DOCSLIB.ORG

Supplementary Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Electronic Supplementary Material (ESI) for Molecular BioSystems. This journal is © The Royal Society of Chemistry 2014 Supplementary Information Supplementary table S1- Hu-PPI and Hu-Vir PPI data before and after the removal of ambiguous and redundant protein identifiers (those with identities >98% and ±20 of protein length in BLAST searches). ‘*’ strains not merged and ‘**’ strains merged. Identity cut off DATA Interactions Interactions after Proteins in BLAST before BLAST BLAST (no. of proteins involved) 98% Hu-PPI 49879 49772 10446 (10658) 98% Hu-Vir PPI 12649 12623 1735 – Human (human (1754 human 763 – Viral proteins) +763 viral) 98% Hu-Vir PPI 12623 9732* 1735 – Human (viral proteins) (1735 human + 518 – Viral 763 viral) 30% Hu-Vir PPI 12623 3389** 1735 – Human (viral proteins) (1735 human 267** – Viral +763 viral) Supplementary table S2 - Salient features of viruses used in the study. This table gives number of proteins encoded by virus, number of Hu-Vir PPI for that virus, virus host or disease caused, site and type of infection caused by virus and virus classification. Virus No. of No. of Virus host /disease Site and type of infection Classification ORFs or Hu- protein Vir encode PPI by virus Adeno associated 7 2 no known disease found in semen ssDNA, virus 2 Parvoviridae Autographa californica 156 1 insect virus coelum dsDNA, nuclear polyhedrosis Baculoviridae virus Avian sarcoma virus NA 2 Bird lymphoma and connective tissue, ssRNA-RT, mammals lymphatic tissue Retroviridae Bovine herpes virus 1 70 1 cattle rhinotracheitis, vaginitis, dsDNA, conjunctivitis Herpesviridae Bovine leukemia virus 6 7 cattle B-cell leukemia ssRNA-RT, Retroviridae Bovine papilloma 8 28 cattle skin, bladder cancer dsDNA, virus 1 Papillomaviridae Bovine papilloma 9 1 cattle skin, bladder cancer dsDNA, virus 2 Papillomaviridae Bovine Rotavirus NA 1 cattle diarrhoea intestinal tract dsRNA, Reoviridae Chicken anemia virus 4 1 birds bone marrow atrophy ssDNA, Circoviridae Cotton tail rabbit 10 5 rabbit skin, bladder cancer dsDNA, papilloma virus Papillomaviridae Dengue virus 7 140 humans, dengue hemorrhagic, fever, (+)ssRNA, fever diarrhoea Flaviviridae Epstein barr virus 94 315 humans, cancer, B-cells and epithelial cells dsDNA, Burkitt's lymphoma Herpesviridae Equine herpes virus 1 NA 1 horse, pneumonia pneumonia, paralysis dsDNA, Herpesviridae Equine herpes virus 4 NA 2 horse conjuctivitis, swollen dsDNA, lymph nodes Herpesviridae Equine infectious 4 1 horse, anemia and break down of blood cells ssRNA-RT, anemia virus fever Retroviridae Foamy virus NA 1 humans, simians, lymhoblastoid, carcinoma ssRNA-RT, camcer Retroviridae Fowl adenovirus A 39 2 fowl, infection respiratory dsDNA, Adenoviridae Hantaan virus 1 4 human, blood vessels, kidney, (-)ssRNA, hemorrhagic fever lungs, liver Bunyaviridae Hepatitis B virus 7 27 humans, hepatitis B liver and pancreas cancer, dsDNA-RT, cirrhosis Hepadnaviridae Hepatitis C virus 2 91 humans, hepatitis C hepatocytes (+)ssRNA, Flaviviridae Hepatitis D virus 2 2 humans, alongwith liver and pancreas cancer, (-)ssRNA, hepatitis B cirrhosis unassigned Hepatitis E virus 10 2 humans, hepatitis E liver (+)ssRNA, Hepeviridae Human adenovirus A 36 19 human, infection respiratory dsDNA, Adenoviridae Human adenovirus B 38 4 human, infection respiratory dsDNA, Adenoviridae Human adenovirus C 38 62 human, infection respiratory dsDNA, Adenoviridae Human adenovirus D 38 1 human, infection respiratory dsDNA, Adenoviridae Human adenovirus E 38 3 human, infection respiratory dsDNA, Adenoviridae Human adenovirus F 34 1 human, infection respiratory dsDNA, Adenoviridae Human entero virus B, 1 1 humans, menigitis brain, meingitis (+)ssRNA, Echovirus Picornaviridae Human herpes virus 3 73 1 humans, mucoepithelial, skin and dsDNA, chickenpox and nerve cells Herpesviridae shingles Human herpes virus 1 77 76 humans, oral and mucoepithelial and nerve dsDNA, genital herpes cells Herpesviridae Human herpes virus 2 77 4 humans, oral and mucoepithelial and nerve dsDNA, genital herpes cells Herpesviridae Human herpes virus 165 6 humans, infectious Monocyte, lymphocyte, dsDNA, 5(cytomegalovirus) mononucleosis-like and epithelial cells Herpesviridae syndrome