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Christensen T, Dyer LA, Forister ML, Bowers MD, Carper A, Teglas MB, Hurtado P, Smilanich AM. Host plant-mediation of viral transmission and its consequences for a native butterfly. Ecology 2024; 105:e4282. [PMID: 38483138 DOI: 10.1002/ecy.4282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/11/2023] [Accepted: 01/18/2024] [Indexed: 04/04/2024]
Abstract
Pathogens play a key role in insect population dynamics, contributing to short-term fluctuations in abundance as well as long-term demographic trends. Two key factors that influence the effects of entomopathogens on herbivorous insect populations are modes of pathogen transmission and larval host plants. In this study, we examined tritrophic interactions between a sequestering specialist lepidopteran, Euphydryas phaeton, and a viral pathogen, Junonia coenia densovirus, on its native host plant, Chelone glabra, and a novel host plant, Plantago lanceolata, to explore whether host plant mediates viral transmission, survival, and viral loads. A two-factor factorial experiment was conducted in the laboratory with natal larval clusters randomly assigned to either the native or novel host plant and crossed with either uninoculated controls or viral inoculation (20% of individuals in the cluster inoculated). Diapausing clusters were overwintered in the laboratory and checked weekly for mortality. At the end of diapause, all surviving individuals were reared to adulthood to estimate survivorship. All individuals were screened to quantify viral loads, and estimate horizontal transmission postmortem. To test for vertical transmission, adults were mated, and the progeny were screened for viral presence. Within virus-treated groups, we found evidence for both horizontal and vertical transmission. Larval clusters reared on the native host plant had slightly higher horizontal transmission. Survival probability was lower in clusters feeding on the native host plant, with inoculated groups reared on the native host plant experiencing complete mortality. Viral loads did not differ by the host plant, although viral loads decreased with increased sequestration of secondary compounds on both host plants. Our results indicate that the use of a novel host plant may confer fitness benefits in terms of survival and reduced viral transmission when larvae feeding on it are infected with this pathogen, supporting hypotheses of potential evolutionary advantages of a host range expansion in the context of tritrophic interactions.
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Affiliation(s)
- Tara Christensen
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
- Department of Biology, University of Nevada, Reno, Nevada, USA
| | - Lee A Dyer
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
- Department of Biology, University of Nevada, Reno, Nevada, USA
| | - Matthew L Forister
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
- Department of Biology, University of Nevada, Reno, Nevada, USA
| | - M Deane Bowers
- Department of Ecology and Evolutionary Biology and Museum of Natural History, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Adrian Carper
- Department of Ecology and Evolutionary Biology and Museum of Natural History, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Mike B Teglas
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, Nevada, USA
| | - Paul Hurtado
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
- Department of Mathematics and Statistics, University of Nevada, Reno, Nevada, USA
| | - Angela M Smilanich
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
- Department of Biology, University of Nevada, Reno, Nevada, USA
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2
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Rozo-Lopez P, Brewer W, Käfer S, Martin MM, Parker BJ. Untangling an insect's virome from its endogenous viral elements. BMC Genomics 2023; 24:636. [PMID: 37875824 PMCID: PMC10594914 DOI: 10.1186/s12864-023-09737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. METHODS In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. RESULTS We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the 'virome' of this insect can be attributed to EVEs in the host genome. CONCLUSION Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
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Affiliation(s)
- Paula Rozo-Lopez
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
| | - William Brewer
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Simon Käfer
- Institut Für Biologie Und Umweltwissenschaften, Carl Von Ossietzky Universität Oldenburg, 26129, Oldenburg, Germany
| | - McKayla M Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Benjamin J Parker
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
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Zhao S, Hu H, Lan J, Yang Z, Peng Q, Yan L, Luo L, Wu L, Lang Y, Yan Q. Characterization of a fatal feline panleukopenia virus derived from giant panda with broad cell tropism and zoonotic potential. Front Immunol 2023; 14:1237630. [PMID: 37662912 PMCID: PMC10469695 DOI: 10.3389/fimmu.2023.1237630] [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: 06/09/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Represented by feline panleukopenia virus (FPV) and canine parvovirus (CPV), the species carnivore protoparvovirus 1 has a worldwide distribution through continuous ci13rculation in companion animals such as cats and dogs. Subsequently, both FPV and CPV had engaged in host-to-host transfer to other wild animal hosts of the order Carnivora. In the present study, we emphasized the significance of cross-species transmission of parvoviruses with the isolation and characterization of an FPV from giant panda displaying severe and fatal symptoms. The isolated virus, designated pFPV-sc, displayed similar morphology as FPV, while phylogenetic analysis indicated that the nucleotide sequence of pFPV-sc clades with Chinese FPV isolates. Despite pFPV-sc is seemingly an outcome of a spillover infection event from domestic cats to giant pandas, our study also provided serological evidence that FPV or other parvoviruses closely related to FPV could be already prevalent in giant pandas in 2011. Initiation of host transfer of pFPV-sc is likely with association to giant panda transferrin receptor (TfR), as TfR of giant panda shares high homology with feline TfR. Strikingly, our data also indicate that pFPV-sc can infect cell lines of other mammal species, including humans. To sum up, observations from this study shall promote future research of cross-host transmission and antiviral intervention of Carnivore protoparvovirus 1, and necessitate surveillance studies in thus far unacknowledged potential reservoirs.
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Affiliation(s)
- Shan Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huanyuan Hu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | | | - Qianling Peng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Liheng Yan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Lin Wu
- Sichuan Academy of Giant Panda, Chengdu, China
| | - Yifei Lang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qigui Yan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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4
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Desingu PA, Rubeni TP, Sundaresan NR. Deciphering the Origin of DNA Viruses (Replication-Associated Parvo-NS1) That Infect Vertebrates from Invertebrate-Infecting Viruses. Microbiol Spectr 2023; 11:e0457022. [PMID: 37347193 PMCID: PMC10433990 DOI: 10.1128/spectrum.04570-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/21/2023] [Indexed: 06/23/2023] Open
Abstract
DNA replication is a standard and essential function among DNA viruses; however, this functional domain's common ancestor, origin, and evolutionary path in invertebrate- and vertebrate-infecting viruses are not yet fully understood. Here, we present evidence, using a combination of phylogenetic relationships, coevolution, and CLANS (cluster analysis of sequences) analysis, that the parvo-NS1 domain (nonstructural protein NS1, DNA helicase domain) of these DNA viruses that infect vertebrates potentially originated from the invertebrate (Platyhelminthes) parvo-NS1 domain of parvovirus-related sequences (PRSs). Our results suggest that papillomaviruses and the parvovirus subfamilies Densovirinae and Hamaparvovirinae DNA helicase evolved directly from the Platyhelminthes NS1 domain (PRSs). Similarly, the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the PRSs through Hamaparvovirinae. Further, our analysis also clarified that herpesviruses and adenoviruses independently obtained the parvo-NS1 domain from Dependoparvovirus (Parvovirinae). Furthermore, virus-host coevolution analysis revealed that the parvovirus NS1 domain has coevolved with hosts, from flatworms to humans, and it appears that the papillomavirus may have obtained the DNA helicase during the early stages of parvovirus evolution and later led to the development of the DNA helicase of adomavirus and polyomavirus. Finally, herpesviruses and adenoviruses likely inherited the parvo-NS1 domain from Dependoparvovirus in the later stages of evolution. To the best of our knowledge, this is the first evolutionary evidence to suggest that the DNA helicase of viruses that infect vertebrates originated from the invertebrate PRSs. IMPORTANCE DNA replication of DNA viruses is an essential function. This allows DNA replication of viruses to form virus particles. The DNA helicase domain is responsible for this primary function. This domain is present in parvoviruses, papillomaviruses, polyomaviruses, herpesviruses, and adenoviruses. But little is known about the common ancestor, origin, and evolutionary path of DNA helicase in invertebrate- and vertebrate-infecting viruses. Here, we report the possibility of the origin of DNA viruses (DNA helicase) infecting vertebrates from Platyhelminthes (invertebrate) PRSs. Our study established that the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the Platyhelminthes PRSs through Hamaparvovirinae. Furthermore, our study suggests that the papillomavirus DNA helicase may have evolved in the early stages of parvovirus evolution and then led to the development of the adomavirus and polyomavirus. Our study suggests that the herpesviruses and adenoviruses likely inherited the parvo-NS1 domain through gene capture from Dependoparvovirus in the later stages of parvovirus evolution in their hosts.
