DOCSLIB.ORG

1 Replication Strategies

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1 Replication Strategies Course in Virology Rotterdam 2018 VIRUSES IN DIFFERENT SHAPES AND FLAVORS REPLICATION STRATEGIES THE VIRAL LIFE CYCLE Raoul J. de Groot Division of Virology Faculty of Veterinary Medicine Utrecht University VIRUS CLASSIFICATION BALTIMORE CLASSIFICATION central phenomenon – de novo mRNA synthesis • HOST PLANT / ANIMAL / BACTERIUM • MORPHOLOGY NAKED OR ENVELOPED SPHERICAL OR FILAMENTOUS VII NUCLEOCAPID: HELICAL OR ICOSAHEDRAL • GENOME DNA OR RNA SINGLE OR DOUBLE STRANDED LINEAR OR CIRCULAR SEGMENTED OR NON-SEGMENTED • REPLICATION ‘BALTIMORE’ CLASSIFICATION STRATEGY REPLICATION IN EUKARYOTIC CELLS A DIVERSITY OF VIRUSES a variety of replication sites ONE GENERAL REPLICATION SCHEME • ALL VIRUSES PACKAGE THEIR GENOME INSIDE A PARTICLE THAT MEDIATES TRANSMISSION FROM HOST TO HOST • THE VIRAL GENOME CONTAINS THE INFORMATION FOR INITIATING AND COMPLETING AN INFECTIOUS CYCLE WITHIN A HOST CELL 1 THE VIRAL LIFE CYCLE ENTRY the six steps… • Attachment • Penetration • Uncoating FIRST CONTACT: ADSORPTION ENTRY REQUIRES BREACHING OF THE PLASMA MEMBRANE IN ORDER TO INTRODUCE THE VIRAL GENOME IN THE CYTOPLASM • virions equiped with metastable proteins • enveloped viruses: fusion proteins SARS coronavirus: ACE2 MERS coronavirus: DPP4 • naked viruses: pore-forming proteins Influenza virus: sialic acid • membrane fusion/pore formation requires conformational changes in virion (proteins) • triggered by the appropriate cue CELL CORTEX HOW TO OVERCOME THE CELL CORTEX? • plasma membrane-associated cytoskeleton • gel-like mesh of actin filaments, at the perimeter of the cell • mechanical strength – cell surface movement • a barrier to virus entry Sleeping Beauty – Hedge of Thorns Julius Diez (~1900) 2 A VARIETY OF ENDOCYTIC PATHWAYS ENTRY VIA ENDOCYTOSIS: SEMLIKI FOREST VIRUS TO ENTER CELLS Lopez, S. & Arias, C. (2010) How Viruses Hijack Endocytic Machinery. Nature Education Parton, R. G. & Simons, K. (2007) The multiple faces of caveolae. Nature Reviews Molecular Cell Biology ENVELOPED VIRUSES: ROUTES OF ENTRY HERPESVIRUSES – BI-DIRECTIONAL TRAFFICKING OF CAPSIDS ALONG UNIPOLAR AXONAL MICROTUBULES Scale drawing of an herpesvirus capsid, transported along a microtubule by dynein motors ENTRY The Viral Life Cycle ATTACHMENT – PENETRATION - UNCOATING • transport along microtubular network • delivery of virions in endosomes and subviral particles deep in the interior of the cell, in the perinuclear region • optimal site for virus replication • triggering of fusion proteins to induce escape from endosome (cues: a.o. low pH, proteolytic cleaveage) 3 VIRAL REPLICATION….. BALTIMORE CLASSIFICATION True DNA viruses: replication via DNA intermediates Parvoviridae Retroviridae Hepadnaviridae • Transcription VII • Translation Herpesviridae • Genome replication Reoviridae Coronaviridae Picornaviridae Togaviridae Orthomyxoviridae Paramyxoviridae Rhabdoviridae VIRAL REPLICATION….. BALTIMORE CLASSIFICATION true RNA viruses: replication via RNA intermediates Parvoviridae • Most DNA viruses replicate in the nucleus Retroviridae Hepadnaviridae VII exception: poxviruses (cytoplasm) Herpesviridae • Most DNA viruses possess a ds genome exception: parvovirus (linear single strand) Reoviridae Coronaviridae Picornaviridae Togaviridae Orthomyxoviridae Paramyxoviridae Rhabdoviridae RNA VIRUSES: GENOME POLARITY • Positive strand viruses: genome is mRNA sense: can be translated • Negative strand viruses: genome is anti-sense: cannot be translated genome non-infectious – RdRp in virion • Ambisense genome: contains genes in both orientations 4 BALTIMORE CLASSIFICATION retroviruses: replication via DNA intermediates Parvoviridae Retroviridae Hepadnaviridae VII Herpesviridae Reoviridae Coronaviridae Picornaviridae Togaviridae Orthomyxoviridae Paramyxoviridae Rhabdoviridae Retroviridae Subfamily Characteristic members Oncovirinae Oncogenic viruses Genera Oncornavirus B Leukemia virus Rous Sarcoma virus Oncornavirus C Mouse mammary Tumor virus Mason-Pfizer Monkey virus Oncornavirus D Lentivirinae Human Immuno deficiency virus Feline Immuno deficiency virus Visna virus The HIV-1 capsid pore is strongly electropositive and recruits dNTPs with rapid association and dissociation kinetics D A Jacques et al. Nature 1–5 (2016) doi:10.1038/nature19098 5 VIRAL GENES AND GENE EXPRESSION Two types of proteins: Structural and non-structural ARE REPLICATION ENZYMES NON-STRUCTURAL PER SE? structural proteins end up in the virion non-structural proteins: replication enzymes accessory proteins VIRAL GENES AND GENE EXPRESSION VIRAL GENES AND GENE EXPRESSION Two types of proteins: Essential and non-essential Viral genes are expressed to produce either: • Essential proteins: absolutely required • Individual proteins (1 mRNA, 1 protein) for replication in tissue culture cells replication enzymes • Polyproteins virion proteins processing by viral and/or host proteinases • Non-essential proteins: dispensible in vitro accessory proteins SYNTHESIS AND PROTEOLYTIC PROCESSING OF THE POLIOVIRUS POLYPROTEIN VIRAL REPLICATION TYPICALLY OCCURS IN MEMBRANOUS VIRUS-INDUCED COMPARTMENTS “VIRAL FACTORIES” 6 3D-ANALYSIS OF FLOCK-HOUSE VIRUS RNA CORONAVIRUS RNA SYNTHESIS ASSOCIATED REPLICATION COMPLEX REVEALS WITH ER-DERIVED DOUBLE MEMBRANE VESICLES A VIRUS-INDUCED MINI-ORGANELLE Kopek et al. (2007) PLOS Biol. Knoops et al. (2008) PLOS Biol. TWO TYPES OF VIRAL FACTORIES? VIRAL FACTORIES: ALSO SITES OF VIRION ASSEMBLY Flock-house virus Poliovirus Rubella virus SARS coronavirus Potato virus X virion “cages” encasing the X-body. Dengue virus Hepatitis C virus Linnik et al. (2013) Front. Plant Sci. Paul and Bartenschlager (2013) Unraveling the structure of viral replication complexes at super-resolution World J. Virol. The Viral Life Cycle VIRAL ASSEMBLY.... • production of virions • naked viruses: assembly in cytoplasms release through cell lysis 7 VIRAL ASSEMBLY.... • production of virions • enveloped viruses: budding release from intact cells BUDDING • stage of virus assembly during which the membrane is acquired • wrapping of NC in a cellular membrane, modified by virus-specific envelope proteins 8 Budding Retroviruses Fission - Maturation Viruses may differ in the location of the budding site REPLICATION STRATEGIES THE VIRAL LIFE CYCLE • insight into the diversity of viruses and their replication strategies • classification of viruses • six steps of the viral life cycle • general impression of the processes that occur during each of these steps 9.
Load more

Recommended publications
  • 10.2.2 Nomenclature of Viruses and Taxonomic Groups Bacterial Viruses Such As T1, T2 and Φx174
    Classification and nomenclature of viruses History of virus classification • Type of host • Type of disease • Transmition by an arthropod vector • Nucleic acid type • SS or DS • Segmented • Size of the virion • Capsid simmetry • Envelope Nomenclature • Small, icosahedral, single-stranded DNA viruses of animals were called parvoviruses (Latin parvus = small) • Nematode-transmitted polyhedral (icosahedral) viruses of plants were called nepoviruses • Phages T2, T4 and T6 were called T even phages • Serological relationships between viruses were investigated • Distinct strains (serotypes) could be distinguished in serological tests • Antisera against purified virions • Serotypes reflect differences in virus proteins International Committee on Taxonomy of Viruses • Order had to be brought • ICTV was formed in 1966 • Many working groups and is advised by virologists around the world • Rules for the nomenclature and classification of viruses • Considers proposals for new taxonomic groups and virus names • Approved are published in book form and on the web Modern virus classification and nomenclature • Each order, family, subfamily and genus is defined by viral characteristics that are necessary for membership of that group. Classification based on genome sequences • Similarity is represented in diagrams known as phylogenetic trees. • Rooted- the tree begins at a root which is assumed to be the ancestor of the viruses in the tree. • Unrooted- no assumption is made about the ancestor of the viruses in the tree. 10.2.2 Nomenclature of viruses and taxonomic groups Bacterial viruses such as T1, T2 and ϕX174. Viruses of humans and other vertebrates diseases that they cause Examples: measles virus, smallpox virus, foot and mouth disease virus Some viruses city, town or river Examples: Newcastle disease virus, Norwalk virus, Ebola virus Insect viruses Many insect viruses were named after the insect, with an indication of the effect of infection on the host.
