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Molina IS, Jimenez-Vasquez V, Lizarraga W, Sevilla N, Hurtado V, Padilla-Rojas C. Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology. J Med Virol 2023; 95:e29056. [PMID: 37671858 DOI: 10.1002/jmv.29056] [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: 04/29/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.
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Affiliation(s)
- Iris S Molina
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Victor Jimenez-Vasquez
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Wendy Lizarraga
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nieves Sevilla
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Veronica Hurtado
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Carlos Padilla-Rojas
- Area de Innovacion y Desarrollo Tecnológico, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
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Nyirakanani C, Tamisier L, Bizimana JP, Rollin J, Nduwumuremyi A, Bigirimana VDP, Selmi I, Lasois L, Vanderschuren H, Massart S. Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda. Virus Evol 2023; 9:vead053. [PMID: 37692897 PMCID: PMC10491861 DOI: 10.1093/ve/vead053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/14/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023] Open
Abstract
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in thirteen cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in twelve districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 per cent divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNPs) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNP patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100 per cent occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes' associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.
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Affiliation(s)
- Chantal Nyirakanani
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Lucie Tamisier
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Jean Pierre Bizimana
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Johan Rollin
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, DNAVision, Gosselies, Charleroi 6041, Belgium
| | - Athanase Nduwumuremyi
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Vincent de Paul Bigirimana
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Ilhem Selmi
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Ludivine Lasois
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Tropical Crop Improvement Laboratory, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven 3001, Belgium
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
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Crespo-Bellido A, Duffy S. The how of counter-defense: viral evolution to combat host immunity. Curr Opin Microbiol 2023; 74:102320. [PMID: 37075547 DOI: 10.1016/j.mib.2023.102320] [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: 01/07/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Viruses are locked in an evolutionary arms race with their hosts. What ultimately determines viral evolvability, or capacity for adaptive evolution, is their ability to efficiently explore and expand sequence space while under the selective regime imposed by their ecology, which includes innate and adaptive host defenses. Viral genomes have significantly higher evolutionary rates than their host counterparts and should have advantages relative to their slower-evolving hosts. However, functional constraints on virus evolutionary landscapes along with the modularity and mutational tolerance of host defense proteins may help offset the advantage conferred to viruses by high evolutionary rates. Additionally, cellular life forms from all domains of life possess many highly complex defense mechanisms that act as hurdles to viral replication. Consequently, viruses constantly probe sequence space through mutation and genetic exchange and are under pressure to optimize diverse counter-defense strategies.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.
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4
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Okeke ES, Olovo CV, Nkwoemeka NE, Okoye CO, Nwankwo CEI, Onu CJ. Microbial ecology and evolution is key to pandemics: using the coronavirus model to mitigate future public health challenges. Heliyon 2022; 8:e09449. [PMID: 35601228 PMCID: PMC9113781 DOI: 10.1016/j.heliyon.2022.e09449] [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: 09/23/2021] [Revised: 01/03/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. The recent coronavirus model was used to study issues leading to microbial evolution, towards preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious diseases.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences and Environmental Biology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, 212013, PR China
| | - Chinasa Valerie Olovo
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University Zhenjiang, 212013, Jiangsu, PR China
| | - Ndidi Ethel Nkwoemeka
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
| | - Charles Obinwanne Okoye
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Biofuels Institute, School of Environment and Safety Engineering Jiangsu University, Zhenjiang, 212013, China
| | - Chidiebele Emmanuel Ikechukwu Nwankwo
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
| | - Chisom Joshua Onu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
- Department of Biological Sciences, College of Liberal Arts and Sciences, Detroit, Michigan, 48202, USA
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5
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Hill T, Unckless RL, Perlmutter JI. Positive Selection and Horizontal Gene Transfer in the Genome of a Male-Killing Wolbachia. Mol Biol Evol 2022; 39:msab303. [PMID: 34662426 PMCID: PMC8763111 DOI: 10.1093/molbev/msab303] [Citation(s) in RCA: 4] [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] [Indexed: 12/28/2022] Open
Abstract
Wolbachia are a genus of widespread bacterial endosymbionts in which some strains can hijack or manipulate arthropod host reproduction. Male killing is one such manipulation in which these maternally transmitted bacteria benefit surviving daughters in part by removing competition with the sons for scarce resources. Despite previous findings of interesting genome features of microbial sex ratio distorters, the population genomics of male-killers remain largely uncharacterized. Here, we uncover several unique features of the genome and population genomics of four Arizonan populations of a male-killing Wolbachia strain, wInn, that infects mushroom-feeding Drosophila innubila. We first compared the wInn genome with other closely related Wolbachia genomes of Drosophila hosts in terms of genome content and confirm that the wInn genome is largely similar in overall gene content to the wMel strain infecting D. melanogaster. However, it also contains many unique genes and repetitive genetic elements that indicate lateral gene transfers between wInn and non-Drosophila eukaryotes. We also find that, in line with literature precedent, genes in the Wolbachia prophage and Octomom regions are under positive selection. Of all the genes under positive selection, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes. These dynamics of selection and horizontal gene transfer across the genomes of several Wolbachia strains and diverse host species may be important underlying factors in Wolbachia's success as a male-killer of divergent host species.
