate human health risks. There are rising concerns that emergent JEV genotype V (GV) is circulating in Asia, against which current vaccines may not be efficacious. To ascertain if JEV GV and other arboviruses are circulating in East Asia, we conducted next-generation sequencing on 260 pools of Culex tritaeniorhynchus and Culex bitaeniorhynchus mosquitoes (6540 specimens) collected at Camp Humphreys, Republic of Korea (ROK) in 2018. Interrogation of our data revealed a highly abundant and diverse virosphere that contained sequences from 122 distinct virus species. Our statistical and hierarchical analysis uncovered correlates of potential health, virological, and ecological relevance. Furthermore, we obtained evidence that JEV GV was circulating in Pyeongtaek and, retrospectively, in Seoul in 2016 and placed these findings within the context of human and fowl reservoir activity. Sequence-based analysis of JEV GV showed a divergent genotype that is the most distant from the GIII-derived live attenuated SA14-14-2 vaccine strain and indicated regions probably responsible for reduced antibody affinity. These results emphasize recent concerns of shifting JEV genotype in East Asia and highlight the critical need for a vaccine proven efficacious against this re-emergent virus. Together, our one-health approach to Culex viral metagenomics uncovered novel insights into virus ecology and human health.
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Affiliation(s)
- Mark A Sanborn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Heung-Chul Kim
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, 65th Medical Brigade, Unit #15281, APO AP 96271-5281, USA
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Simon D Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Terry A Klein
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, 65th Medical Brigade, Unit #15281, APO AP 96271-5281, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Abstract
The enormous diversity of RNA viruses in insects is continuously validated. Parasitoid wasps, as biocontrol insects which are widely used against insect pests in agroecosystems, may also carry many “good” RNA viruses. In this study, many virus-like fragments were obtained from transcriptomes of three wasp species, including Anisopteromalus calandrae (8), Lariophagus distinguendus (3), and Theocolax elegans (18), which can parasitize and control rice weevil Sitophilus oryzae, a serious insect pest of farm-stored grains. By further bioinformatic analysis and sequencing, we identified six novel RNA viruses with complete genomes and named them WWPSRV-1, WWPSRV-2, AcPSRV-1, AcNSRV-1, AcNSRV-2, and LdNSRV-1. PCR-based detection revealed that WWPSRV-1 and WWPSRV-2 had the possibility of interspecies virus transmission, especially WWPSRV-2, which was also present in the rice weevil adults. Phylogenetically, three out of these six viruses appeared to be members of order Picornavirales: WWPSRV-1 belonged to unassigned virus families of this order, whereas WWPSRV-2 and AcPSRV-1 belonged to families Iflaviridae and Dicistroviridae, respectively. The conserved picornavirus-typical domains helicase, protease, and RNA-dependent RNA polymerase could be found in the nonstructural protein encoded by the three viruses, whose genomes consisted of the different numbers of open reading frames (ORFs). The other three RNA viruses could be classified to order Mononegavirales: AcNSRV-1 and AcNSRV-2 belonged to family Lispiviridae, whereas LdNSRV-1 belonged to a big family Rhabdoviridae. The genomes of the three viruses contained at least five ORFs, encoding deduced proteins in the following order: 3′-N-P-M-G-L-5′. All the ORFs were separated by conserved intergenic sequences which likely regulated the transcription termination and initiation. Our findings enhance the understanding of RNA viruses in weevil wasps and set the foundation for the future study of the association among weevils, weevil wasps, and RNA viruses. IMPORTANCE The enormous diversity of RNA viruses in insects is continuously validated. Parasitoid wasps, as biocontrol insects which are widely used against insect pests in agroecosystems, may also carry many “good” RNA viruses. Some RNA viruses in parasitoid wasps have been reported to affect the host wasps or the wasps’ host. Here, six novel RNA viruses with complete genomes were identified in three parasitoid wasps of the rice weevil. One of these viruses was also detected in the rice weevil adults. Phylogenetically, WWPSRV-1 was the first unambiguous detection of Nora-like virus in insect parasitoids. WWPSRV-2 and AcPSRV-1 belong to families Iflaviridae and Dicistroviridae, some viruses of which can result in lethal infections in silkworms and honeybees. The other three RNA viruses belong to order Mononegavirales, which comprises many well-known insect-associated viruses.