Human herpes virus 6 104 2 humans, sixth T-cells dsDNA, disease or rose rash Herpesviridae disease Human 15 1399 humans, T-cells SsRNA-RT, immunodeficiency AIDS(global) Retroviridae virus 1 Human 9 85 humans, T-cells ssRNA-RT, immunodeficiency AIDS(west Africa) Retroviridae virus 2 Human Papilloma 9 115 humans, cervical keratinocytes and epithelial dsDNA, virus High risk cancer and warts cells Papillomaviridae Human papilloma 9 53 humans, cervical keratinocytes and epithelial dsDNA, virus type Low Risk cancer and warts cells Papillomaviridae Human T-lymphocytic 6 232 humans, HTLV T-cells, B-cells and ssRNA-RT, virus 1 myelopathy, dendritic cells Retroviridae leukemia Human T-lymphocytic 6 75 humans, HTLV T-cells, B-cells and ssRNA-RT, virus 2 myelopathy dendritic cells Retroviridae Influenza A virus 9 293 humans, Influenza bronchial epithelial cells (-)ssRNA, H1N1 Orthomyxoviridae Influenza A virus 9 2 humans, Influenza bronchial epithelial cells (-)ssRNA, H3N2 Orthomyxoviridae Influenza A virus 9 1 humans, Influenza bronchial epithelial cells (-)ssRNA, H7N3 Orthomyxoviridae JC polyomavirus 6 3 humans, tonsils, gastrointestinal dsDNA, progressive tract, nervous tissue Polyomaviridae multifocal leukoencephalopath y Kaposi sarcoma 2 10 humans, kaposi Lymphocyte dsDNA, associated herpes virus sarcoma Herpesviridae Measles virus 7 6 humans, measles respiratory tract (-)ssRNA, Paramyxoviridae Mokola virus 5 1 humans and nervous system (-)ssRNA, animals, Rhabdoviridae encephalitis Murine adenovirus 26 1 mice, acute CNS hemorrhage in brain and dsDNA, disease spinal cord Adenoviridae Murine herpes virus 4 74 2 mice, infection nasal passages dsDNA, Herpesviridae Murine polyoma virus 6 5 mice, leukemia gangliosides dsDNA, Polyomaviridae Nipah virus 8 1 humans and respiratory and nervous (-)ssRNA, mammals, infection system Paramyxoviridae Orf virus 130 1 sheep and humans, skin dsDNA, Poxvidae sheep pox Papiine herpes virus 75 4 baboon, infection neuro-virulent dsDNA, Herpesviridae Para influenza virus 9 2 humans, Croup respiratory tract (-)ssRNA, Paramyxoviridae Polio virus 1 2 humans, nervous system (+)ssRNA, poliomyelitis Picornaviridae Puumala virus 1 2 human, hemorrhagic fever with (-)ssRNA, hemorrhagic fever renal syndrome Bunyaviridae Rabies virus 5 1 humans and dogs, Nervous system (-)ssRNA, Rabies Rhabdoviridae Rous sarcoma virus 4 9 chicken, sarcoma connective tissue ssRNA-RT, Retroviridae Saimiriine herpesvirus 76 6 sqirrel monkeys, skin and epithelial cells dsDNA, 2 humans in Herpesviridae laboratory SARS 14 4 humans, SARS respiratory tract (+)ssRNA, Coronaviridae Sendai virus 9 1 mammals, infection respiratory tract and lungs (-)ssRNA, Paramyxoviridae Seoul virus NA 3 humans hemorrhagic fever (-)ssRNA, Bunyaviridae Simian 7 2 primates, related to T-cell ssRNA-RT, immunodeficiency HIV Retroviridae virus Simian rotavirus NA 2 primates, diarrhoea gut and intestine dsRNA, Reoviridae Simian virus 40 7 46 primates, latent vacuolating dsDNA, infection Polyomaviridae Stomatitis virus 5 2 mammals(infection cytolytic (-)ssRNA, ), Rhabdoviridae humans(oncolytic) Tula virus 1 1 humans, fever NA (-)ssRNA, Bunyaviridae Vaccinia virus 223 198 humans, smallpox skin dsDNA, Poxvidae vaccine West nile virus 1 1 mammals, nervous system and (+)ssRNA, meningitis and lymphatic tisse Flaviviridae encephalitis Zaire ebolavirus 9 1 humans, endothelial lining and (-)ssRNA, hemorrhage blood vessels Filoviridae Supplementary Figure S1- Venn diagram showing distribution of human proteins in Hu-PPI and Hu-Vir PPI data Supplementary Figure S2 – Gene Ontology (GO) molecular function enrichment for peripheral proteins in Hu-PPI network (a) and 176 human proteins interacting with viruses but not part of Hu-PPI network (b). Supplementary Figure S3 – Gene Ontology (GO) biological process enrichment for peripheral proteins in Hu-PPI network (a) and 176 human proteins interacting with viruses but not part of Hu-PPI network(b). Supplementary Figure S4 – Gene Ontology (GO) cellular component enrichment for peripheral proteins in Hu-PPI network (a) and 176 human proteins interacting with viruses but not part of Hu-PPI network (b)..
Recommended publications
  • Survival of Human Norovirus Surrogates in Juices and Their Inactivation Using Novel Methods