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Affiliation(s)
| | - T. P. Rubeni
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
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5
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López-Astacio RA, Adu OF, Lee H, Hafenstein SL, Parrish CR. The Structures and Functions of Parvovirus Capsids and Missing Pieces: the Viral DNA and Its Packaging, Asymmetrical Features, Nonprotein Components, and Receptor or Antibody Binding and Interactions. J Virol 2023; 97:e0016123. [PMID: 37367301 PMCID: PMC10373561 DOI: 10.1128/jvi.00161-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Parvoviruses are among the smallest and superficially simplest animal viruses, infecting a broad range of hosts, including humans, and causing some deadly infections. In 1990, the first atomic structure of the canine parvovirus (CPV) capsid revealed a 26-nm-diameter T=1 particle made up of two or three versions of a single protein, and packaging about 5,100 nucleotides of single-stranded DNA. Our structural and functional understanding of parvovirus capsids and their ligands has increased as imaging and molecular techniques have advanced, and capsid structures for most groups within the Parvoviridae family have now been determined. Despite those advances, significant questions remain unanswered about the functioning of those viral capsids and their roles in release, transmission, or cellular infection. In addition, the interactions of capsids with host receptors, antibodies, or other biological components are also still incompletely understood. The parvovirus capsid's apparent simplicity likely conceals important functions carried out by small, transient, or asymmetric structures. Here, we highlight some remaining open questions that may need to be answered to provide a more thorough understanding of how these viruses carry out their various functions. The many different members of the family Parvoviridae share a capsid architecture, and while many functions are likely similar, others may differ in detail. Many of those parvoviruses have not been experimentally examined in detail (or at all in some cases), so we, therefore, focus this minireview on the widely studied protoparvoviruses, as well as the most thoroughly investigated examples of adeno-associated viruses.
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Affiliation(s)
- Robert A. López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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6
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Campbell MA, Loncar S, Kotin RM, Gifford RJ. Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates. PLoS Biol 2022; 20:e3001867. [PMID: 36445931 PMCID: PMC9707805 DOI: 10.1371/journal.pbio.3001867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Parvoviruses (family Parvoviridae) are small DNA viruses that cause numerous diseases of medical, veterinary, and agricultural significance and have important applications in gene and anticancer therapy. DNA sequences derived from ancient parvoviruses are common in animal genomes and analysis of these endogenous parvoviral elements (EPVs) has demonstrated that the family, which includes twelve vertebrate-specific genera, arose in the distant evolutionary past. So far, however, such "paleovirological" analysis has only provided glimpses into the biology of ancient parvoviruses and their long-term evolutionary interactions with hosts. Here, we comprehensively map EPV diversity in 752 published vertebrate genomes, revealing defining aspects of ecology and evolution within individual parvovirus genera. We identify 364 distinct EPV sequences and show these represent approximately 200 unique germline incorporation events, involving at least five distinct parvovirus genera, which took place at points throughout the Cenozoic Era. We use the spatiotemporal and host range calibrations provided by these sequences to infer defining aspects of long-term evolution within individual parvovirus genera, including mammalian vicariance for genus Protoparvovirus, and interclass transmission for genus Dependoparvovirus. Moreover, our findings support a model of virus evolution in which the long-term cocirculation of multiple parvovirus genera in vertebrates reflects the adaptation of each viral genus to fill a distinct ecological niche. Our findings show that efforts to develop parvoviruses as therapeutic tools can be approached from a rational foundation based on comparative evolutionary analysis. To support this, we published our data in the form of an open, extensible, and cross-platform database designed to facilitate the wider utilisation of evolution-related domain knowledge in parvovirus research.
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Affiliation(s)
- Matthew A. Campbell
- University of Alaska Museum of the North, Fishes and Marine Invertebrates, Fairbanks, Alaska, United States of America
- * E-mail:
| | - Shannon Loncar
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, Worcester, Massachusetts, United States of America
| | - Robert M. Kotin
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, Worcester, Massachusetts, United States of America
- Carbon Biosciences, Lexington, Massachusetts, United States of America
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, United Kingdom
- * E-mail:
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Wagemans J, Holtappels D, Vainio E, Rabiey M, Marzachì C, Herrero S, Ravanbakhsh M, Tebbe CC, Ogliastro M, Ayllón MA, Turina M. Going Viral: Virus-Based Biological Control Agents for Plant Protection. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:21-42. [PMID: 35300520 DOI: 10.1146/annurev-phyto-021621-114208] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The most economically important biotic stresses in crop production are caused by fungi, oomycetes, insects, viruses, and bacteria. Often chemical control is still the most commonly used method to manage them. However, the development of resistance in the different pathogens/pests, the putative damage on the natural ecosystem, the toxic residues in the field, and, thus, the contamination of the environment have stimulated the search for saferalternatives such as the use of biological control agents (BCAs). Among BCAs, viruses, a major driver for controlling host populations and evolution, are somewhat underused, mostly because of regulatory hurdles that make the cost of registration of such host-specific BCAs not affordable in comparison with the limited potential market. Here, we provide a comprehensive overview of the state of the art of virus-based BCAs against fungi, bacteria, viruses, and insects, with a specific focus on new approaches that rely on not only the direct biocidal virus component but also the complex ecological interactions between viruses and their hosts that do not necessarily result in direct damage to the host.
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Affiliation(s)
| | | | - Eeva Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Mojgan Rabiey
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Cristina Marzachì
- Istituto per la Protezione Sostenibile delle Piante, CNR, Torino, Italy;
| | - Salvador Herrero
- Department of Genetics and University Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, Burjassot, Spain
| | | | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Torino, Italy;
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8
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Cerqueira de Araujo A, Huguet E, Herniou EA, Drezen JM, Josse T. Transposable element repression using piRNAs, and its relevance to endogenous viral elements (EVEs) and immunity in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100876. [PMID: 35065285 DOI: 10.1016/j.cois.2022.100876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
The piRNA system controls transposable element (TE) mobility by transcriptional gene silencing and post-transcriptional gene silencing. Dispersed in insect genomes, piRNA clusters contain TE copies, from which they produce piRNAs (specific small RNAs). These piRNAs can both target the nascent transcripts produced by active TE copies and directly repress them by heterochromatinization. They can also target mature transcripts and cleave them following amplification by the so-called 'ping-pong' loop mechanism. Moreover, piRNA clusters contain endogenous viral elements (EVEs), from which they produce piRNAs. The current idea is that these piRNAs could participate in the antiviral response against exogenous viral infection. In this review, we show that among insects, to date, this antiviral response by the piRNA system appears mainly restricted to mosquitoes, but this could be due to the focus of most studies on arboviruses.
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Affiliation(s)
- Alexandra Cerqueira de Araujo
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France.
