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Hamza W, Hazzouri KM, Sudalaimuthuasari N, Amiri KMA, Neretina AN, Al Neyadi SES, Kotov AA. Genome Assembly of a Relict Arabian Species of Daphnia O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life. Int J Mol Sci 2023; 24:ijms24010889. [PMID: 36614331 PMCID: PMC9820869 DOI: 10.3390/ijms24010889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
The water flea Daphnia O.F. Müller 1776 (Crustacea: Cladocera) is an important model of recent evolutionary biology. Here, we report a complete genome of Daphnia (Ctenodaphnia) arabica (Crustacea: Cladocera), recently described species endemic to deserts of the United Arab Emirates. In this study, genome analysis of D. arabica was carried out to investigate its genomic differences, complexity as well as its historical origins within the subgenus Daphnia (Ctenodaphnia). Hybrid genome assembly of D. arabica resulted in ~116 Mb of the assembled genome, with an N50 of ~1.13 Mb (BUSCO score of 99.2%). From the assembled genome, in total protein coding, 5374 tRNA and 643 rRNA genes were annotated. We found that the D. arabica complete genome differed from those of other Daphnia species deposited in the NCBI database but was close to that of D. cf. similoides. However, its divergence time estimate sets D. arabica in the Mesozoic, and our demographic analysis showed a great reduction in its genetic diversity compared to other Daphnia species. Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in D. arabica, which is missing in all other studied species of Daphnia. This complex consists of a few subunits (A, B, C) working together to maintain the genome stability (i.e., promoting the reparation of DNA under stress). We propose that this domain could play a role in maintaining the fitness and survival of this species in the desert environment. The present study will pave the way for future research to identify the genes that were gained or lost in this species and identify which of these were key factors to its adaptation to the harsh desert environment.
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Affiliation(s)
- Waleed Hamza
- Biology Department, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Correspondence: (W.H.); (A.A.K.)
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Biology Department, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Anna N. Neretina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Shamma E. S. Al Neyadi
- Biology Department, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Alexey A. Kotov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: (W.H.); (A.A.K.)
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2
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Behl A, Nair A, Mohagaonkar S, Yadav P, Gambhir K, Tyagi N, Sharma RK, Butola BS, Sharma N. Threat, challenges, and preparedness for future pandemics: A descriptive review of phylogenetic analysis based predictions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105217. [PMID: 35065303 DOI: 10.1016/j.meegid.2022.105217] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 12/01/2021] [Accepted: 01/14/2022] [Indexed: 11/27/2022]
Abstract
For centuries the world has been confronted with many infectious diseases, with a potential to turn into a pandemic posing a constant threat to human lives. Some of these pandemics occurred due to the emergence of new disease or re-emergence of previously known diseases with a few mutations. In such scenarios their optimal prevention and control options were not adequately developed. Most of these diseases are highly contagious and for their timely control, knowledge about the pathogens and disease progression is the basic necessity. In this review, we have presented a documented chronology of the earlier pandemics, evolutionary analysis of the infectious disease with pandemic potential, the role of RNA, difficulties in controlling pandemics, and the likely pathogens that could trigger future pandemics. In this study, the evolutionary history of the pathogens was identified by carrying out phylogenetic analysis. The percentage similarity between different infectious diseases is critically analysed for the identification of their correlation using online sequence matcher tools. The Baltimore classification system was used for finding the genomic nature of the viruses. It was observed that most of the infectious pathogens rise from their animal hosts with some mutations in their genome composition. The phylogenetic tree shows that the single-stranded RNA diseases have a common origin and many of them are having high similarity percentage. The outcomes of this study will help in the identification of potential pathogens that can cause future pandemics. This information will be helpful in the development of early detection techniques, devising preventive mechanism to limit their spread, prophylactic measures, Infection control and therapeutic options, thereby, strengthening our approach towards global preparedness against future pandemics.
