Cloning and Rescue of the Genome of Bombyx Mori Bidensovirus, And
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Discovery and Molecular Characterisation of the First Ambidensovirus in Honey Bees
doi:10.14720/aas.2020.116.2.1832 Original research article / izvirni znanstveni članek Discovery and molecular characterisation of the first ambidensovirus in honey bees Sabina OTT RUTAR 1, Dušan KORDIŠ 1, 2 Received Avgust 13, 2020; accepted December 13, 2020. Delo je prispelo 13. avgusta 2020, sprejeto 13. decembra 2020 Discovery and molecular characterisation of the first am- Odkritje in molekularna karakterizacija prvega ambidenso- bidensovirus in honey bees virusa pri čebelah Abstract: Honey bees play a critical role in global food Izvleček: Čebele igrajo ključno vlogo v svetovni proizvo- production as pollinators of numerous crops. Several stressors dnji hrane kot opraševalci številnih poljščin. Številni stresorji cause declines in populations of managed and wild bee species, povzročajo upad populacij gojenih in divjih vrst čebel, kot so such as habitat degradation, pesticide exposure and patho- degradacija habitata, izpostavljenost pesticidom in patogeni. gens. Viruses act as key stressors and can infect a wide range of Virusi delujejo kot glavni stresorji in lahko okužijo številne species. The majority of honey bee-infecting viruses are RNA viruses of the Picornavirales order. Although some ssDNA vi- vrste. Večina virusov, ki okužijo čebele, so RNA virusi iz reda ruses are common in insects, such as densoviruses, they have Picornavirales. Čeprav so nekateri ssDNA virusi pogosti pri not yet been found in honey bees. Densoviruses were however žuželkah, na primer densovirusi, jih pri čebelah doslej še niso found in bumblebees and ants. Here, we show that densoviruses našli. Densovirusi pa so bili najdeni pri čmrljih in mravljah. Po- are indeed present in the transcriptome of the eastern honey kazali smo, da so densovirusi prisotni v transkriptomu azijskih bee (Apis cerana) from southern China. -
ICTV Virus Taxonomy Profile: Parvoviridae
ICTV VIRUS TAXONOMY PROFILES Cotmore et al., Journal of General Virology 2019;100:367–368 DOI 10.1099/jgv.0.001212 ICTV ICTV Virus Taxonomy Profile: Parvoviridae Susan F. Cotmore,1,* Mavis Agbandje-McKenna,2 Marta Canuti,3 John A. Chiorini,4 Anna-Maria Eis-Hubinger,5 Joseph Hughes,6 Mario Mietzsch,2 Sejal Modha,6 Mylene Ogliastro,7 Judit J. Penzes, 2 David J. Pintel,8 Jianming Qiu,9 Maria Soderlund-Venermo,10 Peter Tattersall,1,11 Peter Tijssen12 and ICTV Report Consortium Abstract Members of the family Parvoviridae are small, resilient, non-enveloped viruses with linear, single-stranded DNA genomes of 4–6 kb. Viruses in two subfamilies, the Parvovirinae and Densovirinae, are distinguished primarily by their respective ability to infect vertebrates (including humans) versus invertebrates. Being genetically limited, most parvoviruses require actively dividing host cells and are host and/or tissue specific. Some cause diseases, which range from subclinical to lethal. A few require co-infection with helper viruses from other families. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the Parvoviridae, which is available at www.ictv.global/report/parvoviridae. Table 1. Characteristics of the family Parvoviridae Typical member: human parvovirus B19-J35 G1 (AY386330), species Primate erythroparvovirus 1, genus Erythroparvovirus, subfamily Parvovirinae Virion Small, non-enveloped, T=1 icosahedra, 23–28 nm in diameter Genome Linear, single-stranded DNA of 4–6 kb with short terminal hairpins Replication Rolling hairpin replication, a linear adaptation of rolling circle replication. Dynamic hairpin telomeres prime complementary strand and duplex strand-displacement synthesis; high mutation and recombination rates Translation Capped mRNAs; co-linear ORFs accessed by alternative splicing, non-consensus initiation or leaky scanning Host range Parvovirinae: mammals, birds, reptiles. -
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
viruses Article Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics Ashleigh F. Porter 1, Mang Shi 1, John-Sebastian Eden 1,2 , Yong-Zhen Zhang 3,4 and Edward C. Holmes 1,3,* 1 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (A.F.P.); [email protected] (M.S.); [email protected] (J.-S.E.) 2 Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia 3 Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 201500, China; [email protected] 4 Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China * Correspondence: [email protected]; Tel.: +61-2-9351-5591 Received: 17 October 2019; Accepted: 23 November 2019; Published: 25 November 2019 Abstract: DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. -
