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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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Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC. Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics. PLoS Pathog 2023; 19:e1011588. [PMID: 37651317 PMCID: PMC10470969 DOI: 10.1371/journal.ppat.1011588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.
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Affiliation(s)
- Brandon D Hollingsworth
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Nathan D Grubaugh
- Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale University, New Haven, Connecticut, United States of America
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Courtney C Murdock
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
- Northeast Regional Center for Excellence in Vector-borne Diseases, Cornell University, Ithaca, New York, United States of America
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Miranda TDS, Schiffler FB, D'arc M, Moreira FRR, Cosentino MAC, Coimbra A, Mouta R, Medeiros G, Girardi DL, Wanderkoke V, Soares CFA, Francisco TM, Henry MD, Afonso BC, Soffiati FL, Ferreira SS, Ruiz-Miranda CR, Soares MA, Santos AFA. Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil. Virus Res 2023; 325:199017. [PMID: 36565815 DOI: 10.1016/j.virusres.2022.199017] [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: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
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Affiliation(s)
- Thamiris Dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Déa Luiza Girardi
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Victor Wanderkoke
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Caique Ferreira Amaral Soares
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talitha Mayumi Francisco
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Malinda Dawn Henry
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Bianca Cardozo Afonso
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | | | - Carlos Ramon Ruiz-Miranda
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - André Felipe Andrade Santos
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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Moonen JP, Schinkel M, van der Most T, Miesen P, van Rij RP. Composition and global distribution of the mosquito virome - A comprehensive database of insect-specific viruses. One Health 2023; 16:100490. [PMID: 36817977 PMCID: PMC9929601 DOI: 10.1016/j.onehlt.2023.100490] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Mosquitoes are vectors for emerging and re-emerging infectious viral diseases of humans, livestock and other animals. In addition to these arthropod-borne (arbo)viruses, mosquitoes are host to an array of insect-specific viruses, collectively referred to as the mosquito virome. Mapping the mosquito virome and understanding if and how its composition modulates arbovirus transmission is critical to understand arboviral disease emergence and outbreak dynamics. In recent years, next-generation sequencing as well as PCR and culture-based methods have been extensively used to identify mosquito-associated viruses, providing insights into virus ecology and evolution. Until now, the large amount of mosquito virome data, specifically those acquired by metagenomic sequencing, has not been comprehensively integrated. We have constructed a searchable database of insect-specific viruses associated with vector mosquitoes from 175 studies, published between October 2000 and February 2022. We identify the most frequently detected and widespread viruses of the Culex, Aedes and Anopheles mosquito genera and report their global distribution. In addition, we highlight the challenges of extracting and integrating published virome data and we propose that a standardized reporting format will facilitate data interpretation and re-use by other scientists. We expect our comprehensive database, summarizing mosquito virome data collected over 20 years, to be a useful resource for future studies.
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da Silva H, Oliveira TMP, Sabino EC, Alonso DP, Sallum MAM. Bacterial diversity in Haemagogus leucocelaenus (Diptera: Culicidae) from Vale do Ribeira, São Paulo, Brazil. BMC Microbiol 2022; 22:161. [PMID: 35733096 PMCID: PMC9215073 DOI: 10.1186/s12866-022-02571-5] [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: 04/07/2022] [Accepted: 06/06/2022] [Indexed: 01/29/2023] Open
Abstract
INTRODUCTION Mosquitoes (Diptera: Culicidae) are vectors that transmit numerous pathogens to humans and other vertebrates. Haemagogus leucocelaenus is a mosquito associated with transmission of yellow fever virus. The insect gut harbors a variety of microorganisms that can live and multiply within it, thus contributing to digestion, nutrition, and development of its host. The composition of bacterial communities in mosquitoes can be influenced by both biotic and abiotic factors. The goal of this study was to investigate the bacterial diversity of Hg. leucocelaenus and verify the differences between the bacterial communities in Hg. leucocelaenus from three different locations in the Atlantic tropical rain forest and southeastern state of São Paulo State, Brazil. RESULTS The phylum Proteobacteria was found in mosquitoes collected from the three selected study sites. More than 50% of the contigs belong to Wolbachia, followed by 5% Swaminathania, and 3% Acinetobacter. The genus Serratia was found in samples from two locations. CONCLUSIONS Wolbachia was reported for the first time in this species and may indicates that the vector competence of the populations of the species can vary along its geographical distribution area. The presence of Serratia might facilitate viral invasion caused by the disruption of the midgut barrier via action of the SmEnhancin protein, which digests the mucins present in the intestinal epithelium.