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Thongsripong P, Chandler JA, Kittayapong P, Wilcox BA, Kapan DD, Bennett SN. Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes. Sci Rep 2021; 11:8448. [PMID: 33875673 PMCID: PMC8055903 DOI: 10.1038/s41598-021-87122-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
High-throughput nucleic acid sequencing has greatly accelerated the discovery of viruses in the environment. Mosquitoes, because of their public health importance, are among those organisms whose viromes are being intensively characterized. Despite the deluge of sequence information, our understanding of the major drivers influencing the ecology of mosquito viromes remains limited. Using methods to increase the relative proportion of microbial RNA coupled with RNA-seq we characterize RNA viruses and other symbionts of three mosquito species collected along a rural to urban habitat gradient in Thailand. The full factorial study design allows us to explicitly investigate the relative importance of host species and habitat in structuring viral communities. We found that the pattern of virus presence was defined primarily by host species rather than by geographic locations or habitats. Our result suggests that insect-associated viruses display relatively narrow host ranges but are capable of spreading through a mosquito population at the geographical scale of our study. We also detected various single-celled and multicellular microorganisms such as bacteria, alveolates, fungi, and nematodes. Our study emphasizes the importance of including ecological information in viromic studies in order to gain further insights into viral ecology in systems where host specificity is driving both viral ecology and evolution.
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Affiliation(s)
- Panpim Thongsripong
- Department of Microbiology, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA.
| | - James Angus Chandler
- Department of Microbiology, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Pattamaporn Kittayapong
- Center of Excellence for Vectors and Vector-Borne Diseases, Faculty of Science, Mahidol University At Salaya, Nakhon Pathom, Thailand
| | - Bruce A Wilcox
- Global Health Group International, ASEAN Institute for Health Development, Mahidol University At Salaya, Nakhon Pathom, Thailand
| | - Durrell D Kapan
- Department of Entomology and Center for Comparative Genomics, Institute for Biodiversity Sciences and Sustainability, California Academy of Sciences, San Francisco, CA, USA
- Center for Conservation and Research Training, Pacific Biosciences Research Center, University of Hawai'i At Manoa, Honolulu, HI, USA
| | - Shannon N Bennett
- Department of Microbiology, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
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Larvicidal composite alginate hydrogel combined with a Pickering emulsion of essential oil. Carbohydr Polym 2021; 254:117381. [PMID: 33357888 DOI: 10.1016/j.carbpol.2020.117381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/13/2020] [Accepted: 11/03/2020] [Indexed: 01/09/2023]
Abstract
Sulfonated cellulose nanocrystals (S-CNCs) can be used to encapsulate thyme white essential oil (EO) that is volatile and immiscible with water. S-CNCs form a Pickering emulsion (PE) with EOs and the micron-scale PEs are embedded in sodium alginate (SA) to form macroscale hydrogel beads. The incorporation of PEs with SA is confirmed with FTIR, XRD, SEM and confocal microscopic characterizations and the release behavior is monitored to understand the time-dependent biological activity of the EOs. The larvicidal performance of the SA-PE composite hydrogel beads is investigated with Aedes albopictus (Skuse) larvae. The larvicidal activity is higher for SA/PE hydrogel beads prepared at 0.5 % CaCl2 than 0.75 or 1.0 % CaCl2 due to their higher release rate.
