DOCSLIB.ORG

Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts Shelley Cook1*☯, Betty Y.-W. Chung2☯, David Bass1, Gregory Moureau3, Shuoya Tang2, Erica McAlister1, C. Lorna Culverwell1, Edvard Glücksman4, Hui Wang5, T. David K. Brown6, Ernest A. Gould3,5, Ralph E. Harbach1, Xavier de Lamballerie3, Andrew E. Firth6* 1 Department of Life Sciences, Natural History Museum, London, United Kingdom, 2 Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, 3 UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France, 4 Department of General Botany, University Duisburg-Essen, Essen, Germany, 5 Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom, 6 Department of Pathology, University of Cambridge, Cambridge, United Kingdom Abstract We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected. Citation: Cook S, Chung BY-W, Bass D, Moureau G, Tang S, et al. (2013) Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts. PLoS ONE 8(11): e80720. doi:10.1371/journal.pone.0080720 Editor: Houssam Attoui, The Pirbright Institute, United Kingdom Received June 14, 2013; Accepted October 7, 2013; Published November 18, 2013 Copyright: © 2013 Cook et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: SC was funded by a Wellcome Trust Sir Henry Wellcome Postdoctoral Fellowship [082744]. See www.wellcome.ac.uk. Work in the AEF lab is funded by grants from the Wellcome Trust [088789] and the U.K. Biotechnology and Biological Research Council (BBSRC) [BB/J007072/1 and BB/ J015652/1]. See www.wellcome.ac.uk and www.bbscr.ac.uk respectively. BYWC is funded by an EMBO Long-Term Postdoctoral Fellowship and a Sir Henry Wellcome Postdoctoral Fellowship [096082]. See www.embo.org and www.wellcome.ac.uk respectively. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. * E-mail: [email protected] (SC); [email protected] (AEF) ☯ These authors contributed equally to this work. Introduction research has demonstrated that there exists a vast diversity of previously undiscovered viruses in the natural environment [1]. The emergence of new infectious diseases, many of which For example, a large number of “insect-specific” flaviviruses are caused by RNA viruses, is a major threat to human, animal have been discovered recently in numerous culicine mosquito and plant health and agriculture. RNA viruses demonstrate species (Diptera: Culicidae: Culicinae) and these viral strains remarkable capacity to evolve due to large population size, are likely to vastly outnumber the pathogenic strains present in short generation times and high mutation and recombination the natural environment, including those flaviviruses that cause rates. Many are also vector-borne, potentially increasing the diseases such as yellow fever and dengue fever in humans prevalence and range of a given virus in natural ecosystems. [2,3,4,5]. A variety of other novel RNA and DNA viruses have Understanding the mechanisms underlying viral emergence is been recently identified in insects [6,7]. Deep sequencing key for the rational design of antiviral therapies and control technologies have the potential to provide an unprecedented strategies. A first step in this process is the characterisation of description of this genetic background, and thus to begin to the true distribution of virus genetic variability, both spatially understand the interactions of pathogenic and “silent” viruses in and taxonomically across different host species. Recent nature, which may include competitive exclusion, PLOS ONE | www.plosone.org 1 November 2013 | Volume 8 | Issue 11 | e80720 RNA Reconstruction of Novel Viruses from Diptera superinfection, recombination and other mechanisms that may pooling aims was to collect (i) adult anophelines, (ii) adult be involved in the generation of viral diversity [8,9,30]. culicines, (iii) immature anophelines and (iv) immature Invertebrates, including dipterans (order Diptera, the two- culicines, from each collection site, plus (v) a pooled sample of winged flies) such as mosquitoes, respond to viral infection via chironomids from across all sites, for comparison of viral RNA interference (RNAi) or RNA silencing, leading to diversity. suppression or elimination of the pathogen via sequence- specific degradation of homologous RNA sequences into small Total and small RNA preparation, library construction RNAs (sRNAs) of discrete sizes. This has been demonstrated and Illumina sequencing in Stegomyia aegypti [=Aedes aegypti] mosquitoes infected RNA was purified from 0.5 g of flies using the Ambion with dengue virus (DENV) or Sindbis virus (SINV), Culex mirVana miRNA Isolation Kit (PE Applied BioSystems, quinquefasciatus mosquitoes orally exposed to West Nile virus Warrington, England) according to the manufacturer’s (WNV) and Drosophila infected with flock