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Affiliation(s)
- Amanpreet Behl
- Department of Molecular Medicine, Jamia Hamdard Univeristy, Hamdard Nagar, New Delhi, Delhi 110062, India
| | - Ashrit Nair
- Department of Textile and Fibre Engineering, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
| | - Sanika Mohagaonkar
- Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom
| | - Pooja Yadav
- Department of Medical Elementology and Toxicology, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Kirtida Gambhir
- Stem cell and Gene Therapy Research Group, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organisation, Delhi 110054, India
| | - Nishant Tyagi
- Stem cell and Gene Therapy Research Group, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organisation, Delhi 110054, India
| | - Rakesh Kumar Sharma
- Saveetha Institute of Medical and Technical Sciences, 162, Poonamallee High Road, Chennai 600077, Tamil Nadu, India
| | - Bhupendra Singh Butola
- Department of Textile and Fibre Engineering, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
| | - Navneet Sharma
- Department of Textile and Fibre Engineering, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
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3
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Zuykova EI, Bochkarev NA, Kotov AA. Specific and Genetic Structure of the Daphnia longispina s. l. Complex (Cladocera, Daphniidae) in Water Bodies of Southern Siberia. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021070323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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4
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Carvalho VL, Long MT. Insect-Specific Viruses: An overview and their relationship to arboviruses of concern to humans and animals. Virology 2021; 557:34-43. [PMID: 33631523 DOI: 10.1016/j.virol.2021.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 02/08/2023]
Abstract
The group of Insect-specific viruses (ISVs) includes viruses apparently restricted to insects based on their inability to replicate in the vertebrates. Increasing numbers of ISVs have been discovered and characterized representing a diverse number of viral families. However, most studies have focused on those ISVs belonging to the family Flaviviridae, which highlights the importance of ISV study from other viral families, which allow a better understanding for the mechanisms of transmission and evolution used for this diverse group of viruses. Some ISVs have shown the potential to modulate arboviruses replication and vector competence of mosquitoes. Based on this, ISVs may be used as an alternative tool for biological control, development of vaccines, and diagnostic platforms for arboviruses. In this review, we provide an update of the general characteristics of ISVs and their interaction with arboviruses that infect vertebrates.
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Affiliation(s)
- Valéria L Carvalho
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, College of Veterinary Medicine, 1945 SW 16th Ave, Gainesville, FL, 32608, USA; Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Rodovia BR-316, Km 7, S/n, Ananindeua, Para, 67030-000, Brazil.
| | - Maureen T Long
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, College of Veterinary Medicine, 1945 SW 16th Ave, Gainesville, FL, 32608, USA.
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Neretina AN, Karabanov DP, Sacherova V, Kotov AA. Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere. PeerJ 2021; 9:e10804. [PMID: 33585083 PMCID: PMC7860113 DOI: 10.7717/peerj.10804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 02/05/2023] Open
Abstract
Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.
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Affiliation(s)
- Anna N. Neretina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- I.D. Papanin Institute for Biology of Inland Waters, Borok, Yaroslavl State, Russia
| | | | - Alexey A. Kotov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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6
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Klimentov AS, Belova OA, Kholodilov IS, Butenko AM, Bespyatova LA, Bugmyrin SV, Chernetsov N, Ivannikova AY, Kovalchuk IV, Nafeev AA, Oorzhak ND, Pilikova OM, Polienko AE, Purmak KA, Romanenko EN, Romanova LI, Saryglar AA, Solomashchenko NI, Shamsutdinov AF, Vakalova EV, Lukashev AN, Karganova GG, Gmyl AP. Phlebovirus sequences detected in ticks collected in Russia: Novel phleboviruses, distinguishing criteria and high tick specificity. INFECTION GENETICS AND EVOLUTION 2020; 85:104524. [PMID: 32891876 DOI: 10.1016/j.meegid.2020.104524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Phlebovirus is an abundant and rather heterogeneous genus within the Phenuiviridae family (order Bunyavirales). The genus Phlebovirus is divided into two antigenic complexes, which also correspond to the main vector: sandflies/mosquitoes and ticks. Previously, only sandfly/mosquito-borne phleboviruses were associated with human disease, such as Rift Valley fever virus, Toscana virus, Sicilian and Naples Sandfly fever viruses and others. Until recently, tick-borne phleboviruses were not considered as human pathogens. After the discovery of severe fever with thrombocytopenia syndrome, interest to tick-borne phleboviruses has increased dramatically. In the last decade, many novel phleboviruses have been reported in different regions. Despite this, the diversity, ecology and pathogenicity of these viruses still remain obscure. The aim of this work was to study the diversity of phleboviruses in ticks collected in several regions of Russia. We used pan-phlebovirus RT-PCR assays based on multiple degenerate primers targeting the polymerase gene fragment. Arthropod specimens were collected from 2005 to 2018. A total of 5901 Ixodidae ticks combined into 1116 pools were screened. A total of 160 specific amplicons were produced. In three cases RT-PCR assays amplified two distinct viruses from same tick pools. Direct sequencing of amplicons and subsequent phylogenetic analysis revealed twelve representatives of divergent phlebovirus groups. Based on the distribution of pairwise nucleotide sequence identity values, a cut-off (88%) was suggested to distinguish tick-borne phleboviruses. According to this provisional criterion, two viruses found here could be termed novel, while ten viruses have been described in previous studies. Detected phleboviruses demonstrated almost perfect specificity to a tick species or, at least, a genus. The same pattern was observed for tick-borne phleboviruses found in different studies around the world. Viruses that grouped together on a phylogenetic tree and differed less than this sequence identity threshold suggested above were hosted by ticks from the same genus.