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Hwang MJ, Kim HC, Klein TA, Chong ST, Sim K, Chung Y, Cheong HK. Comparison of climatic factors on mosquito abundance at US Army Garrison Humphreys, Republic of Korea. PLoS One 2020; 15:e0240363. [PMID: 33085720 PMCID: PMC7577452 DOI: 10.1371/journal.pone.0240363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/24/2020] [Indexed: 01/05/2023] Open
Abstract
Introduction A number of studies have been conducted on the relationship between the distribution of mosquito abundance and meteorological variables. However, few studies have specifically provided specific ranges of temperatures for estimating the maximum abundance of mosquitoes as an empirical basis for climatic dynamics for estimating mosquito-borne infectious disease risks. Methods Adult mosquitoes were collected for three consecutive nights/week using Mosquito Magnet® Independence® model traps during 2018 and 2019 at US Army Garrison (USAG) Humphreys, Pyeongtaek, Gyeonggi Province, Republic of Korea (ROK). An estimate of daily mean temperatures (provided by the Korea Meteorological Administration) were distributed at the maximum abundance for selected species of mosquitoes using daily mosquito collection data after controlling for mosquito ecological cycles and environmental factors. Results Using the Monte-Carlo simulation, the overall mosquito population abundance peaked at 22.7°C (2.5th—97.5th: 21.7°C–23.8°C). Aedes albopictus, vector of Zika, chikungunya, dengue fever and other viruses, abundance peaked at 24.6°C (2.5th–97.5th, 22.3°C–25.6°C), while Japanese encephalitis virus (JEV) vectors, e.g., Culex tritaeniorhynchus and Culex pipiens, peaked at 24.3°C (2.5th–97.5th: 21.9°C–26.3°C) and 22.6°C (2.5th–97.5th: 21.9°C–25.2°C), respectively. Members of the Anopheles Hyrcanus Group, some of which are vivax malaria vectors in the ROK, abundance peaked at 22.4°C (2.5th–97.5th: 21.5°C–23.8°C). Conclusion The empirical mean temperature ranges for maximum abundance were determined for each mosquito species collected at USAG Humphreys. These data contributed to the identification of relative mosquito abundance patterns for estimating mosquito-borne disease risks and developing and implementing disease prevention practices.
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Affiliation(s)
- Myung-Jae Hwang
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi-do, Republic of Korea
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th Medical Brigade, Unit 15281, United States of America
| | - Terry A. Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th Medical Brigade, Unit 15281, United States of America
| | - Sung-Tae Chong
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th Medical Brigade, Unit 15281, United States of America
| | - Kisung Sim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yeonseung Chung
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hae-Kwan Cheong
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi-do, Republic of Korea
- * E-mail:
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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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Hewson I, Johnson MR, Tibbetts IR. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses 2020; 12:v12091057. [PMID: 32972018 PMCID: PMC7551563 DOI: 10.3390/v12091057] [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: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: ; Tel.: +1-607-255-0151
| | | | - Ian R. Tibbetts
- School of Biological Sciences, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia;
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18
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Kubacki J, Flacio E, Qi W, Guidi V, Tonolla M, Fraefel C. Viral Metagenomic Analysis of Aedes albopictus Mosquitos from Southern Switzerland. Viruses 2020; 12:v12090929. [PMID: 32846980 PMCID: PMC7552062 DOI: 10.3390/v12090929] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023] Open
Abstract
A metagenomic study was performed on 498 female and 40 male Aedes albopictus mosquitos collected in August and September 2019 in Ticino, a region in southern Switzerland, to address the question regarding the risk of the local transmission of zoonotic viruses. A total of 13 viruses from seven different virus families and several unclassified viral taxa were identified. Reads of insect-specific flaviviruses were present in all pools, and a complete genome of aedes flavivirus was assembled and phylogenetically analysed. The most abundant virus was Wenzhou sobemo-like virus, assembled from 1.3 × 105 to 3.6 × 106 reads in each pool. In a pool of male mosquitos, a complete genome of aedes Iflavi-like virus was detected and phylogenetically analysed. Most importantly, genomes of human pathogenic viruses were not found. This is the first study to determine the virome of Ae. albopictus from Switzerland and forms a baseline for future longitudinal investigations concerning the potential role of Ae. albopictus as a vector of clinically relevant viruses.