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Zhao K, Hao X, Lei B, Dong S, Wang J, Zhang W, Wang J, Yuan W. Emergence and genomic analysis of a novel ostrich-origin GPV-related parvovirus in China. Poult Sci 2022; 101:101929. [PMID: 35691050 PMCID: PMC9194870 DOI: 10.1016/j.psj.2022.101929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
In recent years, ostrich disease characterized by paralysis and diarrhea has been circulating in some regions of China, causing huge economic losses to the ostrich breeding industry. In our study, clinical samples from diseased ostriches were collected, and only parvovirus was detected. The virus distribution analysis by histopathology and quantitative real-time PCR assays indicated that the virus had a wide range of tissue tropisms. The full-length genome of the ostrich parvovirus (OsPV) was sequenced and comprehensively analyzed. Interestingly, the phylogenetic and alignment results indicated that the OsPV and the goose parvovirus (GPV) form a separate branch. In contrast to GPV strains, OsPV showed 2 new 14 nucleotide deletions in the inverted terminal repeat (ITR) region. Furthermore, recombination analysis indicated that OsPV was a recombination strain between the vaccine strain SYG61v and the virulent strain B strain, with the major parent of OsPV as the SYG61v strain and the minor parent as the B strain. The 14 nucleotide deletions in the ITR region as well as recombination may be some of the reasons for the cross-species transmission of parvovirus from goose to ostrich. The above data will contribute to a better understanding of the molecular biology of the novel OsPV and help to develop the vaccine candidate strain.
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10
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Gilbert C, Belliardo C. The diversity of endogenous viral elements in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 49:48-55. [PMID: 34839030 DOI: 10.1016/j.cois.2021.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
We provide an overview of the currently known diversity of viral sequences integrated into insect genomes. Such endogenous viral elements (EVE) have so far been annotated in at least eight insect orders and can be assigned to at least three families of large double-stranded (ds) DNA viruses, at least 22 families of RNA viruses, and three families of single-stranded DNA viruses. The study of these EVE has already produced important insights into insect-virus interactions, including the discovery of a new form of adaptive antiviral immunity. Insect EVE diversity will continue to increase as new insect genomes and exogenous viruses are sequenced, which will continue to make paleovirology a vibrant research field in this group of animals in the years to come.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, 91198, France.
| | - Carole Belliardo
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, 06903, France; MYCOPHYTO, 540 Avenue de la Plaine, Mougins, 06250, France
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The VP1u of Human Parvovirus B19: A Multifunctional Capsid Protein with Biotechnological Applications. Viruses 2020; 12:v12121463. [PMID: 33352888 PMCID: PMC7765992 DOI: 10.3390/v12121463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The viral protein 1 unique region (VP1u) of human parvovirus B19 (B19V) is a multifunctional capsid protein with essential roles in virus tropism, uptake, and subcellular trafficking. These functions reside on hidden protein domains, which become accessible upon interaction with cell membrane receptors. A receptor-binding domain (RBD) in VP1u is responsible for the specific targeting and uptake of the virus exclusively into cells of the erythroid lineage in the bone marrow. A phospholipase A2 domain promotes the endosomal escape of the incoming virus. The VP1u is also the immunodominant region of the capsid as it is the target of neutralizing antibodies. For all these reasons, the VP1u has raised great interest in antiviral research and vaccinology. Besides the essential functions in B19V infection, the remarkable erythroid specificity of the VP1u makes it a unique erythroid cell surface biomarker. Moreover, the demonstrated capacity of the VP1u to deliver diverse cargo specifically to cells around the proerythroblast differentiation stage, including erythroleukemic cells, offers novel therapeutic opportunities for erythroid-specific drug delivery. In this review, we focus on the multifunctional role of the VP1u in B19V infection and explore its potential in diagnostics and erythroid-specific therapeutics.
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12
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Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin. J Virol 2020; 95:JVI.01594-20. [PMID: 32967964 PMCID: PMC7737747 DOI: 10.1128/jvi.01594-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
The primary interest in sea star densoviruses, specifically SSaDV, has been their association with sea star wasting syndrome (SSWS), a disease that has decimated sea star populations across the West Coast of the United States since 2013. The association of SSaDV with SSWS was originally drawn from metagenomic analysis, which was further studied through field surveys using quantitative PCR (qPCR), with the conclusion that it was the most likely viral candidate in the metagenomic data based on its representation in symptomatic sea stars compared to asymptomatic sea stars. We reexamined the original metagenomic data with additional genomic data sets and found that SSaDV was 1 of 10 densoviruses present in the original data set and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations. A viral etiology of sea star wasting syndrome (SSWS) was originally explored with virus-sized material challenge experiments, field surveys, and metagenomics, leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are, however, highly diverse and pervasive among eukaryotic organisms, which we hypothesize may confound the association between densoviruses and SSWS. To test this hypothesis and assess the association of densoviruses with SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study on sea star-associated densovirus (SSaDV), the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained only endogenized densovirus elements similar to the NS1 gene, while numerous extant densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show that SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the West Coast of the United States and globally that are commonly associated with grossly normal (i.e., healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in sea stars confound the original hypothesis that one densovirus is the etiological agent of SSWS. IMPORTANCE The primary interest in sea star densoviruses, specifically SSaDV, has been their association with sea star wasting syndrome (SSWS), a disease that has decimated sea star populations across the West Coast of the United States since 2013. The association of SSaDV with SSWS was originally drawn from metagenomic analysis, which was further studied through field surveys using quantitative PCR (qPCR), with the conclusion that it was the most likely viral candidate in the metagenomic data based on its representation in symptomatic sea stars compared to asymptomatic sea stars. We reexamined the original metagenomic data with additional genomic data sets and found that SSaDV was 1 of 10 densoviruses present in the original data set and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.
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Bačnik K, Kutnjak D, Jerič Kokelj B, Tuta N, Lončar T, Vogelsang M, Ravnikar M. Metagenomic characterization of parental and production CHO cell lines for detection of adventitious viruses. Biologicals 2020; 69:70-75. [PMID: 33246870 DOI: 10.1016/j.biologicals.2020.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022] Open
Abstract
Viral contamination is a major concern for biological products. Therefore, virus testing of raw materials and cells is essential for the safety of the final product. We used high-throughput sequencing to detect viral-like sequences in selected CHO cell lines. Our aim was to test various approaches of sample preparation, to establish a pipeline for metagenomic analysis and to characterize standard viral metagenome of production and parental CHO cell lines. The comparison of the metagenomics composition of the differently prepared samples showed that among four tested approaches sequencing of ribosomal RNA depleted total RNA is the most promising approach. The metagenomics investigation of one production and three parental CHO cell lines of diverse origin did not indicate the presence of adventitious viral agents in the investigated samples. The study revealed an expected background of virus-like nucleic acids in the samples, which originate from remains of expression vectors, endogenized viral elements and residuals of bacteriophages.