house virus (FHV) instructions for total and small-enriched RNA. Additionally, the [10,11,12,13]. Similarly, studies in RNAi-deficient Anopheles latter were DNase-treated. All RNA extractions were stored at gambiae mosquitoes showed increased viral dissemination -80°C and evaluated on a Bioanalyzer (Agilent Technology, rates and titres of inoculated O’nyong-nyong virus [14]. In this Santa Clara, CA, USA). study, we used sRNAs sequenced from mosquitoes and Twelve tagged small-enriched RNA libraries were prepared chironomids sampled from the natural environment to inform for single read sequencing using the HiSeq 2000 platform total RNA deep sequencing of samples of particular interest. (Illumina, San Diego, CA, USA). Briefly, acrylamide gel Within the mosquitoes, the vast majority of flaviviruses purification of RNA bands corresponding to size range ~20–30 discovered to date have been isolated from culicine mosquito nt was conducted. Adaptor sequences were added so that the species (subfamily Culicinae, see examples above) as libraries could be multiplexed, producing 10–19 million reads opposed to anopheline mosquitoes (subfamily Anophelinae, for per tagged library. Based on the sRNA sequencing, we chose example An. gambiae, a major vector for malarial parasites, three samples for further investigation: sample 1 (140 adult see example above), despite the fact that species from both anopheline mosquitoes, female Anopheles maculipennis sensu groups of Culicidae take bloodmeals. In contrast, the lato, from the farm/stables site), sample 7 (adult chironomids chironomids (Diptera: Chironomidae) are non-biting midges. pooled across sites) and sample 9 (25 adult culicine We planned to sample all three groups in order to test whether mosquitoes, female Ochlerotatus caspius and Oc. detritus from related viruses may be discovered in a range of dipterans in the rice farm). Since genome assembly from sRNA alone is the natural environment, potentially related to a shared difficult due to non-uniform and incomplete coverage and short environment and/or transmission and maintenance cycles sequence reads, we subjected total RNA samples to HiSeq aside from blood-feeding. sequencing in an attempt to assemble full-genome virus sequences. Materials and Methods Sequence processing, assembly and virus genome Trapping protocol identification Approximately 600 mosquitoes and chironomids were Sequence read processing, assembly and virus genome collected in June 2011 in the Camargue region of France for identification were conducted using a custom bioinformatics screening. Specimens were sampled from a variety of locations pipeline. Trimmed sRNA reads were assembled using Velvet using different collection methods to maximise species [16] and contigs were compared to a database comprising all diversity. Collections were made within and around (i) an National Center for Biotechnology Information (NCBI) RNA ornithological park, (ii) a rice farm and (iii) a rural farmhouse virus proteins using blastx [17]. For the total RNA samples, raw and stables. CDC fan-augmented light traps were Illumina reads were trimmed using the FASTX-Toolkit (see supplemented
Load more

Recommended publications
  • Using Cell Lines to Study Factors Affecting Transmission of Fish Viruses
    Using cell lines to study factors affecting transmission of fish viruses by Phuc Hoang Pham A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Biology Waterloo, Ontario, Canada, 2014 ©Phuc Hoang Pham 2014 AUTHOR'S DECLARATION I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii ABSTRACT Factors that can influence the transmission of aquatic viruses in fish production facilities and natural environment are the immune defense of host species, the ability of viruses to infect host cells, and the environmental persistence of viruses. In this thesis, fish cell lines were used to study different aspects of these factors. Five viruses were used in this study: viral hemorrhagic septicemia virus (VHSV) from the Rhabdoviridae family; chum salmon reovirus (CSV) from the Reoviridae family; infectious pancreatic necrosis virus (IPNV) from the Birnaviridae family; and grouper iridovirus (GIV) and frog virus-3 (FV3) from the Iridoviridae family. The first factor affecting the transmission of fish viruses examined in this thesis is the immune defense of host species. In this work, infections of marine VHSV-IVa and freshwater VHSV-IVb were studied in two rainbow trout cell lines, RTgill-W1 from the gill epithelium, and RTS11 from spleen macrophages. RTgill-W1 produced infectious progeny of both VHSV-IVa and -IVb. However, VHSV-IVa was more infectious than IVb toward RTgill-W1: IVa caused cytopathic effects (CPE) at a lower viral titre, elicited CPE earlier, and yielded higher titres.