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Affiliation(s)
- Jakub Kubacki
- Institute of Virology, University of Zürich, CH-8057 Zürich, Switzerland
- Correspondence: (J.K.); (C.F.)
| | - Eleonora Flacio
- Laboratory of Applied Microbiology, Department for Environment Constructions and Design, University of Applied Sciences and Arts of Southern Switzerland, CH-6500 Manno, Switzerland; (E.F.); (V.G.); (M.T.)
| | - Weihong Qi
- Functional Genomics Center Zurich, CH-8057 Zürich, Switzerland;
| | - Valeria Guidi
- Laboratory of Applied Microbiology, Department for Environment Constructions and Design, University of Applied Sciences and Arts of Southern Switzerland, CH-6500 Manno, Switzerland; (E.F.); (V.G.); (M.T.)
| | - Mauro Tonolla
- Laboratory of Applied Microbiology, Department for Environment Constructions and Design, University of Applied Sciences and Arts of Southern Switzerland, CH-6500 Manno, Switzerland; (E.F.); (V.G.); (M.T.)
| | - Cornel Fraefel
- Institute of Virology, University of Zürich, CH-8057 Zürich, Switzerland
- Correspondence: (J.K.); (C.F.)
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Parry R, Naccache F, Ndiaye EH, Fall G, Castelli I, Lühken R, Medlock J, Cull B, Hesson JC, Montarsi F, Failloux AB, Kohl A, Schnettler E, Diallo M, Asgari S, Dietrich I, Becker SC. Identification and RNAi Profile of a Novel Iflavirus Infecting Senegalese Aedes vexans arabiensis Mosquitoes. Viruses 2020; 12:E440. [PMID: 32295109 PMCID: PMC7232509 DOI: 10.3390/v12040440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/10/2020] [Accepted: 04/11/2020] [Indexed: 01/16/2023] Open
Abstract
The inland floodwater mosquito Aedes vexans (Meigen, 1830) is a competent vector of numerous arthropod-borne viruses such as Rift Valley fever virus (Phenuiviridae) and Zika virus (Flaviviridae). Aedes vexans spp. have widespread Afrotropical distribution and are common European cosmopolitan mosquitoes. We examined the virome of Ae. vexans arabiensis samples from Barkédji village, Senegal, with small RNA sequencing, bioinformatic analysis, and RT-PCR screening. We identified a novel 9494 nt iflavirus (Picornaviridae) designated here as Aedes vexans iflavirus (AvIFV). Annotation of the AvIFV genome reveals a 2782 amino acid polyprotein with iflavirus protein domain architecture and typical iflavirus 5' internal ribosomal entry site and 3' poly-A tail. Aedes vexans iflavirus is most closely related to a partial virus sequence from Venturia canescens (a parasitoid wasp) with 56.77% pairwise amino acid identity. Analysis of AvIFV-derived small RNAs suggests that AvIFV is targeted by the exogenous RNA interference pathway but not the PIWI-interacting RNA response, as ~60% of AvIFV reads corresponded to 21 nt Dicer-2 virus-derived small RNAs and the 24-29 nt AvIFV read population did not exhibit a "ping-pong" signature. The RT-PCR screens of archival and current (circa 2011-2020) Ae. vexans arabiensis laboratory samples and wild-caught mosquitoes from Barkédji suggest that AvIFV is ubiquitous in these mosquitoes. Further, we screened wild-caught European Ae. vexans samples from Germany, the United Kingdom, Italy, and Sweden, all of which tested negative for AvIFV RNA. This report provides insight into the diversity of commensal Aedes viruses and the host RNAi response towards iflaviruses.