The Discovery, Distribution and Diversity of DNA Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.16.342956; this version posted March 17, 2021. 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. Title: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe Running title: DNA viruses of European Drosophila Key Words: DNA virus, Endogenous viral element, Drosophila, Nudivirus, Galbut virus, Filamentous virus, Adintovirus, Densovirus, Bidnavirus Authors: Megan A. Wallace 1,2 [email protected] 0000-0001-5367-420X Kelsey A. Coffman 3 [email protected] 0000-0002-7609-6286 Clément Gilbert 1,4 [email protected] 0000-0002-2131-7467 Sanjana Ravindran 2 [email protected] 0000-0003-0996-0262 Gregory F. Albery 5 [email protected] 0000-0001-6260-2662 Jessica Abbott 1,6 [email protected] 0000-0002-8743-2089 Eliza Argyridou 1,7 [email protected] 0000-0002-6890-4642 Paola Bellosta 1,8,9 [email protected] 0000-0003-1913-5661 Andrea J. Betancourt 1,10 [email protected] 0000-0001-9351-1413 Hervé Colinet 1,11 [email protected] 0000-0002-8806-3107 Katarina Eric 1,12 [email protected] 0000-0002-3456-2576 Amanda Glaser-Schmitt 1,7 [email protected] 0000-0002-1322-1000 Sonja Grath 1,7 [email protected] 0000-0003-3621-736X Mihailo Jelic 1,13 [email protected] 0000-0002-1637-0933 Maaria Kankare 1,14 [email protected] 0000-0003-1541-9050 Iryna Kozeretska 1,15 [email protected] 0000-0002-6485-1408 Volker Loeschcke 1,16 [email protected] 0000-0003-1450-0754 Catherine Montchamp-Moreau 1,4 [email protected] 0000-0002-5044-9709 Lino Ometto 1,17 [email protected] 0000-0002-2679-625X Banu Sebnem Onder 1,18 [email protected] 0000-0002-3003-248X Dorcas J. -
The Discovery, Distribution and Diversity of DNA Viruses Associated with Drosophila Melanogaster in Europe Authors: Megan A
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.16.342956; this version posted October 16, 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. DNA viruses of European Drosophila The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe Authors: Megan A. Wallace 1,2 [email protected] 0000-0001-5367-420X Kelsey A. Coffman 3 [email protected] 0000-0002-7609-6286 Clément Gilbert 1,4 [email protected] 0000-0002-2131-7467 Sanjana Ravindran 2 [email protected] 0000-0003-0996-0262 Gregory F. Albery 5 [email protected] 0000-0001-6260-2662 Jessica Abbott 1,6 [email protected] 0000-0002-8743-2089 Eliza Argyridou 1,7 [email protected] 0000-0002-6890-4642 Paola Bellosta 1,8,9 [email protected] 0000-0003-1913-5661 Andrea J. Betancourt 1,10 [email protected] 0000-0001-9351-1413 Hervé Colinet 1,11 [email protected] 0000-0002-8806-3107 Katarina Eric 1,12 [email protected] 0000-0002-3456-2576 Amanda Glaser-Schmitt 1,7 [email protected] 0000-0002-1322-1000 Sonja Grath 1,7 [email protected] 0000-0003-3621-736X Mihailo Jelic 1,13 [email protected] 0000-0002-1637-0933 Maaria Kankare 1,14 [email protected] 0000-0003-1541-9050 Iryna Kozeretska 1,15 [email protected] 0000-0002-6485-1408 Volker Loeschcke 1,16 [email protected] 0000-0003-1450-0754 Catherine Montchamp-Moreau 1,4 [email protected] 0000-0002-5044-9709 Lino Ometto 1,17 [email protected] 0000-0002-2679-625X Banu Sebnem Onder 1,18 [email protected] 0000-0002-3003-248X Dorcas J. -
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 -
Culex Virome V34
Page 1 of 31 Virome of >12 thousand Culex mosquitoes from throughout California Mohammadreza Sadeghi1,2,3; Eda Altan1,2; Xutao Deng12; Christopher M. Barker4, Ying Fang4, Lark L Coffey4; Eric Delwart1,2 1Blood Systems Research Institute, San Francisco, CA, USA. 2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. 3Department of Virology, University of Turku, Turku, Finland. 4Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA. §Reprints or correspondence: Eric Delwart 270 Masonic Ave. San Francisco, CA 94118 Phone: (415) 923-5763 Fax: (415) 276-2311 Email: [email protected] Page 2 of 31 Abstract Metagenomic analysis of mosquitoes allows the genetic characterization of all associated viruses, including arboviruses and insect-specific viruses, plus those in their diet or infecting their parasites. We describe here the virome in mosquitoes, primarily Culex pipiens complex, Cx. tarsalis and Cx. erythrothorax, collected in 2016 from 23 counties in California, USA. The nearly complete genomes of 54 different virus species, including 28 novel species and some from potentially novel RNA and DNA viral