    [Show full text]
  • (LRV1) Pathogenicity Factor
    Antiviral screening identifies adenosine analogs PNAS PLUS targeting the endogenous dsRNA Leishmania RNA virus 1 (LRV1) pathogenicity factor F. Matthew Kuhlmanna,b, John I. Robinsona, Gregory R. Bluemlingc, Catherine Ronetd, Nicolas Faseld, and Stephen M. Beverleya,1 aDepartment of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; bDepartment of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; cEmory Institute for Drug Development, Emory University, Atlanta, GA 30329; and dDepartment of Biochemistry, University of Lausanne, 1066 Lausanne, Switzerland Contributed by Stephen M. Beverley, December 19, 2016 (sent for review November 21, 2016; reviewed by Buddy Ullman and C. C. Wang) + + The endogenous double-stranded RNA (dsRNA) virus Leishmaniavirus macrophages infected in vitro with LRV1 L. guyanensis or LRV2 (LRV1) has been implicated as a pathogenicity factor for leishmaniasis Leishmania aethiopica release higher levels of cytokines, which are in rodent models and human disease, and associated with drug-treat- dependent on Toll-like receptor 3 (7, 10). Recently, methods for ment failures in Leishmania braziliensis and Leishmania guyanensis systematically eliminating LRV1 by RNA interference have been − infections. Thus, methods targeting LRV1 could have therapeutic ben- developed, enabling the generation of isogenic LRV1 lines and efit. Here we screened a panel of antivirals for parasite and LRV1 allowing the extension of the LRV1-dependent virulence paradigm inhibition, focusing on nucleoside analogs to capitalize on the highly to L. braziliensis (12). active salvage pathways of Leishmania, which are purine auxo- A key question is the relevancy of the studies carried out in trophs.
    [Show full text]
  • Detection and Characterization of a Novel Marine Birnavirus Isolated from Asian Seabass in Singapore
    Chen et al. Virology Journal (2019) 16:71 https://doi.org/10.1186/s12985-019-1174-0 RESEARCH Open Access Detection and characterization of a novel marine birnavirus isolated from Asian seabass in Singapore Jing Chen1†, Xinyu Toh1†, Jasmine Ong1, Yahui Wang1, Xuan-Hui Teo1, Bernett Lee2, Pui-San Wong3, Denyse Khor1, Shin-Min Chong1, Diana Chee1, Alvin Wee1, Yifan Wang1, Mee-Keun Ng1, Boon-Huan Tan3 and Taoqi Huangfu1* Abstract Background: Lates calcarifer, known as seabass in Asia and barramundi in Australia, is a widely farmed species internationally and in Southeast Asia and any disease outbreak will have a great economic impact on the aquaculture industry. Through disease investigation of Asian seabass from a coastal fish farm in 2015 in Singapore, a novel birnavirus named Lates calcarifer Birnavirus (LCBV) was detected and we sought to isolate and characterize the virus through molecular and biochemical methods. Methods: In order to propagate the novel birnavirus LCBV, the virus was inoculated into the Bluegill Fry (BF-2) cell line and similar clinical signs of disease were reproduced in an experimental fish challenge study using the virus isolate. Virus morphology was visualized using transmission electron microscopy (TEM). Biochemical analysis using chloroform and 5-Bromo-2′-deoxyuridine (BUDR) sensitivity assays were employed to characterize the virus. Next-Generation Sequencing (NGS) was also used to obtain the virus genome for genetic and phylogenetic analyses. Results: The LCBV-infected BF-2 cell line showed cytopathic effects such as rounding and granulation of cells, localized cell death and detachment of cells observed at 3 to 5 days’ post-infection.
    [Show full text]
  • CHARACTERIZATION of FIELD STRAINS of INFECTIOUS BURSAL DISEASE VIRUS (IBDV) USING MOLECULAR TECHNIQUES by ALEJANDRO BANDA (Under
    CHARACTERIZATION OF FIELD STRAINS OF INFECTIOUS BURSAL DISEASE VIRUS (IBDV) USING MOLECULAR TECHNIQUES by ALEJANDRO BANDA (Under the Direction of Pedro Villegas) ABSTRACT This study was aimed to apply different molecular techniques in the genotyping of field strains of infectious bursal disease virus (IBDV) currently present in the United States and in some other countries. The different techniques included the reverse transcription-polymerase chain reaction / restriction fragment length polymorphism (RT- PCR/RFLP), heteroduplex mobility assay (HMA), nucleotide and amino acid sequence analysis, and riboprobe in situ hybridization (ISH). From 150 samples analyzed from the United States, 80% exhibited RFLP identical to the variant Delaware E strain, other strains detected included Sal-1, D-78, Lukert, PBG-98, Delaware A, GLS IBDV standard challenge strain –like (STC-like). The analysis of the deduced amino acid sequence of the VP2 hypervariable region from six strains classified as Delaware variant E, revealed some amino acid substitutions that make them somewhat different from the original variant E strain isolated in the mid 1980s. The isolate 9109 was classified as a standard strain, but, it exhibited a unique RFLP pattern characterized by the presence of the Ssp I restriction site characteristic of the very virulent IBDV (vvIBDV) strains. The pathogenic properties of this isolate were compared to those of isolate 9865 (variant strain) and the Edgar strain. All three strains induced subclinical disease, however by in situ hybridization some differences in the tissue tropism were observed. The viral replication of the variant isolate 9865 was more restricted to the bursa of Fabricius. Isolate 9109 and the Edgar strain were also observed in thymus, cecal tonsils, spleen, kidney and proventriculus.