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Affiliation(s)
- Rhys Parry
- Australian Infectious Diseases Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.P.); (S.A.)
| | - Fanny Naccache
- Institute for Parasitology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany;
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - El Hadji Ndiaye
- Pole de Zoologie Médicale, Institut Pasteur de Dakar, Dakar BP 220, Senegal; (E.H.N.); (M.D.)
| | - Gamou Fall
- Pole de Virologie, Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar, Dakar BP 220, Senegal;
| | - Ilaria Castelli
- Arboviruses and Insect Vectors, Department of Virology, Institut Pasteur, 75724 Paris, France; (I.C.); (A.-B.F.)
| | - Renke Lühken
- Faculty of Mathematics, Informatics and Natural Sciences, Universiät Hamburg, 20148 Hamburg, Germany; (R.L.); (E.S.)
- Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Jolyon Medlock
- Health Protection Research Unit in Emerging and Zoonotic Infection, Public Health England, Porton Down, Salisbury SP4 0JG, UK;
- Medical Entomology & Zoonoses Ecology, Emergency Response Department Science & Technology, Public Health England, Porton Down, Salisbury SP4 0JG, UK; or
| | - Benjamin Cull
- Medical Entomology & Zoonoses Ecology, Emergency Response Department Science & Technology, Public Health England, Porton Down, Salisbury SP4 0JG, UK; or
| | - Jenny C. Hesson
- Department of Medical Biochemistry and Microbiology/Zoonosis Science Center, Uppsala University, 75237 Uppsala, Sweden;
| | - Fabrizio Montarsi
- Laboratory of Parasitology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro (Padua), Italy;
| | - Anna-Bella Failloux
- Arboviruses and Insect Vectors, Department of Virology, Institut Pasteur, 75724 Paris, France; (I.C.); (A.-B.F.)
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK;
| | - Esther Schnettler
- Faculty of Mathematics, Informatics and Natural Sciences, Universiät Hamburg, 20148 Hamburg, Germany; (R.L.); (E.S.)
- Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Centre for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, 20359 Hamburg, Germany
| | - Mawlouth Diallo
- Pole de Zoologie Médicale, Institut Pasteur de Dakar, Dakar BP 220, Senegal; (E.H.N.); (M.D.)
| | - Sassan Asgari
- Australian Infectious Diseases Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.P.); (S.A.)
| | | | - Stefanie C. Becker
- Institute for Parasitology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany;
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
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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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Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL. Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes. Viruses 2019; 11:v11111027. [PMID: 31694175 PMCID: PMC6893623 DOI: 10.3390/v11111027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 02/06/2023] Open
Abstract
Metagenomic studies of mosquitoes have revealed that their virome is far more diverse and includes many more viruses than just the pathogenic arboviruses vectored by mosquitoes. In this study, the virome of 953 female mosquitoes collected in the summer of 2017, representing six mosquito species from two geographic locations in Mid-Eastern Sweden, were characterized. In addition, the near-complete genome of nine RNA viruses were characterized and phylogenetically analysed. These viruses showed association to the viral orders Bunyavirales, Picornavirales, Articulavirales, and Tymovirales, and to the realm Ribovira. Hence, through this study, we expand the knowledge of the virome composition of different mosquito species in Sweden. In addition, by providing viral reference genomes from wider geographic regions and different mosquito species, future in silico recognition and assembly of viral genomes in metagenomic datasets will be facilitated.
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Affiliation(s)
- Pontus Öhlund
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; (H.L.); (A.-L.B.)
- Correspondence: ; Tel.: +46-18-672-409
| | - Juliette Hayer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre, Box 7023, 750 07 Uppsala, Sweden;
| | - Hanna Lundén
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; (H.L.); (A.-L.B.)
| | - Jenny C. Hesson
- Department of Medical Biochemistry and Microbiology/Zoonosis Science Center, Uppsala University, Box 582, 751 23 Uppsala, Sweden;
| | - Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; (H.L.); (A.-L.B.)
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