families and genera, were assembled and phylogenetically analyzed, significantly expanding the known Culex-associated virome. The majority of detected viral sequences originated from single-stranded RNA viral families with members known to infect insects, plants, or unknown hosts. These reference viral genomes will facilitate the identification of related viruses in other insect species and to monitor changes in the virome of Culex mosquito populations to define factors influencing their transmission and possible impact on their insect hosts. Page 3 of 31 Introduction Mosquitoes transmit numerous arboviruses, many of which result in significant morbidity and/or mortality in humans and animals (Ansari and Shope, 1994; Driggers et al., 2016; Gan and Leo, 2014; Reimann et al., 2008; Weaver and Vasilakis, 2009). -
Downloaded and De Novo Assembled Using CLC
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.11.245274; this version posted August 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Ever-increasing viral diversity associated with the red imported fire ant Solenopsis invicta 2 (Formicidae: Hymenoptera) 3 4 César A.D. Xavier1, Margaret L. Allen2*, and Anna E. Whitfield1* 5 6 1Department of Entomology and Plant Pathology, North Carolina State University, 840 Main Campus 7 Drive, Raleigh, NC 27606, USA 8 2U. S. Department of Agriculture, Agricultural Research Service, Biological Control of Pests Research 9 Unit, 59 Lee Road, Stoneville, MS 38776, USA 10 *Corresponding author: Margaret L. Allen 11 Phone: 1(662) 686-3647 12 E-mail: [email protected] 13 *Corresponding author: Anna E. Whitfield 14 Phone: 1(919) 515-5861 15 E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.11.245274; this version posted August 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 16 Abstract 17 Background: Advances in sequencing and analysis tools have facilitated discovery of many new 18 viruses from invertebrates, including ants. Solenopsis invicta is an invasive ant that has quickly 19 spread around world causing significant ecological and economic impacts. Its virome has begun 20 to be characterized pertaining to potential use of viruses as natural enemies. Although the S. invicta 21 virome is best characterized among ants, most studies have been performed in its native range, 22 with little information from invaded areas. -
Molecular Biology and Structure of a Novel Penaeid Shrimp Densovirus Elucidate Convergent Parvoviral Host Capsid Evolution
Molecular biology and structure of a novel penaeid shrimp densovirus elucidate convergent parvoviral host capsid evolution Judit J. Pénzesa,b, Hanh T. Phama, Paul Chipmanb, Nilakshee Bhattacharyac, Robert McKennab, Mavis Agbandje-McKennab,1,2, and Peter Tijssena,1,2 aInstitut Armand-Frappier, Institut national de la recherche scientifique-Institut Armand-Frappier, Laval, QC H7V 1B7, Canada; bThe McKnight Brain Institute, University of Florida, Gainesville, FL 32610; and cInstitute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 Edited by Kenneth I. Berns, University of Florida College of Medicine, Gainesville, FL, and approved July 8, 2020 (received for review April 27, 2020) The giant tiger prawn (Penaeus monodon) is a decapod crustacean isolated from both proto- and deuterostome invertebrates, mostly widely reared for human consumption. Currently, viruses of two insects and other arthropods (6–18). distinct lineages of parvoviruses (PVs, family Parvoviridae; subfamily To date, parvovirus crustacean pathogens comprise three Hamaparvovirinae) infect penaeid shrimp. Here, a PV was isolated distinct lineages with divergent genome organizations and tran- and cloned from Vietnamese P. monodon specimens, designated scription patterns. Cherax quadricarinatus DV, isolated from the Penaeus monodon metallodensovirus (PmMDV). This is the first freshwater red-clawed crayfish (Cherax quadricarinatus), has an member of a third divergent lineage shown to infect penaeid ambisense genome with a PLA2 domain and is now an assigned decapods. PmMDV has a transcription strategy unique among in- member of genus Aquambidensovirus of the Densovirinae (19). vertebrate PVs, using extensive alternative splicing and incorpo- Genera Hepanhamaparvovirus and Penstylhamaparvovirus are rating transcription elements characteristic of vertebrate-infecting members of subfamily Hamaparvovirinae, each with one species PVs. -
Multipartite Viruses: Organization, Emergence and Evolution