    [Show full text]
  • Novel Viruses in Salivary Glands of Mosquitoes from Sylvatic Cerrado, Midwestern Brazil
    RESEARCH ARTICLE Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil Andressa Zelenski de Lara Pinto1, Michellen Santos de Carvalho1, Fernando Lucas de Melo2, Ana LuÂcia Maria Ribeiro3, Bergmann Morais Ribeiro2, Renata Dezengrini Slhessarenko1* 1 Programa de PoÂs-GraduacËão em Ciências da SauÂde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CuiabaÂ, Mato Grosso, Brazil, 2 Departamento de Biologia Celular, Instituto de Ciências BioloÂgicas, Universidade de BrasõÂlia, BrasõÂlia, Distrito Federal, Brazil, 3 Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, CuiabaÂ, Mato Grosso, Brazil a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Viruses may represent the most diverse microorganisms on Earth. Novel viruses and vari- ants continue to emerge. Mosquitoes are the most dangerous animals to humankind. This OPEN ACCESS study aimed at identifying viral RNA diversity in salivary glands of mosquitoes captured in a sylvatic area of Cerrado at the Chapada dos Guimar es National Park, Mato Grosso, Brazil. Citation: Lara Pinto AZd, Santos de Carvalho M, de ã Melo FL, Ribeiro ALM, Morais Ribeiro B, In total, 66 Culicinae mosquitoes belonging to 16 species comprised 9 pools, subjected to Dezengrini Slhessarenko R (2017) Novel viruses in viral RNA extraction, double-strand cDNA synthesis, random amplification and high- salivary glands of mosquitoes from sylvatic throughput sequencing, revealing the presence of seven insect-specific viruses, six of which Cerrado, Midwestern Brazil. PLoS ONE 12(11): e0187429. https://doi.org/10.1371/journal. represent new species of Rhabdoviridae (Lobeira virus), Chuviridae (Cumbaru and Croada pone.0187429 viruses), Totiviridae (Murici virus) and Partitiviridae (Araticum and Angico viruses).
    [Show full text]
  • A-Lovisolo.Vp:Corelventura
    Acta zoologica cracoviensia, 46(suppl.– Fossil Insects): 37-50, Kraków, 15 Oct., 2003 Searching for palaeontological evidence of viruses that multiply in Insecta and Acarina Osvaldo LOVISOLO and Oscar RÖSLER Received: 31 March, 2002 Accepted for publication: 17 Oct., 2002 LOVISOLO O., RÖSLER O. 2003. Searching for palaeontological evidence of viruses that multiply in Insecta and Acarina. Acta zoologica cracoviensia, 46(suppl.– Fossil Insects): 37-50. Abstract. Viruses are known to be agents of important diseases of Insecta and Acarina, and many vertebrate and plant viruses have arthropods as propagative vectors. There is fossil evidence of arthropod pathogens for some micro-organisms, but not for viruses. Iso- lated virions would be hard to detect but, in fossil material, it could be easier to find traces of virus infection, mainly virus-induced cellular structures (VICS), easily recognisable by electron microscopy, such as virions encapsulated in protein occlusion bodies, aggregates of membrane-bounded virus particles and crystalline arrays of numerous virus particles. The following main taxa of viruses that multiply in arthropods are discussed both for some of their evolutionary aspects and for the VICS they cause in arthropods: A. dsDNA Poxviridae, Asfarviridae, Baculoviridae, Iridoviridae, Polydnaviridae and Ascoviridae, infecting mainly Lepidoptera, Hymenoptera, Coleoptera, Diptera and Acarina; B. ssDNA Parvoviridae, infecting mainly Diptera and Lepidoptera; C. dsRNA Reoviridae and Bir- naviridae, infecting mainly Diptera, Hymenoptera and Acarina, and plant viruses also multiplying in Hemiptera; D. Amb.-ssRNA Bunyaviridae and Tenuivirus, that multiply in Diptera and Hemiptera (animal viruses) and in Thysanoptera and Hemiptera (plant vi- ruses); E. -ssRNA Rhabdoviridae, multiplying in Diptera and Acarina (vertebrate vi- ruses), and mainly in Hemiptera (plant viruses); F.