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Affiliation(s)
- Katarina Bačnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Barbara Jerič Kokelj
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Nika Tuta
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Mengeš, Slovenia
| | - Tan Lončar
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Mengeš, Slovenia
| | - Matjaž Vogelsang
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Mengeš, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia; University of Nova Gorica, Vipavska Cesta, 5000, Nova Gorica, Slovenia
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Endogenous Viral Element-Derived Piwi-Interacting RNAs (piRNAs) Are Not Required for Production of Ping-Pong-Dependent piRNAs from Diaphorina citri Densovirus. mBio 2020; 11:mBio.02209-20. [PMID: 32994324 PMCID: PMC7527727 DOI: 10.1128/mbio.02209-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small RNAs primarily responsible for silencing transposons in the animal germ line. The ping-pong cycle, the posttranscriptional silencing branch of the piRNA pathway, relies on piRNAs produced from endogenous transposon remnants to direct cleavage of transposon RNA via association with Piwi-family Argonaute proteins. In some mosquito species and mosquito-derived cell lines expressing a functionally expanded group of Piwi-family Argonaute proteins, both RNA and DNA viruses are targeted by piRNAs in a manner thought to involve direct processing of exogenous viral RNA into piRNAs. Whether viruses are targeted by piRNAs in nonmosquito species is unknown. Partial integrations of DNA and nonretroviral RNA virus genomes, termed endogenous viral elements (EVEs), are abundant in arthropod genomes and often produce piRNAs that are speculated to target cognate viruses through the ping-pong cycle. Here, we describe a Diaphorina citri densovirus (DcDV)-derived EVE in the genome of Diaphorina citri We found that this EVE gives rise to DcDV-specific primary piRNAs and is unevenly distributed among D. citri populations. Unexpectedly, we found that DcDV is targeted by ping-pong-dependent virus-derived piRNAs (vpiRNAs) in D. citri lacking the DcDV-derived EVE, while four naturally infecting RNA viruses of D. citri are not targeted by vpiRNAs. Furthermore, a recombinant Cricket paralysis virus containing a portion of the DcDV genome corresponding to the DcDV-derived EVE was not targeted by vpiRNAs during infection in D. citri harboring the EVE. These results demonstrate that viruses can be targeted by piRNAs in a nonmosquito species independently of endogenous piRNAs.IMPORTANCE Small RNAs serve as specificity determinants of antiviral responses in insects. Piwi-interacting RNAs (piRNAs) are a class of small RNAs found in animals, and their primary role is to direct antitransposon responses. These responses require endogenous piRNAs complementary to transposon RNA. Additionally, piRNAs have been shown to target RNA and DNA viruses in some mosquito species. In contrast to transposons, targeting of viruses by the piRNA pathway in these mosquito species does not require endogenous piRNAs. Here, we show that piRNAs target a DNA virus, but not RNA viruses, in an agricultural insect pest. We found that targeting of this DNA virus did not require endogenous piRNAs and that endogenous piRNAs did not mediate targeting of an RNA virus with which they shared complementary sequence. Our results highlight differences between mosquitoes and our experimental system and raise the possibility that DNA viruses may be targeted by piRNAs in other species.
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Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association. Viruses 2020; 12:v12091042. [PMID: 32962015 PMCID: PMC7551885 DOI: 10.3390/v12091042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
Influenza viruses (family Orthomyxoviridae) infect a variety of vertebrates, including birds, humans, and other mammals. Recent metatranscriptomic studies have uncovered divergent influenza viruses in amphibians, fish and jawless vertebrates, suggesting that these viruses may be widely distributed. We sought to identify additional vertebrate influenza-like viruses through the analysis of publicly available RNA sequencing data. Accordingly, by data mining, we identified the complete coding segments of five divergent vertebrate influenza-like viruses. Three fell as sister lineages to influenza B virus: salamander influenza-like virus in Mexican walking fish (Ambystoma mexicanum) and plateau tiger salamander (Ambystoma velasci), Siamese algae-eater influenza-like virus in Siamese algae-eater fish (Gyrinocheilus aymonieri) and chum salmon influenza-like virus in chum salmon (Oncorhynchus keta). Similarly, we identified two influenza-like viruses of amphibians that fell as sister lineages to influenza D virus: cane toad influenza-like virus and the ornate chorus frog influenza-like virus, in the cane toad (Rhinella marina) and ornate chorus frog (Microhyla fissipes), respectively. Despite their divergent phylogenetic positions, these viruses retained segment conservation and splicing consistent with transcriptional regulation in influenza B and influenza D viruses, and were detected in respiratory tissues. These data suggest that influenza viruses have been associated with vertebrates for their entire evolutionary history.
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Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks. Sci Rep 2020; 10:12800. [PMID: 32733035 PMCID: PMC7393117 DOI: 10.1038/s41598-020-69557-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera Sicinivirus, Anativirus, Megrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.
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Lian C, Zhang R, Lan J, Yang Y, Li H, Sui N, Xie Z, Jiang S. Identification of a common conserved neutralizing linear B-cell epitope in the VP3 protein of waterfowl parvoviruses. Avian Pathol 2020; 49:325-334. [PMID: 32208867 DOI: 10.1080/03079457.2020.1746743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Waterfowl parvoviruses (WPVs) including goose parvovirus (GPV), novel GPV-related virus (NGPV) and Muscovy duck parvovirus (MDPV) cause significant economic losses and epizootic threat to the waterfowl industries, and little is known about the B-cell epitopes of WPVs. In this study, a monoclonal antibody (mAb) 5B5 against the VP3 protein of NGPV was used to identify the possible epitope in the three kinds of WPVs. The mAb 5B5 had neutralizing activities to the three viruses, and reacted with the conserved linear B-cell epitopes of 438LHNPPP443 in VP3 protein of GPV, NGPV and MDPV. To the authors' best knowledge, this is the first report on identification of the common conserved neutralizing linear B-cell epitope on VP3 protein of three different WPVs, which would facilitate the development of a novel immunodiagnostic assay for rapid detection of WPV infection.
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Affiliation(s)
- Caiyu Lian
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian, People's Republic of China
| | - Ruihua Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian, People's Republic of China
| | - Jingjing Lan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian, People's Republic of China
| | - Yupeng Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China
| | - Hanqing Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China
| | - Nana Sui
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian, People's Republic of China
| | - Zhijing Xie
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian, People's Republic of China
| | - Shijin Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, People's Republic of China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian, People's Republic of China
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Sosa-Gómez DR, Morgado FS, Corrêa RFT, Silva LA, Ardisson-Araújo DMP, Rodrigues BMP, Oliveira EE, Aguiar RWS, Ribeiro BM. Entomopathogenic Viruses in the Neotropics: Current Status and Recently Discovered Species. NEOTROPICAL ENTOMOLOGY 2020; 49:315-331. [PMID: 32358711 DOI: 10.1007/s13744-020-00770-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
The market for biological control of insect pests in the world and in Brazil has grown in recent years due to the unwanted ecological and human health impacts of chemical insecticides. Therefore, research on biological control agents for pest management has also increased. For instance, insect viruses have been used to protect crops and forests around the world for decades. Among insect viruses, the baculoviruses are the most studied and used viral biocontrol agent. More than 700 species of insects have been found to be naturally infected by baculoviruses, with 90% isolated from lepidopteran insects. In this review, some basic aspects of baculovirus infection in vivo and in vitro infection, gene content, viral replication will be discussed. Furthermore, we provide examples of the use of insect viruses for biological pest control and recently characterized baculoviruses in Brazil.
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Affiliation(s)
- D R Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina, PR, Brasil
| | - F S Morgado
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - R F T Corrêa
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - L A Silva
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - D M P Ardisson-Araújo
- Depto de Bioquímica e Biologia Molecular, Univ Federal de Santa Maria, Santa Maria, RS, Brasil
| | - B M P Rodrigues
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - E E Oliveira
- Depto de Entomologia, Univ Federal de Viçosa, Viçosa, MG, Brasil
| | - R W S Aguiar
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - B M Ribeiro
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil.
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Hildebrandt E, Penzes JJ, Gifford RJ, Agbandje-Mckenna M, Kotin RM. Evolution of dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors. Virus Evol 2020; 6:veaa043. [PMID: 32913662 PMCID: PMC7474932 DOI: 10.1093/ve/veaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.
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Affiliation(s)
- Evin Hildebrandt
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
| | - Judit J Penzes
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Genomics & Bioinformatics, Sir Michael Stoker Building Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Mavis Agbandje-Mckenna
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert M Kotin
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
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Identification of a novel bovine copiparvovirus in pooled fetal bovine serum. Virus Genes 2020; 56:522-526. [PMID: 32306155 PMCID: PMC7329774 DOI: 10.1007/s11262-020-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/03/2020] [Indexed: 01/12/2023]
Abstract
A novel parvovirus was identified as a cell culture contaminant by metagenomic analysis. Droplet digital PCR (ddPCR) was used to determine viral loads in the cell culture supernatant and further analysis, by ddPCR and DNA sequencing, demonstrated that fetal bovine serum (FBS) used during cell culture was the source of the parvovirus contamination. The FBS contained ~ 50,000 copies of the novel parvovirus DNA per ml of serum. The viral DNA was resistant to DNAse digestion. Near-full length sequence of the novel parvovirus was determined. Phylogenetic analysis demonstrated that virus belongs to the Copiparvovirus genus, being most closely related to bovine parvovirus 2 (BPV2) with 41% identity with the non-structural protein NS1 and 47% identity with the virus capsid protein of BPV2. A screen of individual and pooled bovine sera identified a closely related variant of the novel virus in a second serum pool. For classification purposes, the novel virus has been designated bovine copiparvovirus species 3 isolate JB9 (bocopivirus 3-JB9).