    [Show full text]
  • 2020 Taxonomic Update for Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
    Archives of Virology https://doi.org/10.1007/s00705-020-04731-2 VIROLOGY DIVISION NEWS 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Daniela Alioto3 · Sergey V. Alkhovsky4 · Gaya K. Amarasinghe5 · Simon J. Anthony6,7 · Tatjana Avšič‑Županc8 · María A. Ayllón9,10 · Justin Bahl11 · Anne Balkema‑Buschmann12 · Matthew J. Ballinger13 · Tomáš Bartonička14 · Christopher Basler15 · Sina Bavari16 · Martin Beer17 · Dennis A. Bente18 · Éric Bergeron19 · Brian H. Bird20 · Carol Blair21 · Kim R. Blasdell22 · Steven B. Bradfute23 · Rachel Breyta24 · Thomas Briese25 · Paul A. Brown26 · Ursula J. Buchholz27 · Michael J. Buchmeier28 · Alexander Bukreyev18,29 · Felicity Burt30 · Nihal Buzkan31 · Charles H. Calisher32 · Mengji Cao33,34 · Inmaculada Casas35 · John Chamberlain36 · Kartik Chandran37 · Rémi N. Charrel38 · Biao Chen39 · Michela Chiumenti40 · Il‑Ryong Choi41 · J. Christopher S. Clegg42 · Ian Crozier43 · John V. da Graça44 · Elena Dal Bó45 · Alberto M. R. Dávila46 · Juan Carlos de la Torre47 · Xavier de Lamballerie38 · Rik L. de Swart48 · Patrick L. Di Bello49 · Nicholas Di Paola50 · Francesco Di Serio40 · Ralf G. Dietzgen51 · Michele Digiaro52 · Valerian V. Dolja53 · Olga Dolnik54 · Michael A. Drebot55 · Jan Felix Drexler56 · Ralf Dürrwald57 · Lucie Dufkova58 · William G. Dundon59 · W. Paul Duprex60 · John M. Dye50 · Andrew J. Easton61 · Hideki Ebihara62 · Toufc Elbeaino63 · Koray Ergünay64 · Jorlan Fernandes195 · Anthony R. Fooks65 · Pierre B. H. Formenty66 · Leonie F. Forth17 · Ron A. M. Fouchier48 · Juliana Freitas‑Astúa67 · Selma Gago‑Zachert68,69 · George Fú Gāo70 · María Laura García71 · Adolfo García‑Sastre72 · Aura R. Garrison50 · Aiah Gbakima73 · Tracey Goldstein74 · Jean‑Paul J. Gonzalez75,76 · Anthony Grifths77 · Martin H. Groschup12 · Stephan Günther78 · Alexandro Guterres195 · Roy A.
    [Show full text]
  • The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
    PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA.
    [Show full text]
  • 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.