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Affiliation(s)
- Alexander S Klimentov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Gamaleya Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow 123098, Russia.
| | - Oxana A Belova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Ivan S Kholodilov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Alexander M Butenko
- Gamaleya Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow 123098, Russia
| | - Liubov A Bespyatova
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk 185910, Russia
| | - Sergey V Bugmyrin
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk 185910, Russia
| | - Nikita Chernetsov
- Zoological Institute of RAS, St. Petersburg 199034, Russia; Dept. Vertebrate Zoology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Anna Y Ivannikova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Irina V Kovalchuk
- Office of Rospotrebnadzor in the Stavropol Territory, Stavropol 355008, Russia; Stavropol State Medical University, Stavropol 355017, Russia
| | - Alexander A Nafeev
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, Ulyanovsk 432005, Russia
| | | | - Olga M Pilikova
- Black Sea Anti-Plague Station of Rospotrebnadzor, Novorossiysk 353919, Russia
| | - Alexandra E Polienko
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Kristina A Purmak
- Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Evgeniya N Romanenko
- Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Lidiya Iu Romanova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Institute for Translational Medicine and Biotechnology, Sechenov University, Moscow 119991, Russia
| | | | - Nataliya I Solomashchenko
- Stavropol State Medical University, Stavropol 355017, Russia; Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Anton F Shamsutdinov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, Kazan 420015, Russia
| | - Elena V Vakalova
- Astrakhan Anti-Plague Station of Rospotrebnadzor, Astrakhan 414000, Russia
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow 119435, Russia
| | - Galina G Karganova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Institute for Translational Medicine and Biotechnology, Sechenov University, Moscow 119991, Russia
| | - Anatoly P Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
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7
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The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses 2019; 11:v11111032. [PMID: 31698764 PMCID: PMC6893659 DOI: 10.3390/v11111032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/05/2022] Open
Abstract
Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.
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8
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Warner BE, Ballinger MJ, Yerramsetty P, Reed J, Taylor DJ, Smith TJ, Bruenn JA. Cellular production of a counterfeit viral protein confers immunity to infection by a related virus. PeerJ 2018; 6:e5679. [PMID: 30280045 PMCID: PMC6166632 DOI: 10.7717/peerj.5679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022] Open
Abstract
DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this appears to occur through the piRNA system, but in others by way of counterfeit viral proteins encoded by NIRVs. In the fungi, NIRVs may be as long as 1,400 uninterrupted codons. In one such case in the yeast Debaryomyces hansenii, one of these genes provides immunity to a related virus by virtue of expression of a counterfeit viral capsid protein, which interferes with assembly of viral capsids by negative complementation. The widespread occurrence of non-retroviral RNA virus genes in eukaryotes may reflect an underappreciated method of host resistance to infection. This work demonstrates for the first time that an endogenous host protein encoded by a gene that has been naturally acquired from a virus and fixed in a eukaryote can interfere with the replication of a related virus and do so by negative complementation.