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Yuan K, Wang D, Luan Q, Sun J, Gao Q, Jiang Z, Wang S, Han Y, Qu X, Cui Y, Qiu S, Di Y, Wang X, Song S, Wang P, Xia S, Yu Y, Liu W, Yin Y. Whole Genome Characterization and Genetic Evolution Analysis of a New Ostrich Parvovirus. Viruses 2020; 12:v12030334. [PMID: 32204363 PMCID: PMC7150892 DOI: 10.3390/v12030334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
Ostrich diseases characterized by paralysis have been breaking out in broad areas of China since 2015, causing major damage to the ostrich breeding industry in China. This report describes a parvovirus detected in ostriches from four different regions. The entire genomes of four parvovirus strains were sequenced following amplification by PCR, and we conducted comprehensive analysis of the ostrich parvovirus genome. Results showed that the length genomes of the parvovirus contained two open reading frames. Ostrich parvovirus (OsPV) is a branch of goose parvovirus (GPV). Genetic distance analysis revealed a close relationship between the parvovirus and goose parvovirus strains from China, with the closest being the 2016 goose parvovirus RC16 strain from Chongqing. This is the first report of a parvovirus in ostriches. However, whether OsPV is the pathogen of ostrich paralysis remains uncertain. This study contributes new information about the evolution and epidemiology of parvovirus in China, which provides a new way for the study of paralysis in ostriches.
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Affiliation(s)
- Kunpeng Yuan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Dongdong Wang
- Qingdao Bolong Experimental Animal Co., Ltd., Qingdao 266225, China; (D.W.); (J.S.)
| | - Qingdong Luan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Ju Sun
- Qingdao Bolong Experimental Animal Co., Ltd., Qingdao 266225, China; (D.W.); (J.S.)
| | - Qianwen Gao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Zhiyao Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Shouchun Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Yijun Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Xueting Qu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Yueying Cui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Shimei Qiu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Youxia Di
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Xiaoyi Wang
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Shige Song
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Peiheng Wang
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Shilong Xia
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Yongle Yu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Weiquan Liu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China;
- Correspondence: (W.L.); (Y.Y.)
| | - Yanbo Yin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
- Correspondence: (W.L.); (Y.Y.)
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A Highly Prevalent and Pervasive Densovirus Discovered among Sea Stars from the North American Atlantic Coast. Appl Environ Microbiol 2020; 86:AEM.02723-19. [PMID: 31924612 PMCID: PMC7054102 DOI: 10.1128/aem.02723-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/27/2019] [Indexed: 12/04/2022] Open
Abstract
Sea star wasting syndrome is a disease primarily observed on the Pacific and Atlantic Coasts of North America that has significantly impacted sea star populations. The etiology of this disease is unknown, although it is hypothesized to be caused by a densovirus, SSaDV. However, previous studies have not found a correlation between SSaDV and sea star wasting syndrome on the North American Atlantic Coast. This study suggests that this observation may be explained by the presence of a genetically similar densovirus, AfaDV, that may have confounded previous studies. SSaDV was not present in sea stars screened in this study, and instead, AfaDV was commonly found in sea star populations across the New England region, with no apparent signs of disease. These results suggest that sea star densoviruses may be common constituents of the animals’ microbiome, and the diversity and extent of these viruses among wild populations may be greater than previously recognized. The etiology of sea star wasting syndrome is hypothesized to be caused by a densovirus, sea star-associated densovirus (SSaDV), that has previously been reported on the Pacific and Atlantic Coasts of the United States. In this study, we reevaluated the presence of SSaDV among sea stars from the North American Atlantic Coast and in doing so discovered a novel densovirus that we have named Asterias forbesi-associated densovirus (AfaDV), which shares 78% nucleotide pairwise identity with SSaDV. In contrast to previous studies, SSaDV was not detected in sea stars from the North American Atlantic Coast. Using a variety of PCR-based techniques, we investigated the tissue tropism, host specificity, and prevalence of AfaDV among populations of sea stars at five locations along the Atlantic Coast. AfaDV was detected in three sea star species (Asterias forbesi, Asterias rubens, and Henricia sp.) found in this region and was highly prevalent (>80% of individuals tested; n = 134), among sampled populations. AfaDV was detected in the body wall, gonads, and pyloric caeca (digestive gland) of specimens but was not detected in their coelomic fluid. A significant difference in viral load (copies mg−1) was found between tissue types, with the pyloric caeca having the highest viral loads. Further investigation of Asterias forbesi gonad tissue found germ line cells (oocytes) to be virus positive, suggesting a potential route of vertical transmission. Taken together, these observations show that the presence of AfaDV is not an indicator of sea star wasting syndrome because AfaDV is a common constituent of these animals’ microbiome, regardless of health. IMPORTANCE Sea star wasting syndrome is a disease primarily observed on the Pacific and Atlantic Coasts of North America that has significantly impacted sea star populations. The etiology of this disease is unknown, although it is hypothesized to be caused by a densovirus, SSaDV. However, previous studies have not found a correlation between SSaDV and sea star wasting syndrome on the North American Atlantic Coast. This study suggests that this observation may be explained by the presence of a genetically similar densovirus, AfaDV, that may have confounded previous studies. SSaDV was not present in sea stars screened in this study, and instead, AfaDV was commonly found in sea star populations across the New England region, with no apparent signs of disease. These results suggest that sea star densoviruses may be common constituents of the animals’ microbiome, and the diversity and extent of these viruses among wild populations may be greater than previously recognized.
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Obbard DJ, Shi M, Roberts KE, Longdon B, Dennis AB. A new lineage of segmented RNA viruses infecting animals. Virus Evol 2020; 6:vez061. [PMID: 31976084 PMCID: PMC6966834 DOI: 10.1093/ve/vez061] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Mang Shi
- Charles Perkins Center, The University of Sydney, NSW 2006, Australia
| | - Katherine E Roberts
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Ben Longdon
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alice B Dennis
- Department of Evolutionary Biology & Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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24
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Altinli M, Lequime S, Courcelle M, François S, Justy F, Gosselin-Grenet AS, Ogliastro M, Weill M, Sicard M. Evolution and phylogeography of Culex pipiens densovirus. Virus Evol 2019; 5:vez053. [PMID: 31807318 PMCID: PMC6884738 DOI: 10.1093/ve/vez053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses—namely densoviruses—have been largely neglected. Here, we investigated the prevalence and the evolution of the only mosquito-infecting ambidensovirus, Culex pipiens densovirus (CpDV), from laboratory mosquito lines and natural populations collected worldwide. CpDV diversity generally grouped in two clades, here named CpDV-1 and -2. The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. We further investigated the role of selection on the evolution of CpDV genome and detected many individual sites under purifying selection both in non-structural and structural genes. However, some sites in structural genes were under diversifying selection, especially during the divergence of CpDV-1 and -2 clades. These substitutions between CpDV-1 and -2 clades were mostly located in the capsid protein encoding region and might cause changes in host specificity or pathogenicity of CpDV strains from the two clades. However, additional functional and experimental studies are necessary to fully understand the protein conformations and the resulting phenotype of these substitutions between clades of CpDV.
