HTLV-1: a Real Pathogen Or a Runaway Guest of a Diseased Cell?
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An Overview of the Molecular Phylogeny of Lentiviruses
Phylogeny of Lentiviruses 35 An overview of the molecular Reviews phylogeny of lentiviruses Brian T. Foley T10, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545 Introduction Lentiviruses are one of several groups of retroviruses. In early studies of the molecular phylogenetic analysis of endogenous and exogenous retroviruses it was suggested that the retroviruses could be divided into four groups, two complex with several accessory or regulatory genes (lentiviruses; and the bovine and primate leukemia virus group now known as deltaretrovirus) and two simple, with just the gag, pol and env genes and few or no accessory genes (a group including spumaretroviruses, C-type endogenous retroviruses and MMLV; the other group including Rous Sarcoma virus, HERV-K Simian Retrovirus 1 and MMTV) [1–5]. A more recent study, including many more recently discovered exogenous and endogenous retroviruses, illustrates the diversity of retroviruses [6]. The retroviridae are currently officially classified into seven different genera, according to the Seventh Report of the International Committee on Taxonomy of Viruses, 2000 (http://www.ncbi.nlm.nih.gov/ICTV). The seven genera are named alpha through epsilon retroviruses plus lentiviruses and spumaviruses. Phylogenetic trees based on pol gene sequences can be found in several recent papers[6–8]. None of the retroviruses in either group of complex retroviruses have been found in an endogenous state to date. Within the Lentiviruses, the primate lentiviruses discovered to date form a monophyletic cluster (Figure 1). One notable difference between the primate lentiviruses and the non-primate lentiviruses is that all nonprimate lentiviruses, except the BIV/JDV lineage, contain a region of the pol gene encoding a dUTPase, whereas all primate lentiviruses lack this region of pol. -
Guide for Common Viral Diseases of Animals in Louisiana
Sampling and Testing Guide for Common Viral Diseases of Animals in Louisiana Please click on the species of interest: Cattle Deer and Small Ruminants The Louisiana Animal Swine Disease Diagnostic Horses Laboratory Dogs A service unit of the LSU School of Veterinary Medicine Adapted from Murphy, F.A., et al, Veterinary Virology, 3rd ed. Cats Academic Press, 1999. Compiled by Rob Poston Multi-species: Rabiesvirus DCN LADDL Guide for Common Viral Diseases v. B2 1 Cattle Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 2 Deer and Small Ruminants Please click on the principle system involvement Generalized viral disease Respiratory viral disease Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 3 Swine Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 4 Horses Please click on the principle system involvement Generalized viral diseases Neurological viral diseases Respiratory viral diseases Enteric viral diseases Abortifacient/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 5 Dogs Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. -
The Expression of Human Endogenous Retroviruses Is Modulated by the Tat Protein of HIV‐1
The Expression of Human Endogenous Retroviruses is modulated by the Tat protein of HIV‐1 by Marta Jeannette Gonzalez‐Hernandez A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Immunology) in The University of Michigan 2012 Doctoral Committee Professor David M. Markovitz, Chair Professor Gary Huffnagle Professor Michael J. Imperiale Associate Professor David J. Miller Assistant Professor Akira Ono Assistant Professor Christiane E. Wobus © Marta Jeannette Gonzalez‐Hernandez 2012 For my family and friends, the most fantastic teachers I have ever had. ii Acknowledgements First, and foremost, I would like to thank David Markovitz for his patience and his scientific and mentoring endeavor. My time in the laboratory has been an honor and a pleasure. Special thanks are also due to all the members of the Markovitz laboratory, past and present. It has been a privilege, and a lot of fun, to work near such excellent scientists and friends. You all have a special place in my heart. I would like to thank all the members of my thesis committee for all the valuable advice, help and jokes whenever needed. Our collaborators from the Bioinformatics Core, particularly James Cavalcoli, Fan Meng, Manhong Dai, Maureen Sartor and Gil Omenn gave generous support, technical expertise and scientific insight to a very important part of this project. Thank you. Thanks also go to Mariana Kaplan’s and Akira Ono’s laboratory for help with experimental designs and for being especially generous with time and reagents. iii Table of Contents Dedication ............................................................................................................................ ii Acknowledgements ............................................................................................................. iii List of Figures ................................................................................................................... -