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Affiliation(s)
- Benjamin E Warner
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Matthew J Ballinger
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Pradeep Yerramsetty
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Jennifer Reed
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch Galveston, Galveston, TX, United States of America
| | - Jeremy A Bruenn
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
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Sadeghi M, Altan E, Deng X, Barker CM, Fang Y, Coffey LL, Delwart E. Virome of > 12 thousand Culex mosquitoes from throughout California. Virology 2018; 523:74-88. [DOI: 10.1016/j.virol.2018.07.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/25/2022]
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Abstract
Our understanding of the viral world changed just after the first structures of icosahedral viral particles were unveiled. The structural similarities between capsid proteins of distant viral groups were not anticipated, and the findings suggested the existence of common ancestors for viruses with different host range, genomic structure and multiplication strategies. This way, diverse viruses with icosahedral particles can now be grouped based on the structural homology between their capsid proteins. In the last years, the presence of conserved folds between viral proteins in non-icosahedral viruses has also emerged. Viral particles with radically different morphologies, ranging from naked and filamentous to enveloped and pleomorphic, have shown structural homology between the nucleoproteins that bind directly to their genomes. This chapter overviews recent findings regarding the similar structure found between nucleoproteins of eukaryotic ssRNA viruses. The structural homology includes the coat proteins from all known families of flexible filamentous plant viruses, a group with monopartite (+)ssRNA genomes. Their coat proteins share a core domain with nucleoproteins of previously unrelated families of enveloped viruses that have segmented (-)ssRNA genomes. This last group consists of mostly animals viruses, including influenza virus.
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Affiliation(s)
- Mikel Valle
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, Derio, Spain.
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11
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de Lara Pinto AZ, Santos de Carvalho M, de Melo FL, Ribeiro ALM, Morais Ribeiro B, Dezengrini Slhessarenko R. Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil. PLoS One 2017; 12:e0187429. [PMID: 29117239 PMCID: PMC5678729 DOI: 10.1371/journal.pone.0187429] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/19/2017] [Indexed: 12/22/2022] Open
Abstract
Viruses may represent the most diverse microorganisms on Earth. Novel viruses and variants continue to emerge. Mosquitoes are the most dangerous animals to humankind. This study aimed at identifying viral RNA diversity in salivary glands of mosquitoes captured in a sylvatic area of Cerrado at the Chapada dos Guimarães National Park, Mato Grosso, Brazil. In total, 66 Culicinae mosquitoes belonging to 16 species comprised 9 pools, subjected to viral RNA extraction, double-strand cDNA synthesis, random amplification and high-throughput sequencing, revealing the presence of seven insect-specific viruses, six of which represent new species of Rhabdoviridae (Lobeira virus), Chuviridae (Cumbaru and Croada viruses), Totiviridae (Murici virus) and Partitiviridae (Araticum and Angico viruses). In addition, two mosquito pools presented Kaiowa virus sequences that had already been reported in South Pantanal, Brazil. These findings amplify the understanding of viral diversity in wild-type Culicinae. Insect-specific viruses may present a broader diversity than previously imagined and future studies may address their possible role in mosquito vector competence.
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Affiliation(s)
- Andressa Zelenski de Lara Pinto
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Michellen Santos de Carvalho
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Fernando Lucas de Melo
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Ana Lúcia Maria Ribeiro
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Bergmann Morais Ribeiro
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
- * E-mail:
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12
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Nunes MRT, Contreras-Gutierrez MA, Guzman H, Martins LC, Barbirato MF, Savit C, Balta V, Uribe S, Vivero R, Suaza JD, Oliveira H, Nunes Neto JP, Carvalho VL, da Silva SP, Cardoso JF, de Oliveira RS, da Silva Lemos P, Wood TG, Widen SG, Vasconcelos PFC, Fish D, Vasilakis N, Tesh RB. Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus. Virology 2017; 504:152-167. [PMID: 28193550 DOI: 10.1016/j.virol.2017.01.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 11/18/2022]
Abstract
The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses.