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Affiliation(s)
- Mine Altinli
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sebastian Lequime
- KU Leuven, Department of Microbiology, Immunology, and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Maxime Courcelle
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sarah François
- DGIMI, INRA, Université de Montpellier, Montpellier, France.,Department of Zoology, University of Oxford, Oxford, UK
| | - Fabienne Justy
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | | | - Mylene Weill
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Mathieu Sicard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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25
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Pigeyre L, Schatz M, Ravallec M, Gasmi L, Nègre N, Clouet C, Seveno M, El Koulali K, Decourcelle M, Guerardel Y, Cot D, Dupressoir T, Gosselin-Grenet AS, Ogliastro M. Interaction of a Densovirus with Glycans of the Peritrophic Matrix Mediates Oral Infection of the Lepidopteran Pest Spodoptera frugiperda. Viruses 2019; 11:v11090870. [PMID: 31533310 PMCID: PMC6783882 DOI: 10.3390/v11090870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 01/01/2023] Open
Abstract
The success of oral infection by viruses depends on their capacity to overcome the gut epithelial barrier of their host to crossing over apical, mucous extracellular matrices. As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitinous peritrophic matrix, that lines and protects the midgut epithelium; how capsids stick to and cross these barriers to reach their final cell destination where replication goes has been poorly studied in insects. Here, we analyzed the early interaction of the Junonia coenia densovirus (JcDV) with the midgut barriers of caterpillars from the pest Spodoptera frugiperda. Using combination of imaging, biochemical, proteomic and transcriptomic analyses, we examined in vitro, ex vivo and in vivo the early interaction of the capsids with the peritrophic matrix and the consequence of early oral infection on the overall gut function. We show that the JcDV particle rapidly adheres to the peritrophic matrix through interaction with different glycans including chitin and glycoproteins, and that these interactions are necessary for oral infection. Proteomic analyses of JcDV binding proteins of the peritrophic matrix revealed mucins and non-mucins proteins including enzymes already known to act as receptors for several insect pathogens. In addition, we show that JcDV early infection results in an arrest of N-Acetylglucosamine secretion and a disruption in the integrity of the peritrophic matrix, which may help viral particles to pass through. Finally, JcDV early infection induces changes in midgut genes expression favoring an increased metabolism including an increased translational activity. These dysregulations probably participate to the overall dysfunction of the gut barrier in the early steps of viral pathogenesis. A better understanding of early steps of densovirus infection process is crucial to build biocontrol strategies against major insect pests.
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Affiliation(s)
- Laetitia Pigeyre
- Ecole Pratique des Hautes Etudes (EPHE), PSL Research Univ, DGIMI, Univ Montpellier, INRA, 34095 Montpellier, France.
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Malvina Schatz
- Ecole Pratique des Hautes Etudes (EPHE), PSL Research Univ, DGIMI, Univ Montpellier, INRA, 34095 Montpellier, France.
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Marc Ravallec
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Leila Gasmi
- Estructura de Recerca Interdisciplinar en Biotecnologia I Biomedicina (ERI-BIOTECMED, Deaprtment of Genetics Faculty of Biological Sciences Univ Valencia, 46100 Burjassot, Spain.
| | - Nicolas Nègre
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Cécile Clouet
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Martial Seveno
- BioCampus, Univ Montpellier, CNRS, INSERM, 34000 Montpellier, France.
| | | | | | - Yann Guerardel
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) Univ Lille, CNRS, UMR 8576-UGSF, 59000 Lille, France.
| | - Didier Cot
- Institut Européen des Membranes (IEM), Univ Montpellier, CBRS, ENSCM, 34095 Montpellier, France.
| | - Thierry Dupressoir
- Ecole Pratique des Hautes Etudes (EPHE), PSL Research Univ, DGIMI, Univ Montpellier, INRA, 34095 Montpellier, France.
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Anne-Sophie Gosselin-Grenet
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Mylène Ogliastro
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
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26
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A Duarte M, F Silva JM, R Brito C, S Teixeira D, L Melo F, M Ribeiro B, Nagata T, S Campos F. Faecal Virome Analysis of Wild Animals from Brazil. Viruses 2019; 11:E803. [PMID: 31480274 PMCID: PMC6784175 DOI: 10.3390/v11090803] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/15/2022] Open
Abstract
The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal's susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.
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Affiliation(s)
- Matheus A Duarte
- Faculdade de Agronomia e Veterinária, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - João M F Silva
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Clara R Brito
- Faculdade de Agronomia e Veterinária, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Danilo S Teixeira
- Núcleo de Atendimento e Pesquisa de Animais Silvestres, Universidade Estadual de Santa Cruz, Ilhéus-BA 45.662-900, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Fabrício S Campos
- Laboratório de Bioinformática e Biotecnologia, Campus de Gurupi, Universidade Federal do Tocantins, Tocantins-TO 77.410-570, Brazil.
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27
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Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts. J Virol 2019; 93:JVI.00432-19. [PMID: 31068424 DOI: 10.1128/jvi.00432-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Most described flaviviruses (family Flaviviridae) are disease-causing pathogens of vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts. Poor sampling of flaviviruses outside vector-borne flaviviruses such as Zika virus and dengue virus has presented a narrow understanding of flavivirus diversity and evolution. In this study, we discovered three crustacean flaviviruses (Gammarus chevreuxi flavivirus, Gammarus pulex flavivirus, and Crangon crangon flavivirus) and two cephalopod flaviviruses (Southern Pygmy squid flavivirus and Firefly squid flavivirus). Bayesian and maximum likelihood phylogenetic methods demonstrate that crustacean flaviviruses form a well-supported clade and share a more closely related ancestor with terrestrial vector-borne flaviviruses than with classical insect-specific flaviviruses. In addition, we identify variants of Wenzhou shark flavivirus in multiple gazami crab (Portunus trituberculatus) populations, with active replication supported by evidence of an active RNA interference response. This suggests that Wenzhou shark flavivirus moves horizontally between sharks and gazami crabs in ocean ecosystems. Analyses of the mono- and dinucleotide composition of marine flaviviruses compared to that of flaviviruses with known host status suggest that some marine flaviviruses share a nucleotide bias similar to that of vector-borne flaviviruses. Furthermore, we identify crustacean flavivirus endogenous viral elements that are closely related to elements of terrestrial vector-borne flaviviruses. Taken together, these data provide evidence of flaviviruses circulating between marine vertebrates and invertebrates, expand our understanding of flavivirus host range, and offer potential insights into the evolution and emergence of terrestrial vector-borne flaviviruses.IMPORTANCE Some flaviviruses are known to cause disease in vertebrates and are typically transmitted by blood-feeding arthropods such as ticks and mosquitoes. While an ever-increasing number of insect-specific flaviviruses have been described, we have a narrow understanding of flavivirus incidence and evolution. To expand this understanding, we discovered a number of novel flaviviruses that infect a range of crustaceans and cephalopod hosts. Phylogenetic analyses of these novel marine flaviviruses suggest that crustacean flaviviruses share a close ancestor to all terrestrial vector-borne flaviviruses, and squid flaviviruses are the most divergent of all known flaviviruses to date. Additionally, our results indicate horizontal transmission of a marine flavivirus between crabs and sharks. Taken together, these data suggest that flaviviruses move horizontally between invertebrates and vertebrates in ocean ecosystems. This study demonstrates that flavivirus invertebrate-vertebrate host associations have arisen in flaviviruses at least twice and may potentially provide insights into the emergence or origin of terrestrial vector-borne flaviviruses.