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Affiliation(s)
- Tom Hill
- NIAID Collaborative Bioinformatics Resource, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
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Koo ES, Jeong YS. Comparative study of the geographical spread of genogroup II porcine norovirus and human norovirus. J Microbiol 2021; 59:644-650. [PMID: 34212288 DOI: 10.1007/s12275-021-1218-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Livestock pigs and porcine norovirus could be candidate tools for future studies on the geographic isolation of norovirus. In this study, we provide the first evidence for geographic isolation of the host as a determinant of the distribution of subgenotypes of the porcine norovirus genogroup II (GII) genotype 11. Environmental water samples were collected from peri-urban streams and estuaries in South Korea between 2014 and 2020. In total, 488 GII region C sequences of norovirus open reading frame 2 were isolated. A total of 14 genotypes were detected, two of which (GII.11 and GII.18) corresponded to porcine norovirus. Five human norovirus genotypes (GII.2, GII.3, GII.4, GII.6, and GII.17) and one porcine norovirus genotype (GII.11) comprised the subgenotypes. Integrated analysis of seasonal and geographical factors revealed that the possibility of the co-emergence of different GII.11 subgenotypes in the same province was lower than that of human norovirus subgenotypes in the same province. Additional algorithms designed to eliminate potential biases further supported the estimated restricted geographical spread of the GII.11 subgenotypes. Fecal contamination source tracking revealed low detection rates of porcine norovirus in the absence of upstream pig farms. These results suggest that a one-sided viral transmission route, mainly dependent on indirect contact owing to the limited chance of direct contact between geographically separated livestock pig populations, may be responsible for the restricted geographical spread of the GII.11 subgenotypes.
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Affiliation(s)
- Eung Seo Koo
- Molecular Virology Laboratory, Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Yong Seok Jeong
- Molecular Virology Laboratory, Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea.
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7
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Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus. Viruses 2021; 13:v13050901. [PMID: 34068017 PMCID: PMC8152266 DOI: 10.3390/v13050901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
The mulberry silkworm, Bombyx mori (L.), is a model organism of lepidopteran insects with high economic importance. The viral diseases of the silkworm caused by Bombyx mori nucleopolyhedrovirus (BmNPV) and Bombyx mori bidensovirus (BmBDV) inflict huge economic losses and significantly impact the sericulture industry of India and other countries. To understand the distribution of Indian isolates of the BmNPV and to investigate their genetic composition, an in-depth population structure analysis was conducted using comprehensive and newly developed genomic analysis methods. The seven new Indian BmNPV isolates from Anantapur, Dehradun, Ghumarwin, Jammu, Kashmir, Mysore and Salem grouped in the BmNPV clade, and are most closely related to Autographa californica multiple nucleopolyhedrovirus and Rachiplusia ou multiple nucleopolyhedrovirus on the basis of gene sequencing and phylogenetic analyses of the partial polh, lef-8 and lef-9 gene fragments. The whole genome sequencing of three Indian BmNPV isolates from Mysore (-My), Jammu (-Ja) and Dehradun (-De) was conducted, and intra-isolate genetic variability was analyzed on the basis of variable SNP positions and the frequencies of alternative nucleotides. The results revealed that the BmNPV-De and BmNPV-Ja isolates are highly similar in their genotypic composition, whereas the population structure of BmNPV-My appeared rather pure and homogenous, with almost no or few genetic variations. The BmNPV-De and BmNPV-Ja samples further contained a significant amount of BmBDV belonging to the Bidnaviridae family. We elucidated the genotype composition within Indian BmNPV and BmBDV isolates, and the results presented have broad implications for our understanding of the genetic diversity and evolution of BmNPV and co-occurring BmBDV isolates.
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8
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Hill T, Unckless RL. Adaptation, ancestral variation and gene flow in a 'Sky Island' Drosophila species. Mol Ecol 2021; 30:83-99. [PMID: 33089581 PMCID: PMC7945764 DOI: 10.1111/mec.15701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south-western USA separated by large expanses of desert. Using population genomic data from more than 300 wild-caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30-100 KYA) and have recently expanded even further (0.2-2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long-term recurrent selection in these genes. In contrast, we find evidence of long-term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll-regulated antimicrobial peptides.
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Affiliation(s)
- Tom Hill
- 4055 Haworth Hall, The Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045
| | - Robert L. Unckless
- 4055 Haworth Hall, The Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045
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9
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Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evol 2021; 7:veab031. [PMID: 34408913 PMCID: PMC8363768 DOI: 10.1093/ve/veab031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.
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Affiliation(s)
- Megan A Wallace
- The European Drosophila Population Genomics Consortium (DrosEU)
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Kelsey A Coffman
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Clément Gilbert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Sanjana Ravindran
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Paola Bellosta
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Cellular, Computational and Integrative Biology, CIBIO University of Trento, Via Sommarive 9, Trento 38123, Italy
- Department of Medicine & Endocrinology, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Hervé Colinet
- The European Drosophila Population Genomics Consortium (DrosEU)
- UMR CNRS 6553 ECOBIO, Université de Rennes1, Rennes, France
| | - Katarina Eric
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Amanda Glaser-Schmitt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Mihailo Jelic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Genetics, Ecology and Evolution, Aarhus University, Ny Munkegade 116, Aarhus C DK-8000, Denmark
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Lino Ometto
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Aleksandra Patenkovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, St Andrews University, St Andrews HY15 4SS, UK
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Center, Fondazione E. Mach, San Michele all’Adige (TN) 38010, Italy
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige (TN) 38010, Italy
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Svitlana V Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine
- Taras Shevchenko National University of Kyiv, 64 Volodymyrska str, Kyiv 01601, Ukraine
| | - Marina Stamenkovic-Radak
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Marija Tanaskovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Marija Savic Veselinovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, i3S, Porto, Portugal
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, i3S, Porto, Portugal
| | - Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution and Ecology, University of Freiburg, Freiburg 79104, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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