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Affiliation(s)
- Marcio R T Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - María Angélica Contreras-Gutierrez
- Programa de Estudio y Control de Enfermedades Tropicales - PECET - SIU-Sede de Investigación Universitaria - Universidad de Antioquia, Medellín, Colombia; Grupo de Investigación en Sistemática Molecular-GSM, Facultad de Ciencias,Ciencias, Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
| | - Hilda Guzman
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States; Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Livia C Martins
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | | | - Chelsea Savit
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States
| | - Victoria Balta
- School of Public Health, University of Washington, Seattle, WA 98195, United States
| | - Sandra Uribe
- Grupo de Investigación en Sistemática Molecular-GSM, Facultad de Ciencias,Ciencias, Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
| | - Rafael Vivero
- Programa de Estudio y Control de Enfermedades Tropicales - PECET - SIU-Sede de Investigación Universitaria - Universidad de Antioquia, Medellín, Colombia; Grupo de Investigación en Sistemática Molecular-GSM, Facultad de Ciencias,Ciencias, Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
| | - Juan David Suaza
- Programa de Estudio y Control de Enfermedades Tropicales - PECET - SIU-Sede de Investigación Universitaria - Universidad de Antioquia, Medellín, Colombia; Grupo de Investigación en Sistemática Molecular-GSM, Facultad de Ciencias,Ciencias, Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
| | - Hamilton Oliveira
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Joaquin P Nunes Neto
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | | | - Sandro Patroca da Silva
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Jedson F Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Rodrigo Santo de Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Poliana da Silva Lemos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0645, United States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0645, United States
| | - Pedro F C Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Durland Fish
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, United States
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States; Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil.
| | - Robert B Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States; Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil.
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13
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Ballinger MJ, Medeiros AS, Qin J, Taylor DJ. Unexpected differences in the population genetics of phasmavirids ( Bunyavirales) from subarctic ponds. Virus Evol 2017; 3:vex015. [PMID: 28744370 PMCID: PMC5518175 DOI: 10.1093/ve/vex015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Little is known of the evolution of RNA viruses in aquatic systems. Here, we assess the genetic connectivity of two bunyaviruses (Kigluaik phantom orthophasmavirus or KIGV and Nome phantom orthophasmavirus or NOMV) with zooplanktonic hosts from subarctic ponds. We expected weak genetic structure among populations as the hosts (phantom midges) have a terrestrial winged dispersal stage. To test whether their respective viruses mirror this structure, we collected and analyzed population datasets from 21 subarctic freshwater ponds and obtained sequences from all four genes in the viral genomes. Prevalence averaged 66 per cent for 514 host specimens and was not significantly different between recently formed thaw ponds and glacial ponds. Unexpectedly, KIGV from older ponds showed pronounced haplotype divergence with little evidence of genetic connectivity. However, KIGV populations from recent thaw ponds appeared to be represented by a closely related haplotype group, perhaps indicating a genotypic dispersal bias. Unlike KIGV, NOMV had modest structure and diversity in recently formed thaw ponds. For each virus, we found elevated genetic diversity relative to the host, but similar population structures to the host. Our results suggest that non-random processes such as virus-host interactions, genotypic bias, and habitat effects differ among polar aquatic RNA viruses.
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Affiliation(s)
- Matthew J. Ballinger
- The Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| | | | - Jie Qin
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Derek J. Taylor
- The Department of Biological Sciences, State University of New York, Buffalo, NY, USA
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14
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Occurrence, pathology, and ultrastructure of iridovirus and cytoplasmic polyhedrosis viruses in daphnids from the Czech Republic. J Invertebr Pathol 2016; 140:35-38. [PMID: 27449679 DOI: 10.1016/j.jip.2016.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 11/23/2022]
Abstract
Iridescent (IVs, family Iridoviridae, genus Iridovirus) and cytoplasmic polyhedrosis viruses (CPVs; family Reoviridae, genus Cypovirus) are well known in insects, with thirteen IV species recognized from various orders, and sixteen CPV species known from lepidopterans. In 1975, an IV and CPV were reported in the daphnid, Simocehpalus expinosus, in Florida, but other reported daphnid virus infections seem to be rare. Here we report infected daphnids from woodland and carp ponds in the Czech Republic, Daphnia curvirostris with an IV, and D. pulex and D. ambigua, with CPVs. This suggests these viruses are more common in daphnids, the rarity of reports due to few surveys.