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28
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Flynn PJ, Moreau CS. Assessing the Diversity of Endogenous Viruses Throughout Ant Genomes. Front Microbiol 2019; 10:1139. [PMID: 31191479 PMCID: PMC6540820 DOI: 10.3389/fmicb.2019.01139] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
Abstract
Endogenous viral elements (EVEs) can play a significant role in the evolution of their hosts and have been identified in animals, plants, and fungi. Additionally, EVEs potentially provide an important snapshot of the evolutionary frequency of viral infection. The purpose of this study is to take a comparative host-centered approach to EVE discovery in ant genomes to better understand the relationship of EVEs to their ant hosts. Using a comprehensive bioinformatic pipeline, we screened all nineteen published ant genomes for EVEs. Once the EVEs were identified, we assessed their phylogenetic relationships to other closely related exogenous viruses. A diverse group of EVEs were discovered in all screened ant host genomes and in many cases are similar to previously identified exogenous viruses. EVEs similar to ssRNA viral proteins are the most common viral lineage throughout the ant hosts, which is potentially due to more chronic infection or more effective endogenization of certain ssRNA viruses in ants. In addition, both EVEs similar to viral glycoproteins and retrovirus-derived proteins are also abundant throughout ant genomes, suggesting their tendency to endogenize. Several of these newly discovered EVEs are found to be potentially functional within the genome. The discovery and analysis of EVEs is essential in beginning to understand viral–ant interactions over evolutionary time.
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Affiliation(s)
- Peter J Flynn
- Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, United States.,Department of Science and Education, Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States
| | - Corrie S Moreau
- Department of Science and Education, Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States.,Departments of Entomology and Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
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29
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A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite ( Tetranychus urticae) Populations. Viruses 2019; 11:v11030233. [PMID: 30866521 PMCID: PMC6466187 DOI: 10.3390/v11030233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/19/2019] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.
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30
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Endogenous Viral Elements Are Widespread in Arthropod Genomes and Commonly Give Rise to PIWI-Interacting RNAs. J Virol 2019; 93:JVI.02124-18. [PMID: 30567990 DOI: 10.1128/jvi.02124-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/14/2018] [Indexed: 12/31/2022] Open
Abstract
Arthropod genomes contain sequences derived from integrations of DNA and nonretroviral RNA viruses. These sequences, known as endogenous viral elements (EVEs), have been acquired over the course of evolution and have been proposed to serve as a record of past viral infections. Recent evidence indicates that EVEs can function as templates for the biogenesis of PIWI-interacting RNAs (piRNAs) in some mosquito species and cell lines, raising the possibility that EVEs may serve as a source of immunological memory in these organisms. However, whether piRNAs are derived from EVEs or serve an antiviral function in other arthropod species is unknown. Here, we used publicly available genome assemblies and small RNA sequencing data sets to characterize the repertoire and function of EVEs across 48 arthropod genomes. We found that EVEs are widespread in arthropod genomes and primarily correspond to unclassified single-stranded RNA (ssRNA) viruses and viruses belonging to the Rhabdoviridae and Parvoviridae families. Additionally, EVEs were enriched in piRNA clusters in a majority of species, and we found that production of primary piRNAs from EVEs is common, particularly for EVEs located within piRNA clusters. While the abundance of EVEs within arthropod genomes and the frequency with which EVEs give rise to primary piRNAs generally support the hypothesis that EVEs contribute to an antiviral response via the piRNA pathway, limited nucleotide identity between currently described viruses and EVEs identified here likely limits the extent to which this process plays a role during infection with known viruses in the arthropod species analyzed.IMPORTANCE Our results greatly expand the knowledge of EVE abundance, diversity, and function in an exceptionally wide range of arthropod species. We found that while previous findings in mosquitoes regarding the potential of EVEs to serve as sources of immunological memory via the piRNA pathway may be generalized to other arthropod species, speculation regarding the antiviral function of EVE-derived piRNAs should take into context the fact that EVEs are, in the vast majority of cases, not similar enough to currently described viruses at the nucleotide level to serve as sources of antiviral piRNAs against them.
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31
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Altinli M, Soms J, Ravallec M, Justy F, Bonneau M, Weill M, Gosselin-Grenet AS, Sicard M. Sharing cells with Wolbachia: the transovarian vertical transmission of Culex pipiens densovirus. Environ Microbiol 2018; 21:3284-3298. [PMID: 30585387 DOI: 10.1111/1462-2920.14511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/19/2022]
Abstract
Culex pipiens densovirus (CpDV), a single stranded DNA virus, has been isolated from Culex pipiens mosquitoes but differs from other mosquito densoviruses in terms of genome structure and sequence identity. Its transmission from host to host, the nature of its interactions with both its host and host's endosymbiotic bacteria Wolbachia are not known. Here, we report the presence of CpDV in the ovaries and eggs of Cx. pipiens mosquitoes in close encounters with Wolbachia. In the ovaries, CpDV amount significantly differed between mosquito lines harbouring different strains of Wolbachia and these differences were not linked to variations in Wolbachia densities. CpDV was vertically transmitted in all laboratory lines to 17%-20% of the offspring. For some females, however, the vertical transmission reached 90%. Antibiotic treatment that cured the host from Wolbachia significantly decreased both CpDV quantity and vertical transmission suggesting an impact of host microbiota, including Wolbachia, on CpDV transmission. Overall our results show that CpDV is transmitted vertically via transovarian path along with Wolbachia with which it shares the same cells. Our results are primordial to understand the dynamics of densovirus infection, their persistence and spread in populations considering their potential use in the regulation of mosquito vector populations.
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Affiliation(s)
- Mine Altinli
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Julien Soms
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Marc Ravallec
- DGIMI, University of Montpellier, INRA, Montpellier, France
| | - Fabienne Justy
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Manon Bonneau
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Mylene Weill
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | | | - Mathieu Sicard
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
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32
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Abstract
Roediger et al. (2018) demonstrate that a kidney disease characterized by apparently spontaneous nephropathy that had been recognized in laboratory mice for many years is caused by a newly recognized virus named the mouse kidney parvovirus (MKPV). That virus appears to be widespread in mouse colonies as it is not detected by current diagnostic tools, and its recognition presents new opportunities for understanding the pathology of tubulointerstitial fibrosis.
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Affiliation(s)
- Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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Obbard DJ. Expansion of the metazoan virosphere: progress, pitfalls, and prospects. Curr Opin Virol 2018; 31:17-23. [PMID: 30237139 DOI: 10.1016/j.coviro.2018.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/15/2018] [Accepted: 08/17/2018] [Indexed: 12/22/2022]
Abstract
Metagenomic sequencing has led to a recent and rapid expansion of the animal virome. It has uncovered a multitude of new virus lineages from under-sampled host groups, including many that break up long branches in the virus tree, and many that display unexpected genome sizes and structures. Although there are challenges to inferring the existence of a virus from a `virus-like sequence', in the absence of an isolate the analysis of nucleic acid (including small RNAs) and sequence data can provide considerable confidence. As a consequence, this period of molecular natural history is helping to reshape our views of deep virus evolution.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
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Insect-specific viruses: from discovery to potential translational applications. Curr Opin Virol 2018; 33:33-41. [PMID: 30048906 DOI: 10.1016/j.coviro.2018.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022]
Abstract
Over the past decade the scientific community has experienced a new age of virus discovery in arthropods in general, and in insects in particular. Next generation sequencing and advanced bioinformatics tools have provided new insights about insect viromes and viral evolution. In this review, we discuss some high-throughput sequencing technologies used to discover viruses in insects and the challenges raised in data interpretations. Additionally, the discovery of these novel viruses that are considered as insect-specific viruses (ISVs) has gained increasing attention in their potential use as biological agents. As example, we show how the ISV Nhumirim virus was used to reduce West Nile virus transmission when co-infecting the mosquito vector. We also discuss new translational opportunities of using ISVs to limit insect vector competence by using them to interfere with pathogen acquisition, to directly target the insect vector or to confer pathogen resistance by the insect vector.