VMC 321: Systematic Veterinary Virology Retroviridae Retro: from Latin Retro,"Backwards”
VMC 321: Systematic Veterinary Virology Retroviridae Retro: from Latin retro,"backwards” - refers to the activity of reverse RETROVIRIDAE transcriptase and the transfer of genetic information from RNA to DNA. Retroviruses Viral RNA Viral DNA Viral mRNA, genome (integrated into host genome) Reverse (retro) transfer of genetic information Usually, well adapted to their hosts Endogenous retroviruses • RNA viruses • single stranded, positive sense, enveloped, icosahedral. • Distinguished from all other RNA viruses by presence of an unusual enzyme, reverse transcriptase. Retroviruses • Retro = reversal • RNA is serving as a template for DNA synthesis. • One genera of veterinary interest • Alpharetrovirus • • Family - Retroviridae • Subfamily - Orthoretrovirinae [Ortho: from Greek orthos"straight" • Genus -. Alpharetrovirus • Genus - Betaretrovirus Family- • Genus - Gammaretrovirus • Genus - Deltaretrovirus Retroviridae • Genus - Lentivirus [ Lenti: from Latin lentus, "slow“ ]. • Genus - Epsilonretrovirus • Subfamily - Spumaretrovirinae • Genus - Spumavirus Retroviridae • Subfamily • Orthoretrovirinae • Genus • Alpharetrovirus Alpharetrovirus • Species • Avian leukosis virus(ALV) • Rous sarcoma virus (RSV) • Avian myeloblastosis virus (AMV) • Fujinami sarcoma virus (FuSV) • ALVs have been divided into 10 envelope subgroups - A , B, C, D, E, F, G, H, I & J based on • host range Avian • receptor interference patterns • neutralization by antibodies leukosis- • subgroup A to E viruses have been divided into two groups sarcoma • Noncytopathic (A, C, and E) • Cytopathic (B and D) virus (ALV) • Cytopathic ALVs can cause a transient cytotoxicity in 30- 40% of the infected cells 1. The viral envelope formed from host cell membrane; contains 72 spiked knobs. 2. These consist of a transmembrane protein TM (gp 41), which is linked to surface protein SU (gp 120) that binds to a cell receptor during infection. 3. The virion has cone-shaped, icosahedral core, Structure containing the major capsid protein 4. -
Effects of Retroviruses on Host Genome Function
ANRV361-GE42-20 ARI 1 August 2008 18:2 V I E E W R S I E N C N A D V A Effects of Retroviruses on Host Genome Function Patric Jern and John M. Coffin Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111; email: [email protected], John.Coffi[email protected] Annu. Rev. Genet. 2008. 42:20.1–20.23 Key Words The Annual Review of Genetics is online at Human Endogenous Retrovirus, LTR, transcription, recombination, genet.annualreviews.org methylation This article’s doi: 10.1146/annurev.genet.42.110807.091501 Abstract Copyright c 2008 by Annual Reviews. For millions of years, retroviral infections have challenged vertebrates, All rights reserved occasionally leading to germline integration and inheritance as ERVs, 0066-4197/08/1201-0001$20.00 genetic parasites whose remnants today constitute some 7% to 8% of the human genome. Although they have had significant evolutionary side effects, it is useful to view ERVs as fossil representatives of retro- viruses extant at the time of their insertion into the germline, not as direct players in the evolutionary process itself. Expression of particu- lar ERVs is associated with several positive physiological functions as well as certain diseases, although their roles in human disease as etio- logical agents, possible contributing factors, or disease markers—well demonstrated in animal models—remain to be established. Here we discuss ERV contributions to host genome structure and function, in- cluding their ability to mediate recombination, and physiological effects on the host transcriptome resulting from their integration, expression, and other events. -
Lentiviral Integration Site Targeting: Host Determinants and Consequences
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Spring 2010 Lentiviral Integration Site Targeting: Host Determinants and Consequences Keshet Ronen University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Virology Commons Recommended Citation Ronen, Keshet, "Lentiviral Integration Site Targeting: Host Determinants and Consequences" (2010). Publicly Accessible Penn Dissertations. 