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15
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Smith RH, Hallwirth CV, Westerman M, Hetherington NA, Tseng YS, Cecchini S, Virag T, Ziegler ML, Rogozin IB, Koonin EV, Agbandje-McKenna M, Kotin RM, Alexander IE. Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus. Sci Rep 2016; 6:28965. [PMID: 27377618 PMCID: PMC4932596 DOI: 10.1038/srep28965] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/07/2016] [Indexed: 12/21/2022] Open
Abstract
Germline endogenous viral elements (EVEs) genetically preserve viral nucleotide sequences useful to the study of viral evolution, gene mutation, and the phylogenetic relationships among host organisms. Here, we describe a lineage-specific, adeno-associated virus (AAV)-derived endogenous viral element (mAAV-EVE1) found within the germline of numerous closely related marsupial species. Molecular screening of a marsupial DNA panel indicated that mAAV-EVE1 occurs specifically within the marsupial suborder Macropodiformes (present-day kangaroos, wallabies, and related macropodoids), to the exclusion of other Diprotodontian lineages. Orthologous mAAV-EVE1 locus sequences from sixteen macropodoid species, representing a speciation history spanning an estimated 30 million years, facilitated compilation of an inferred ancestral sequence that recapitulates the genome of an ancient marsupial AAV that circulated among Australian metatherian fauna sometime during the late Eocene to early Oligocene. In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. Characterisation of AAV-EVE loci among disparate species affords insight into AAV evolution and, in the case of macropodoid species, may offer an additional genetic basis for assignment of phylogenetic relationships among the Macropodoidea. From an applied perspective, the identified AAV “fossils” provide novel capsid sequences for use in translational research and clinical applications.
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Affiliation(s)
- Richard H Smith
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michael Westerman
- Department of Biochemistry and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Nicola A Hetherington
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Yu-Shan Tseng
- The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Sylvain Cecchini
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Tamas Virag
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Mona-Larissa Ziegler
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Igor B Rogozin
- Evolutionary Genomics Research Group, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eugene V Koonin
- Evolutionary Genomics Research Group, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mavis Agbandje-McKenna
- The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Robert M Kotin
- Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, New South Wales, Australia
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16
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Gilbert C, Meik JM, Dashevsky D, Card DC, Castoe TA, Schaack S. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes. Proc Biol Sci 2015; 281:20141122. [PMID: 25080342 DOI: 10.1098/rspb.2014.1122] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake, Crotalus mitchellii, the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. Cross-species PCR screening of orthologous loci and computational scanning of the python and king cobra genomes reveals that circoviruses integrated most recently (within the last approx. 10 Myr), whereas bornaviruses and hepadnaviruses integrated at least approximately 13 and approximately 50 Ma, respectively. This is, to our knowledge, the first report of circo-, borna- and hepadnaviruses in snakes and the first characterization of non-retroviral EVEs in non-avian reptiles. Our study provides a window into the historical dynamics of viruses in these host lineages and shows that their evolution involved multiple host-switches between mammals and reptiles.
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Affiliation(s)
- C Gilbert
- Université de Poitiers, UMR CNRS 7267, Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - J M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - D Dashevsky
- Department of Biology, Reed College, Portland, OR, USA
| | - D C Card
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
| | - T A Castoe
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
| | - S Schaack
- Department of Biology, Reed College, Portland, OR, USA Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
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17
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Metegnier G, Becking T, Chebbi MA, Giraud I, Moumen B, Schaack S, Cordaux R, Gilbert C. Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups. Mob DNA 2015; 6:16. [PMID: 26388953 PMCID: PMC4573495 DOI: 10.1186/s13100-015-0047-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Background The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca). Results In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (−ssRNA), Circoviridae (ssDNA), Mononegavirales (−ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses. Conclusions In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Metegnier
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Thomas Becking
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Mohamed Amine Chebbi
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Isabelle Giraud
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR USA
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
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18
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Bolling BG, Weaver SC, Tesh RB, Vasilakis N. Insect-Specific Virus Discovery: Significance for the Arbovirus Community. Viruses 2015; 7:4911-28. [PMID: 26378568 PMCID: PMC4584295 DOI: 10.3390/v7092851] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/31/2015] [Accepted: 07/31/2015] [Indexed: 01/23/2023] Open
Abstract
Arthropod-borne viruses (arboviruses), especially those transmitted by mosquitoes, are a significant cause of morbidity and mortality in humans and animals worldwide. Recent discoveries indicate that mosquitoes are naturally infected with a wide range of other viruses, many within taxa occupied by arboviruses that are considered insect-specific. Over the past ten years there has been a dramatic increase in the literature describing novel insect-specific virus detection in mosquitoes, which has provided new insights about viral diversity and evolution, including that of arboviruses. It has also raised questions about what effects the mosquito virome has on arbovirus transmission. Additionally, the discovery of these new viruses has generated interest in their potential use as biological control agents as well as novel vaccine platforms. The arbovirus community will benefit from the growing database of knowledge concerning these newly described viral endosymbionts, as their impacts will likely be far reaching.