    Survival of Human Norovirus Surrogates in Juices and Their Inactivation Using Novel Methods

    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 5-2011 Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods Katie Marie Horm [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Recommended Citation Horm, Katie Marie, "Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods. " Master's Thesis, University of Tennessee, 2011. https://trace.tennessee.edu/utk_gradthes/882 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Katie Marie Horm entitled "Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Master of Science, with a major in Food Science and Technology. Doris H. D'Souza, Major Professor We have read this thesis and recommend its acceptance: Federico M. Harte, Gina M. Pighetti Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods A Thesis Presented for the Master of Science Degree The University of Tennessee, Knoxville Katie Marie Horm May 2011 Acknowledgments I would like to think my major professor/advisor Dr.
  • Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats

    Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats

    viruses Article Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats Laura M. Bergner 1,2,* , Nardus Mollentze 1,2 , Richard J. Orton 2 , Carlos Tello 3,4, Alice Broos 2, Roman Biek 1 and Daniel G. Streicker 1,2 1 Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; [email protected] (N.M.); [email protected] (R.B.); [email protected] (D.G.S.) 2 MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; [email protected] (R.J.O.); [email protected] (A.B.) 3 Association for the Conservation and Development of Natural Resources, Lima 15037, Peru; [email protected] 4 Yunkawasi, Lima 15049, Peru * Correspondence: [email protected] Abstract: The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely Citation: Bergner, L.M.; Mollentze, applied to viruses at the time of their discovery. Here, we characterized viral genomes detected N.; Orton, R.J.; Tello, C.; Broos, A.; through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) Biek, R.; Streicker, D.G. and used these data as a case study in evaluating zoonotic potential using molecular sequencing Characterizing and Evaluating the data.
  • Opportunistic Intruders: How Viruses Orchestrate ER Functions to Infect Cells

    Opportunistic Intruders: How Viruses Orchestrate ER Functions to Infect Cells

    REVIEWS Opportunistic intruders: how viruses orchestrate ER functions to infect cells Madhu Sudhan Ravindran*, Parikshit Bagchi*, Corey Nathaniel Cunningham and Billy Tsai Abstract | Viruses subvert the functions of their host cells to replicate and form new viral progeny. The endoplasmic reticulum (ER) has been identified as a central organelle that governs the intracellular interplay between viruses and hosts. In this Review, we analyse how viruses from vastly different families converge on this unique intracellular organelle during infection, co‑opting some of the endogenous functions of the ER to promote distinct steps of the viral life cycle from entry and replication to assembly and egress. The ER can act as the common denominator during infection for diverse virus families, thereby providing a shared principle that underlies the apparent complexity of relationships between viruses and host cells. As a plethora of information illuminating the molecular and cellular basis of virus–ER interactions has become available, these insights may lead to the development of crucial therapeutic agents. Morphogenesis Viruses have evolved sophisticated strategies to establish The ER is a membranous system consisting of the The process by which a virus infection. Some viruses bind to cellular receptors and outer nuclear envelope that is contiguous with an intri‑ particle changes its shape and initiate entry, whereas others hijack cellular factors that cate network of tubules and sheets1, which are shaped by structure. disassemble the virus particle to facilitate entry. After resident factors in the ER2–4. The morphology of the ER SEC61 translocation delivering the viral genetic material into the host cell and is highly dynamic and experiences constant structural channel the translation of the viral genes, the resulting proteins rearrangements, enabling the ER to carry out a myriad An endoplasmic reticulum either become part of a new virus particle (or particles) of functions5.
  • Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris Spelaea)

    Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris Spelaea)

    viruses Article Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris spelaea) Ian H Mendenhall 1,* , Dolyce Low Hong Wen 1,2, Jayanthi Jayakumar 1, Vithiagaran Gunalan 3, Linfa Wang 1 , Sebastian Mauer-Stroh 3,4 , Yvonne C.F. Su 1 and Gavin J.D. Smith 1,5,6 1 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; [email protected] (D.L.H.W.); [email protected] (J.J.); [email protected] (L.W.); [email protected] (Y.C.F.S.) [email protected] (G.J.D.S.) 2 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore 3 Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore; [email protected] (V.G.); [email protected] (S.M.-S.) 4 Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore 5 SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore 6 Duke Global Health Institute, Duke University, Durham, NC 27710, USA * Correspondence: [email protected] Received: 30 January 2019; Accepted: 7 March 2019; Published: 12 March 2019 Abstract: Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission.
  • Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection?

    Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection?

    viruses Review Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection? Solène Grayo Institut Pasteur de Guinée, BP 4416 Conakry, Guinea; [email protected] or [email protected] Abstract: The emergence of the Zika virus (ZIKV) mirrors its evolutionary nature and, thus, its ability to grow in diversity or complexity (i.e., related to genome, host response, environment changes, tropism, and pathogenicity), leading to it recently joining the circle of closed congenital pathogens. The causal relation of ZIKV to microcephaly is still a much-debated issue. The identification of outbreak foci being in certain endemic urban areas characterized by a high-density population emphasizes that mixed infections might spearhead the recent appearance of a wide range of diseases that were initially attributed to ZIKV. Globally, such coinfections may have both positive and negative effects on viral replication, tropism, host response, and the viral genome. In other words, the possibility of coinfection may necessitate revisiting what is considered to be known regarding the pathogenesis and epidemiology of ZIKV diseases. ZIKV viral coinfections are already being reported with other arboviruses (e.g., chikungunya virus (CHIKV) and dengue virus (DENV)) as well as congenital pathogens (e.g., human immunodeficiency virus (HIV) and cytomegalovirus (HCMV)). However, descriptions of human latent viruses and their impacts on ZIKV disease outcomes in hosts are currently lacking. This review proposes to select some interesting human latent viruses (i.e., herpes simplex virus 2 (HSV-2), Epstein–Barr virus (EBV), human herpesvirus 6 (HHV-6), human parvovirus B19 (B19V), and human papillomavirus (HPV)), whose virological features and Citation: Grayo, S.
  • Cellular Entry and Uncoating of Naked and Quasi-Enveloped Human

    Cellular Entry and Uncoating of Naked and Quasi-Enveloped Human

    RESEARCH ARTICLE Cellular entry and uncoating of naked and quasi-enveloped human hepatoviruses Efraı´nE Rivera-Serrano1,2, Olga Gonza´ lez-Lo´ pez1,2, Anshuman Das2, Stanley M Lemon2,3* 1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 2Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 3Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, United States Abstract Many ‘non-enveloped’ viruses, including hepatitis A virus (HAV), are released non- lytically from infected cells as infectious, quasi-enveloped virions cloaked in host membranes. Quasi-enveloped HAV (eHAV) mediates stealthy cell-to-cell spread within the liver, whereas stable naked virions shed in feces are optimized for environmental transmission. eHAV lacks virus- encoded surface proteins, and how it enters cells is unknown. We show both virion types enter by clathrin- and dynamin-dependent endocytosis, facilitated by integrin b1, and traffic through early and late endosomes. Uncoating of naked virions occurs in late endosomes, whereas eHAV undergoes ALIX-dependent trafficking to lysosomes where the quasi-envelope is enzymatically degraded and uncoating ensues coincident with breaching of endolysosomal membranes. Neither virion requires PLA2G16, a phospholipase essential for entry of other picornaviruses. Thus naked and quasi-enveloped virions enter via similar endocytic pathways, but uncoat in different compartments and release their genomes to the cytosol in a manner mechanistically distinct from other Picornaviridae. DOI: https://doi.org/10.7554/eLife.43983.001 *For correspondence: [email protected] Competing interests: The Introduction authors declare that no The presence or absence of an external lipid envelope has featured strongly in the systematic classi- competing interests exist.
  • Origins and Evolution of the Global RNA Virome