174. https://repository.upenn.edu/edissertations/174 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/174 For more information, please contact [email protected]. Lentiviral Integration Site Targeting: Host Determinants and Consequences Abstract A necessary step in the retroviral lifecycle is integration, the covalent insertion of the viral cDNA into the genome of the infected cell. This means that retroviruses, for example HIV, establish life-long infection. It also means that retroviruses are used as gene-delivery vectors to treat genetic diseases. Integration events are distributed non-randomly in the genome of the infected cell, with characteristic genus-specific preferences. In this dissertation, we focus on the lentiviral class of retroviruses, and explore two aspects of their integration: the means by which integration is targeted to its favored sites, and the consequences of integration at these sites for the host cell. The host protein LEDGF/p75 has been shown to interact with lentiviral integrases and contribute to their preference for integration in genes. We sought to establish the extent to which integration site selection is determined by LEDGF/p75 tethering. We first asked whether LEDGF/p75 was an essential integration tether, by analyzing integration site distribution in cells stringently depleted for LEDGF/p75. -
TNPO3-Mediated Nuclear Entry of the Rous Sarcoma Virus Gag Protein Is Independent
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.12.989608; this version posted April 21, 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 TNPO3-mediated nuclear entry of the Rous sarcoma virus Gag protein is independent 2 of the cargo-binding domain 3 4 Breanna L. Ricea, Matthew S. Stakea*, and Leslie J. Parenta,b,# 5 6 aDivision of Infectious Diseases and Epidemiology, Department of Medicine, Penn State 7 College of Medicine, Hershey, PA, USA 8 bDepartment of Microbiology and Immunology, Penn State College of Medicine, 9 Hershey, PA, USA 10 11 Running Head: TNPO3-mediated nuclear entry of alpharetrovirus Gag 12 13 #Address correspondence to Leslie Parent, [email protected]. 14 *Present address: 15 Matthew S. Stake 16 UPMC Hanover Medical Group, Hanover, PA, USA 17 18 B.L.R and M.S.S. contributed equally to this work. 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.12.989608; this version posted April 21, 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. 21 Abstract 22 Retroviral Gag polyproteins orchestrate the assembly and release of nascent 23 virus particles from the plasma membranes of infected cells. -
Emergence of Unique Primate T-Lymphotropic Viruses Among Central African Bushmeat Hunters
Emergence of unique primate T-lymphotropic viruses among central African bushmeat hunters Nathan D. Wolfe*†‡, Walid Heneine§, Jean K. Carr¶, Albert D. Garcia§, Vedapuri Shanmugam§, Ubald Tamoufe*ʈ, Judith N. Torimiroʈ, A. Tassy Prosser†, Matthew LeBretonʈ, Eitel Mpoudi-Ngoleʈ, Francine E. McCutchan*¶, Deborah L. Birx**, Thomas M. Folks§, Donald S. Burke*†, and William M. Switzer§†† Departments of *Epidemiology, †International Health, and ‡Molecular Microbiology and Immunology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205; §Laboratory Branch, Division of HIV͞AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333; ¶Henry M. Jackson Foundation, Rockville, MD 20850; ʈArmy Health Research Center, Yaounde, Cameroon; and **Walter Reed Army Institute of Research, Rockville, MD 20850 Edited by John M. Coffin, Tufts University School of Medicine, Boston, and approved April 11, 2005 (received for review March 2, 2005) The human T-lymphotropic viruses (HTLVs) types 1 and 2 origi- There has been no evidence that STLVs cross into people nated independently and are related to distinct lineages of simian occupationally exposed to NHPs in laboratories and primate T-lymphotropic viruses (STLV-1 and STLV-2, respectively). These centers, as has been documented for other primate retroviruses, facts, along with the finding that HTLV-1 diversity appears to have including simian immunodeficiency virus, simian foamy virus resulted from multiple cross-species transmissions of STLV-1, sug- (SFV), and simian type D retrovirus (12–15). Nevertheless, gest that contact between humans and infected nonhuman pri- zoonotic transmission of STLV to human populations naturally mates (NHPs) may result in HTLV emergence. -
Retroviruses:Retroviruses: Endogenousendogenous MLVMLV Andand XMRVXMRV
Retroviruses:Retroviruses: EndogenousEndogenous MLVMLV andand XMRVXMRV JohnJohn M.M. CoffinCoffin TuftsTufts UniversityUniversity Tufts University Presented at the 1st Intl. Workshop on XMRV 7-8 September, Bethesda USA The Retrovirus Family Tree Virus Genus HFV Spumaretrovirinae bel1, bel2 MLV GammaretrovirusGammaretroviru FeLV HERV-C WDS Epsilonretrovirus orfA, orfB, orfC HIV-1 tat, rev HIV-2 Lentivirus EIAV VMV dut MPMV sag new env MMTV Betaretrovirus HERV-K IAP ASLV Alpharetrovirus BLV HTLV-1 Deltaretrovirus tax, rex HTLV-2 New Genes Presented at the 1st Intl. Workshop on XMRV At least 30 million years ago! 7-8 September, Bethesda USA EndogenousEndogenous RetrovirusesRetroviruses 1.1. Remnants Remnants ofof germgerm lineline infectionsinfections byby exogenousexogenous (infectious)(infectious) retroviruses.retroviruses. 2.2. BecameBecame fixedfixed inin thethe hosthost speciespecies.Somes.Some conferconfer protectionprotection againstagainst futurefuture infectionsinfections byby thethe samesame oror similarsimilar viviruses.ruses. AA fewfew othersothers havehave salutarysalutary effects.effects. 