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Affiliation(s)
- Herculano da Silva
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
| | - Tatiane M. P. Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
| | - Ester C. Sabino
- Departamento de Moléstias Infecciosas e Parasitarias, Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Eneas de Carvalho 470, 1º andar, São Paulo, 05403-000 Brazil
| | - Diego Peres Alonso
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
- Biotechnology Institute and Bioscience Institute, Sao Paulo State University (UNESP), Botucatu, 18618-689 Brazil
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
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Celone M, Okech B, Han BA, Forshey BM, Anyamba A, Dunford J, Rutherford G, Mita-Mendoza NK, Estallo EL, Khouri R, de Siqueira IC, Pollett S. A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus. PLoS Negl Trop Dis 2021; 15:e0010016. [PMID: 34898602 PMCID: PMC8699665 DOI: 10.1371/journal.pntd.0010016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/23/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Improving our understanding of Mayaro virus (MAYV) ecology is critical to guide surveillance and risk assessment. We conducted a PRISMA-adherent systematic review of the published and grey literature to identify potential arthropod vectors and non-human animal reservoirs of MAYV. We searched PubMed/MEDLINE, Embase, Web of Science, SciELO and grey-literature sources including PAHO databases and dissertation repositories. Studies were included if they assessed MAYV virological/immunological measured occurrence in field-caught, domestic, or sentinel animals or in field-caught arthropods. We conducted an animal seroprevalence meta-analysis using a random effects model. We compiled granular georeferenced maps of non-human MAYV occurrence and graded the quality of the studies using a customized framework. Overall, 57 studies were eligible out of 1523 screened, published between the years 1961 and 2020. Seventeen studies reported MAYV positivity in wild mammals, birds, or reptiles and five studies reported MAYV positivity in domestic animals. MAYV positivity was reported in 12 orders of wild-caught vertebrates, most frequently in the orders Charadriiformes and Primate. Sixteen studies detected MAYV in wild-caught mosquito genera including Haemagogus, Aedes, Culex, Psorophora, Coquillettidia, and Sabethes. Vertebrate animals or arthropods with MAYV were detected in Brazil, Panama, Peru, French Guiana, Colombia, Trinidad, Venezuela, Argentina, and Paraguay. Among non-human vertebrates, the Primate order had the highest pooled seroprevalence at 13.1% (95% CI: 4.3-25.1%). From the three most studied primate genera we found the highest seroprevalence was in Alouatta (32.2%, 95% CI: 0.0-79.2%), followed by Callithrix (17.8%, 95% CI: 8.6-28.5%), and Cebus/Sapajus (3.7%, 95% CI: 0.0-11.1%). We further found that MAYV occurs in a wide range of vectors beyond Haemagogus spp. The quality of evidence behind these findings was variable and prompts calls for standardization of reporting of arbovirus occurrence. These findings support further risk emergence prediction, guide field surveillance efforts, and prompt further in-vivo studies to better define the ecological drivers of MAYV maintenance and potential for emergence.
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Affiliation(s)
- Michael Celone
- Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Department of Preventive Medicine & Biostatistics, Bethesda, Maryland, United States of America
| | - Bernard Okech
- Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Department of Preventive Medicine & Biostatistics, Bethesda, Maryland, United States of America
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
| | - Brett M. Forshey
- Armed Forces Health Surveillance Division, Silver Spring, Maryland, United States of America
| | - Assaf Anyamba
- University Space Research Association & NASA/Goddard Space Flight Center, Biospheric Sciences Laboratory, Greenbelt, Maryland, United States of America
| | - James Dunford
- Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Department of Preventive Medicine & Biostatistics, Bethesda, Maryland, United States of America
| | - George Rutherford
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | | | - Elizabet Lilia Estallo
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT) CONICET-Universidad Nacional de Córdoba, Centro de Investigaciones Entomológicas de Córdoba, Córdoba, Argentina
| | - Ricardo Khouri
- Instituto Gonçalo Moniz-Fiocruz, R. Waldemar Falcão, Salvador, Bahia, Brazil
| | | | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
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