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Cholleti H, Hayer J, Mulandane FC, Falk K, Fafetine J, Berg M, Blomström AL. Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique. Infect Ecol Epidemiol 2018; 8:1478585. [PMID: 29868166 PMCID: PMC5974704 DOI: 10.1080/20008686.2018.1478585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/14/2018] [Indexed: 01/17/2023] Open
Abstract
Background: Ticks are primary vectors for many well-known disease-causing agents that affect human and animal populations globally such as tick-borne encephalitis, Crimean-Congo hemorrhagic fever and African swine fever. In this study, viral metagenomics was used to identify what viruses are present in Rhipicephalus spp. ticks collected in the Zambezi Valley of Mozambique. Methods: The RNA was amplified with sequence-independent single primer amplification (SISPA) and high-throughput sequencing was performed on the Ion Torrent platform. The generated sequences were subjected to quality check and classfied by BLAST. CodonCode aligner and SeqMan were used to assemble the sequences. Results: The majority of viral sequences showed closest sequence identity to the Orthomyxoviridae family, although viruses similar to the Parvoviridae and Coronaviridae were also identified. Nearly complete sequences of five orthomyxoviral segments (HA, NP, PB1, PB2, and PA) were obtained and these showed an amino acid identity of 32–52% to known quaranjaviruses. The sequences were most closely related to the Wellfleet Bay virus, detected and isolated from common eider during a mortality event in the USA. Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Further genetic and biological studies are needed in order to investigate potential pathogenesis of the identified orthomyxovirus.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fernando Chanisso Mulandane
- Division of Molecular Diagnostics and Epidemiology, Biotechnology Center, Eduardo Mondlane University, Maputo, Mozambique
| | - Kerstin Falk
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden
| | - Jose Fafetine
- Division of Molecular Diagnostics and Epidemiology, Biotechnology Center, Eduardo Mondlane University, Maputo, Mozambique
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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Laffy PW, Wood‐Charlson EM, Turaev D, Jutz S, Pascelli C, Botté ES, Bell SC, Peirce TE, Weynberg KD, van Oppen MJH, Rattei T, Webster NS. Reef invertebrate viromics: diversity, host specificity and functional capacity. Environ Microbiol 2018; 20:2125-2141. [DOI: 10.1111/1462-2920.14110] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Patrick W. Laffy
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | | | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Sabrina Jutz
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Cecilia Pascelli
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- College of Science and EngineeringJames Cook UniversityTownsville QLD Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook UniversityTownsville QLD Australia
| | | | - Sara C. Bell
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Tyler E. Peirce
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Karen D. Weynberg
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- School of BiosciencesUniversity of Melbourne, ParkvilleMelbourneVIC 3010 Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Nicole S. Webster
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- Austalian Centre for Ecogenomics, University of QueenslandBrisbaneQLD 4072 Australia
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Kobayashi Y, Shimazu T, Murata K, Itou T, Suzuki Y. An endogenous adeno-associated virus element in elephants. Virus Res 2018; 262:10-14. [PMID: 29702129 DOI: 10.1016/j.virusres.2018.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/17/2018] [Accepted: 04/23/2018] [Indexed: 11/19/2022]
Abstract
An endogenous viral element derived from adeno-associated virus containing a nearly intact open reading frame (ORF) of the rep gene (enAAV-rep) has been identified in the genomes of various mammals including degu and African elephant. Particularly, in degu, mRNA expression of enAAV-rep has been observed specifically in the liver. Here we newly identified enAAV-rep in Asian elephant and rock hyrax, both of which are afrotherians. The enAAV-rep of African and Asian elephants appeared to be orthologous and originated from an integration event of the entire genome of AAV into the ancestral genome of elephants more than 6 million years ago, whereas that of rock hyrax appeared to have originated independently. Negative selection operating at the amino acid sequence level was detected for the ORF of enAAV-rep in elephants. As in degu, mRNA expression of enAAV-rep was specifically observed in the liver in Asian elephant. Integrations of enAAV-rep appeared to have occurred independently on the evolutionary lineages of elephants and degu, suggesting that the AAV Rep protein has been co-opted repeatedly in the mammalian liver.
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Affiliation(s)
- Yuki Kobayashi
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan.
| | - Tsukika Shimazu
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan
| | - Koichi Murata
- Department of Animal Resource Science, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Takuya Itou
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi 467-8501, Japan
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38
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de Souza WM, Dennis T, Fumagalli MJ, Araujo J, Sabino-Santos G, Maia FGM, Acrani GO, Carrasco ADOT, Romeiro MF, Modha S, Vieira LC, Ometto T, Queiroz LH, Durigon EL, Nunes MRT, Figueiredo LTM, Gifford RJ. Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity. Viruses 2018; 10:E143. [PMID: 29565808 PMCID: PMC5923437 DOI: 10.3390/v10040143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022] Open
Abstract
Parvoviruses (family Parvoviridae) are small, single-stranded DNA viruses. Many parvoviral pathogens of medical, veterinary and ecological importance have been identified. In this study, we used high-throughput sequencing (HTS) to investigate the diversity of parvoviruses infecting wild and domestic animals in Brazil. We identified 21 parvovirus sequences (including twelve nearly complete genomes and nine partial genomes) in samples derived from rodents, bats, opossums, birds and cattle in Pernambuco, São Paulo, Paraná and Rio Grande do Sul states. These sequences were investigated using phylogenetic and distance-based approaches and were thereby classified into eight parvovirus species (six of which have not been described previously), representing six distinct genera in the subfamily Parvovirinae. Our findings extend the known biogeographic range of previously characterized parvovirus species and the known host range of three parvovirus genera (Dependovirus, Aveparvovirus and Tetraparvovirus). Moreover, our investigation provides a window into the ecological dynamics of parvovirus infections in vertebrates, revealing that many parvovirus genera contain well-defined sub-lineages that circulate widely throughout the world within particular taxonomic groups of hosts.
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Affiliation(s)
- William Marciel de Souza
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
| | - Tristan Dennis
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
| | - Marcílio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
| | - Jansen Araujo
- Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, SP, Brazil.
| | - Gilberto Sabino-Santos
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
| | - Felipe Gonçalves Motta Maia
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
- Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, SP, Brazil.
| | | | | | - Marilia Farignoli Romeiro
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
| | - Luiz Carlos Vieira
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
| | - Tatiana Ometto
- Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, SP, Brazil.
| | - Luzia Helena Queiroz
- Faculty of Veterinary Medicine, São Paulo State University, Araçatuba, SP 16050-680, Brazil.
| | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, SP, Brazil.
| | - Márcio Roberto Teixeira Nunes
- Center for Technological Innovations, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará 67030-000, Pará, Brazil.
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, SP, Brazil.
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Host plant associated enhancement of immunity and survival in virus infected caterpillars. J Invertebr Pathol 2018; 151:102-112. [DOI: 10.1016/j.jip.2017.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/08/2017] [Accepted: 11/07/2017] [Indexed: 01/02/2023]
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Li P, Lin S, Zhang R, Chen J, Sun D, Lan J, Song S, Xie Z, Jiang S. Isolation and characterization of novel goose parvovirus-related virus reveal the evolution of waterfowl parvovirus. Transbound Emerg Dis 2017; 65:e284-e295. [DOI: 10.1111/tbed.12751] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Indexed: 11/28/2022]
Affiliation(s)
- P. Li
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - S. Lin
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
| | - R. Zhang
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - J. Chen
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - D. Sun
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - J. Lan
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - S. Song
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - Z. Xie
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
| | - S. Jiang
- Department of Preventive Veterinary Medicine; College of Veterinary Medicine; Shandong Agricultural University; Taian China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention; Taian China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention; Shandong Agricultural University; Taian China
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41
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Viruses as vectors of horizontal transfer of genetic material in eukaryotes. Curr Opin Virol 2017; 25:16-22. [DOI: 10.1016/j.coviro.2017.06.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/18/2017] [Accepted: 06/13/2017] [Indexed: 01/04/2023]
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