    [Show full text]
  • Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses
    viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified.
    [Show full text]
  • ICTV Code Assigned: 2011.001Ag Officers)
    This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp .
    [Show full text]
  • Meta-Transcriptomic Detection of Diverse and Divergent RNA Viruses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.141184; this version posted June 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Meta-transcriptomic detection of diverse and divergent 2 RNA viruses in green and chlorarachniophyte algae 3 4 5 Justine Charon1, Vanessa Rossetto Marcelino1,2, Richard Wetherbee3, Heroen Verbruggen3, 6 Edward C. Holmes1* 7 8 9 1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 10 Environmental Sciences and School of Medical Sciences, The University of Sydney, 11 Sydney, Australia. 12 2Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical 13 Research, Westmead, NSW 2145, Australia. 14 3School of BioSciences, University of Melbourne, VIC 3010, Australia. 15 16 17 *Corresponding author: 18 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 19 Environmental Sciences and School of Medical Sciences, 20 The University of Sydney, 21 Sydney, NSW 2006, Australia. 22 Tel: +61 2 9351 5591 23 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.141184; this version posted June 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • Viruses Associated with Antarctic Wildlife from Serology Based
    Virus Research 243 (2018) 91–105 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres Review Viruses associated with Antarctic wildlife: From serology based detection to MARK identification of genomes using high throughput sequencing ⁎ Zoe E. Smeelea,b, David G. Ainleyc, Arvind Varsania,b,d, a The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA b School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand c HT Harvey and Associates, Los Gatos, CA 95032, USA d Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa ARTICLE INFO ABSTRACT Keywords: The Antarctic, sub-Antarctic islands and surrounding sea-ice provide a unique environment for the existence of Penguin organisms. Nonetheless, birds and seals of a variety of species inhabit them, particularly during their breeding Seal seasons. Early research on Antarctic wildlife health, using serology-based assays, showed exposure to viruses in Petrel the families Birnaviridae, Flaviviridae, Herpesviridae, Orthomyxoviridae and Paramyxoviridae circulating in seals Sharp spined notothen (Phocidae), penguins (Spheniscidae), petrels (Procellariidae) and skuas (Stercorariidae). It is only during the last Antarctica decade or so that polymerase chain reaction-based assays have been used to characterize viruses associated with Wildlife disease Antarctic animals. Furthermore, it is only during the last five years that full/whole genomes of viruses (ade- noviruses, anelloviruses, orthomyxoviruses, a papillomavirus, paramyoviruses, polyomaviruses and a togavirus) have been sequenced using Sanger sequencing or high throughput sequencing (HTS) approaches.
    [Show full text]
  • Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
    Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person
    [Show full text]
  • Establishment of Neurospora Crassa As a Model Organism for Fungal Virology
    ARTICLE https://doi.org/10.1038/s41467-020-19355-y OPEN Establishment of Neurospora crassa as a model organism for fungal virology Shinji Honda1, Ana Eusebio-Cope2, Shuhei Miyashita3, Ayumi Yokoyama1, Annisa Aulia2, Sabitree Shahi 2, ✉ Hideki Kondo2 & Nobuhiro Suzuki 2 The filamentous fungus Neurospora crassa is used as a model organism for genetics, devel- opmental biology and molecular biology. Remarkably, it is not known to host or to be sus- 1234567890():,; ceptible to infection with any viruses. Here, we identify diverse RNA viruses in N. crassa and other Neurospora species, and show that N. crassa supports the replication of these viruses as well as some viruses from other fungi. Several encapsidated double-stranded RNA viruses and capsid-less positive-sense single-stranded RNA viruses can be experimentally introduced into N. crassa protoplasts or spheroplasts. This allowed us to examine viral replication and RNAi-mediated antiviral responses in this organism. We show that viral infection upregulates the transcription of RNAi components, and that Dicer proteins (DCL-1, DCL-2) and an Argonaute (QDE-2) participate in suppression of viral replication. Our study thus establishes N. crassa as a model system for the study of host-virus interactions. 1 Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan. 2 Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan. 3 Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza- Aoba, Sendai 980-0845, Japan. ✉ email: [email protected] NATURE COMMUNICATIONS | (2020) 11:5627 | https://doi.org/10.1038/s41467-020-19355-y | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-19355-y ungal viruses or mycoviruses are omnipresent in all major mechanism in this fungus35.
    [Show full text]