UNIVERSIDAD AUTÓNOMA DE MADRID FACULTAD DE CIENCIAS DEPARTAMENTO DE BIOLOGÍA MOLECULAR MULTIPARTITE VIRUSES: ORGANIZATION, EMERGENCE AND EVOLUTION TESIS DOCTORAL Adriana Lucía Sanz García Madrid, 2019 MULTIPARTITE VIRUSES Organization, emergence and evolution TESIS DOCTORAL Memoria presentada por Adriana Luc´ıa Sanz Garc´ıa Licenciada en Bioqu´ımica por la Universidad Autonoma´ de Madrid Supervisada por Dra. Susanna Manrubia Cuevas Centro Nacional de Biotecnolog´ıa (CSIC) Memoria presentada para optar al grado de Doctor en Biociencias Moleculares Facultad de Ciencias Departamento de Biolog´ıa Molecular Universidad Autonoma´ de Madrid Madrid, 2019 Tesis doctoral Multipartite viruses: Organization, emergence and evolution, 2019, Madrid, Espana. Memoria presentada por Adriana Luc´ıa-Sanz, licenciada en Bioqumica´ y con un master´ en Biof´ısica en la Universidad Autonoma´ de Madrid para optar al grado de doctor en Biociencias Moleculares del departamento de Biolog´ıa Molecular en la facultad de Ciencias de la Universidad Autonoma´ de Madrid Supervisora de tesis: Dr. Susanna Manrubia Cuevas. Investigadora Cient´ıfica en el Centro Nacional de Biotecnolog´ıa (CSIC), C/ Darwin 3, 28049 Madrid, Espana. to the reader CONTENTS Acknowledgments xi Resumen xiii Abstract xv Introduction xvii I.1 What is a virus? xvii I.2 What is a multipartite virus? xix I.3 The multipartite lifecycle xx I.4 Overview of this thesis xxv PART I OBJECTIVES PART II METHODOLOGY 0.5 Database management for constructing the multipartite and segmented datasets 3 0.6 Analytical -
Insights Into the Antiviral Pathways of the Silkworm Bombyx Mori
MINI REVIEW published: 11 February 2021 doi: 10.3389/fimmu.2021.639092 Insights Into the Antiviral Pathways of the Silkworm Bombyx mori Liang Jiang 1,2* 1 State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China, 2 Biological Science Research Center, Southwest University, Chongqing, China The lepidopteran model silkworm, Bombyx mori, is an important economic insect. Viruses cause serious economic losses in sericulture; thus, the economic importance of these viruses heightens the need to understand the antiviral pathways of silkworm to develop antiviral strategies. Insect innate immunity pathways play a critical role in the outcome of infection. The RNA interference (RNAi), NF-kB-mediated, immune deficiency (Imd), and stimulator of interferon gene (STING) pathways, and Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway are the major antiviral defense mechanisms, and these have been shown to play important roles in the antiviral immunity of silkworms. In contrast, viruses can modulate the prophenol oxidase (PPO), phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt), and the extracellular signal-regulated kinase (ERK) signaling pathways of the host to elevate their proliferation in silkworms. In this review, we present an overview of the current understanding of the main immune pathways in response to viruses and the signaling pathways modulated by Edited by: viruses in silkworms. Elucidation of these pathways involved in the antiviral mechanism Jun-ichi Hikima, University of Miyazaki, Japan of silkworms furnishes a theoretical basis for the enhancement of virus resistance in Reviewed by: economic insects, such as upregulating antiviral immune pathways through transgenic Hiroshi Hamamoto, overexpression, RNAi of virus genes, and targeting these virus-modulated pathways by Teikyo University, Japan gene editing or inhibitors. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID- 19 Pandemic: A
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. March 2021 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Raphael Freitas de Souza, Faculty of Dentistry, McGill University Paul Allison, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University March 31, 2021 1 Contents 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. .................................................................................................................................. 1 Foreword to the second update ............................................................................................. 4 Introduction ............................................................................................................................. 5 Project goal............................................................................................................................. 5 Specific objectives .................................................................................................................. 6 Methods used to identify and include relevant literature ......................................................