    [Show full text]
  • Rapid Protein Sequence Evolution Via Compensatory Frameshift Is Widespread in RNA Virus Genomes
    Park and Hahn BMC Bioinformatics (2021) 22:251 https://doi.org/10.1186/s12859-021-04182-9 RESEARCH Open Access Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes Dongbin Park and Yoonsoo Hahn* *Correspondence: [email protected] Abstract Department of Life Science, Background: RNA viruses possess remarkable evolutionary versatility driven by the Chung-Ang University, Seoul 06794, South Korea high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of proteins, are frequently observed in the coding sequences of various viral genomes. When a secondary indel occurs near the primary indel site, the open reading frame can be restored to produce functional proteins, a phenomenon known as the compensatory frameshift. Results: In this study, we systematically analyzed publicly available viral genome sequences and identifed compensatory frameshift events in hundreds of viral protein- coding sequences. Compensatory frameshift events resulted in large-scale amino acid diferences between the compensatory frameshift form and the wild type even though their nucleotide sequences were almost identical. Phylogenetic analyses revealed that the evolutionary distance between proteins with and without a compensatory frameshift were signifcantly overestimated because amino acid mismatches caused by compensatory frameshifts were counted as substitutions. Further, this could cause compensatory frameshift forms to branch in diferent locations in the protein and nucleotide trees, which may obscure the correct interpretation of phylogenetic rela- tionships between variant viruses. Conclusions: Our results imply that the compensatory frameshift is one of the mecha- nisms driving the rapid protein evolution of RNA viruses and potentially assisting their host-range expansion and adaptation.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Module1: General Concepts
    NPTEL – Biotechnology – General Virology Module1: General Concepts Lecture 1: Virus history The history of virology goes back to the late 19th century, when German anatomist Dr Jacob Henle (discoverer of Henle’s loop) hypothesized the existence of infectious agent that were too small to be observed under light microscope. This idea fails to be accepted by the present scientific community in the absence of any direct evidence. At the same time three landmark discoveries came together that formed the founding stone of what we call today as medical science. The first discovery came from Louis Pasture (1822-1895) who gave the spontaneous generation theory from his famous swan-neck flask experiment. The second discovery came from Robert Koch (1843-1910), a student of Jacob Henle, who showed for first time that the anthrax and tuberculosis is caused by a bacillus, and finally Joseph Lister (1827-1912) gave the concept of sterility during the surgery and isolation of new organism. The history of viruses and the field of virology are broadly divided into three phases, namely discovery, early and modern. The discovery phase (1886-1913) In 1879, Adolf Mayer, a German scientist first observed the dark and light spot on infected leaves of tobacco plant and named it tobacco mosaic disease. Although he failed to describe the disease, he showed the infectious nature of the disease after inoculating the juice extract of diseased plant to a healthy one. The next step was taken by a Russian scientist Dimitri Ivanovsky in 1890, who demonstrated that sap of the leaves infected with tobacco mosaic disease retains its infectious property even after its filtration through a Chamberland filter.
    [Show full text]
  • A Dedicated Platform for Endogenous Viral Elements in Fishes, Amphibians
    bioRxiv preprint doi: https://doi.org/10.1101/529354; this version posted January 24, 2019. 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 4.0 International license. FabriEVEs: A dedicated platform for endogenous viral elements in fishes, amphibians, birds, reptiles and invertebrates Jixing Zhong1,2,3§, Jiacheng Zhu2,3§, Zaoxu Xu2,3, Geng Zou4, JunWei Zhao5, SanJie Jiang2, Wei Zhang6, Jun Xia2,3,7, Lin Yang2,3, Fang Li5, Ya Gao3, Fang Chen3, Yiquan Wu8*, Dongsheng Chen3* 1 School of Biological Sciences and Medical Engineering, Southeast University, Xuanwu District, Nanjing 210096, China 2 BGI Education Center, University of Chinese Academy of Sciences,Beishan Industrial Zone,Shenzhen, 518083, China. 3 BGI-Shenzhen,Beishan Industrial Zone,Shenzhen, 518083, China. 4 State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China 5 Department of Gynaecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China. 6 Sigmovir Biosystems Inc., 9610 Medical Center Drive, Suite 100, Rockville, MD, 20850, USA 7 MGI, BGI-Shenzhen, Beishan Industrial Zone,Shenzhen, 518083, China. 8 Current address: HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; [email protected] §, These authors contribute equally to this work *, Corresponding authors: Dongsheng Chen, [email protected] Yiquan Wu, [email protected] bioRxiv preprint doi: https://doi.org/10.1101/529354; this version posted January 24, 2019.
    [Show full text]
  • Downloaded from Transcriptome Shotgun Assembly (TSA) Database on 29 November 2020 (Ftp://Ftp.Ddbj.Nig.Ac.Jp/Ddbj Database/Tsa/, Table S3)
    viruses Article Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing Xin-Xin Chen, Wei-Chen Wu and Mang Shi * School of Medicine, Sun Yat-sen University, Shenzhen 518107, China; [email protected] (X.-X.C.); [email protected] (W.-C.W.) * Correspondence: [email protected] Abstract: In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray- finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups.
    [Show full text]
  • Non-Invasive Surveys of Mammalian Viruses Using Environmental DNA
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.26.009993; this version posted March 29, 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. Title Non-invasive surveys of mammalian viruses using environmental DNA Highlights Environmental DNA (water and blood-sucking leeches) provided a non- invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre- emergence. bioRxiv preprint doi: https://doi.org/10.1101/2020.03.26.009993; this version posted March 29, 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. Non-invasive surveys of mammalian viruses using environmental DNA Niccolo Alfano1,2*, Anisha Dayaram3,4*, Jan Axtner1, Kyriakos Tsangaras5, Marie- Louise Kampmann1,6, Azlan Mohamed1,7, Seth T.
    [Show full text]