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Affiliation(s)
- Bethany G Bolling
- Institute for Human Infections and Immunity, Center for Tropical Diseases, and Department of Pathology,University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Scott C Weaver
- Institute for Human Infections and Immunity, Center for Tropical Diseases, and Department of Pathology,University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Institute for Human Infections and Immunity, Center for Tropical Diseases, and Department of Pathology,University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, Center for Tropical Diseases, and Department of Pathology,University of Texas Medical Branch, Galveston, TX 77555, USA.
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19
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Bruenn JA, Warner BE, Yerramsetty P. Widespread mitovirus sequences in plant genomes. PeerJ 2015; 3:e876. [PMID: 25870770 PMCID: PMC4393810 DOI: 10.7717/peerj.876] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/13/2015] [Indexed: 11/25/2022] Open
Abstract
The exploration of the evolution of RNA viruses has been aided recently by the discovery of copies of fragments or complete genomes of non-retroviral RNA viruses (Non-retroviral Endogenous RNA Viral Elements, or NERVEs) in many eukaryotic nuclear genomes. Among the most prominent NERVEs are partial copies of the RNA dependent RNA polymerase (RdRP) of the mitoviruses in plant mitochondrial genomes. Mitoviruses are in the family Narnaviridae, which are the simplest viruses, encoding only a single protein (the RdRP) in their unencapsidated viral plus strand. Narnaviruses are known only in fungi, and the origin of plant mitochondrial mitovirus NERVEs appears to be horizontal transfer from plant pathogenic fungi. At least one mitochondrial mitovirus NERVE, but not its nuclear copy, is expressed.
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Affiliation(s)
- Jeremy A Bruenn
- Department of Biological Sciences, State University of New York at Buffalo , Buffalo, NY , USA
| | - Benjamin E Warner
- Department of Biological Sciences, State University of New York at Buffalo , Buffalo, NY , USA
| | - Pradeep Yerramsetty
- Department of Biological Sciences, State University of New York at Buffalo , Buffalo, NY , USA
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20
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Thézé J, Leclercq S, Moumen B, Cordaux R, Gilbert C. Remarkable diversity of endogenous viruses in a crustacean genome. Genome Biol Evol 2015; 6:2129-40. [PMID: 25084787 PMCID: PMC4231630 DOI: 10.1093/gbe/evu163] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent studies in paleovirology have uncovered myriads of endogenous viral elements (EVEs) integrated in the genome of their eukaryotic hosts. These fragments result from endogenization, that is, integration of the viral genome into the host germline genome followed by vertical inheritance. So far, most studies have used a virus-centered approach, whereby endogenous copies of a particular group of viruses were searched in all available sequenced genomes. Here, we follow a host-centered approach whereby the genome of a given species is comprehensively screened for the presence of EVEs using all available complete viral genomes as queries. Our analyses revealed that 54 EVEs corresponding to 10 different viral lineages belonging to 5 viral families (Bunyaviridae, Circoviridae, Parvoviridae, and Totiviridae) and one viral order (Mononegavirales) became endogenized in the genome of the isopod crustacean Armadillidium vulgare. We show that viral endogenization occurred recurrently during the evolution of isopods and that A. vulgare viral lineages were involved in multiple host switches that took place between widely divergent taxa. Furthermore, 30 A. vulgare EVEs have uninterrupted open reading frames, suggesting they result from recent endogenization of viruses likely to be currently infecting isopod populations. Overall, our work shows that isopods have been and are still infected by a large variety of viruses. It also extends the host range of several families of viruses and brings new insights into their evolution. More generally, our results underline the power of paleovirology in characterizing the viral diversity currently infecting eukaryotic taxa.
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Affiliation(s)
- Julien Thézé
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Sébastien Leclercq
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
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21
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Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
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22
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Calisher CH, Tesh RB. Two misleading words in reports of virus discovery: little things mean a lot. Arch Virol 2014; 159:2189-91. [PMID: 24532301 DOI: 10.1007/s00705-014-2008-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/26/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Charles H Calisher
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523-1690, USA,
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