    Origins and Evolution of the Global RNA Virome

    bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. 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 Origins and Evolution of the Global RNA Virome 2 Yuri I. Wolfa, Darius Kazlauskasb,c, Jaime Iranzoa, Adriana Lucía-Sanza,d, Jens H. 3 Kuhne, Mart Krupovicc, Valerian V. Doljaf,#, Eugene V. Koonina 4 aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA 5 b Vilniaus universitetas biotechnologijos institutas, Vilnius, Lithuania 6 c Département de Microbiologie, Institut Pasteur, Paris, France 7 dCentro Nacional de Biotecnología, Madrid, Spain 8 eIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious 9 Diseases, National Institutes of Health, Frederick, Maryland, USA 10 fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA 11 12 #Address correspondence to Valerian V. Dolja, [email protected] 13 14 Running title: Global RNA Virome 15 16 KEYWORDS 17 virus evolution, RNA virome, RNA-dependent RNA polymerase, phylogenomics, horizontal 18 virus transfer, virus classification, virus taxonomy 1 bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. 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. 19 ABSTRACT 20 Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in 21 animals and plants. The recent advances of metaviromics prompted us to perform a detailed 22 phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome.
  • Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements

    Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements

    Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280
  • Chronic Viral Infections Vs. Our Immune System: Revisiting Our View of Viruses As Pathogens

    Chronic Viral Infections Vs. Our Immune System: Revisiting Our View of Viruses As Pathogens

    Chronic Viral Infections vs. Our Immune System: Revisiting our view of viruses as pathogens Tiffany A. Reese Assistant Professor Departments of Immunology and Microbiology Challenge your idea of classic viral infection and disease • Define the microbiome and the virome • Brief background on persistent viruses • Illustrate how viruses change disease susceptibility – mutualistic symbiosis – gene + virus = disease phenotype – virome in immune responses Bacteria-centric view of the microbiome The microbiome defined Definition of microbiome – Merriam-Webster 1 :a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body 2 :the collective genomes of microorganisms inhabiting a particular environment and especially the human body Virome Ø Viral component of the microbiome Ø Includes both commensal and pathogenic viruses Ø Viruses that infect host cells Ø Virus-derived elements in host chromosomes Ø Viruses that infect other organisms in the body e.g. phage/bacteria Viruses are everywhere! • “intracellular parasites with nucleic acids that are capable of directing their own replication and are not cells” – Roossinck, Nature Reviews Microbiology 2011. • Viruses infect all living things. • We are constantly eating and breathing viruses from our environment • Only a small subset of viruses cause disease. • We even carry viral genomes as part of our own genetic material! Diverse viruses all over the body Adenoviridae Picornaviridae
  • High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

    High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

    Edinburgh Research Explorer High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage Citation for published version: Ng, TF, Marine, R, Wang, C, Simmonds, P, Kapusinszky, B, Bodhidatta, L, Oderinde, BS, Wommack, KE & Delwart, E 2012, 'High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage', Journal of Virology, vol. 86, no. 22, pp. 12161-12175. https://doi.org/10.1128/jvi.00869-12 Digital Object Identifier (DOI): 10.1128/jvi.00869-12 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Journal of Virology Publisher Rights Statement: Copyright © 2012, American Society for Microbiology. All Rights Reserved. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage Terry Fei Fan Ng,a,b Rachel Marine,c Chunlin Wang,d Peter Simmonds,e Beatrix Kapusinszky,a,b Ladaporn Bodhidatta,f Bamidele Soji Oderinde,g K.
  • First Insight Into the Viral Community of the Cnidarian Model Metaorganism Aiptasia Using RNA-Seq Data

    First Insight Into the Viral Community of the Cnidarian Model Metaorganism Aiptasia Using RNA-Seq Data

    First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data Jan D. Brüwer and Christian R. Voolstra Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia ABSTRACT Current research posits that all multicellular organisms live in symbioses with asso- ciated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes.
  • Ancient Recombination Events and the Origins of Hepatitis E Virus Andrew G

    Ancient Recombination Events and the Origins of Hepatitis E Virus Andrew G

    Kelly et al. BMC Evolutionary Biology (2016) 16:210 DOI 10.1186/s12862-016-0785-y RESEARCH ARTICLE Open Access Ancient recombination events and the origins of hepatitis E virus Andrew G. Kelly, Natalie E. Netzler and Peter A. White* Abstract Background: Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. Results: To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the “Alpha-like” super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the “Picorna-like” supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family.