3.3. InheritedInherited likelike normalnormal genes.genes. 4.4. PresentPresent inin everyevery vertebratevertebrate andand manymany invertebrates.invertebrates. 5.5. CompriseComprise 6-8%6-8% ofof thethe humanhuman genome.genome. (More(More virusesviruses thanthan us).us). Presented at the 1st Intl. Workshop on XMRV 7-8 September, Bethesda USA EndogenousEndogenous RetrovirusesRetroviruses 6. Provide a fossil record of pathogen-host interactioninteraction unavailableunavailable inin anyany other system. 7. Can participateparticipate in evolutionary processescesses asas wellwell asas informinform usus aboutabout them. 8. Involved in disease in some animals. Humans? Presented at the 1st Intl. Workshop on XMRV 7-8 September, Bethesda USA XMRVXMRV 1.1. First First describeddescribed aboutabout 55 yearsyears agoago inin aa fewfew patientspatients withwith prostateprostate cancer.cancer. 2.2. -
Discovery of Prosimian and Afrotherian Foamy Viruses And
Katzourakis et al. Retrovirology 2014, 11:61 http://www.retrovirology.com/content/11/1/61 RESEARCH Open Access Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution Aris Katzourakis1*†, Pakorn Aiewsakun1†, Hongwei Jia2, Nathan D Wolfe3,4,5, Matthew LeBreton6, Anne D Yoder7 and William M Switzer2* Abstract Background: Foamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of the best-understood viral evolutionary histories ever documented, estimated to have an ancient origin. Nonetheless, our knowledge of some parts of FV evolution, notably that of prosimian and afrotherian FVs, is far from complete due to the lack of sequence data. Results: Here, we report the complete genome of the first extant prosimian FV (PSFV) isolated from a lorisiforme galago (PSFVgal), and a novel partial endogenous viral element with high sequence similarity to FVs, present in the afrotherian Cape golden mole genome (ChrEFV). We also further characterize a previously discovered endogenous PSFV present in the aye-aye genome (PSFVaye). Using phylogenetic methods and available FV sequence data, we show a deep divergence and stable co-evolution of FVs in eutherian mammals over 100 million years. Nonetheless, we found that the evolutionary histories of bat, aye-aye, and New World monkey FVs conflict with the evolutionary histories of their hosts. By combining sequence analysis and biogeographical knowledge, we propose explanations for these mismatches in FV-host evolutionary history. -
An Introduction to Viral Vectors: Safety Considerations
An Introduction to Viral Vectors: Safety Considerations Dawn P. Wooley, Ph.D., SM(NRCM), RBP, CBSP Learning Objectives Recognize hazards associated with viral vectors in research and animal testing laboratories. Interpret viral vector modifications pertinent to risk assessment. Understand the difference between gene delivery vectors and viral research vectors. 2 Outline Introduction to Viral Vectors Retroviral & Lentiviral Vectors (+RNA virus) Adeno and Adeno-Assoc. Vectors (DNA virus) Novel (-)RNA virus vectors NIH Guidelines and Other Resources Conclusions 3 Increased Use of Viral Vectors in Research Difficulties in DNA delivery to mammalian cells <50% with traditional transfection methods Up to ~90% with viral vectors Increased knowledge about viral systems Commercialization has made viral vectors more accessible Many new genes identified and cloned (transgenes) Gene therapy 4 5 6 What is a Viral Vector? Viral Vector: A viral genome with deletions in some or all essential genes and possibly insertion of a transgene Plasmid: Small (~2-20 kbp) circular DNA molecules that replicates in bacterial cells independently of the host cell chromosome 7 Molecular Biology Essentials Flow of genetic information Nucleic acid polarity Infectivity of viral genomes Understanding cDNA cis- vs. trans-acting sequences cis (Latin) – on the same side trans (Latin) – across, over, through 8 Genetic flow & nucleic acid polarity Coding DNA Strand (+) 5' 3' 5' 3' 5' 3' 3' 5' Noncoding DNA Strand (-) mRNA (+) RT 3' 5' cDNA(-) Proteins (Copy DNA aka complementary DNA) 3' 5' 3' 5' 5' 3' mRNA (+) ds DNA in plasmid 9 Virology Essentials Replication-defective vs. infectious virus Helper virus vs. helper plasmids Pathogenesis Original disease Disease caused by transgene Mechanisms of cancer Insertional mutagenesis Transduction 10 Viral Vector Design and Production 1 + Vector Helper Cell 2 + Helper Constructs Vector 3 + + Vector Helper Constructs Note: These viruses are replication-defective but still infectious. -
Vmc 605: Systematic Animal Virology Retroviridae
VMC 605: SYSTEMATIC ANIMAL VIROLOGY RETROVIRIDAE Dr Manoj Kumar Assistant Professor Department of Veterinary Microbiology Bihar Animal Sciences University Retro: from Latin retro,"backwards” - refers to the activity of reverse RETROVIRIDAE transcriptase and the transfer of genetic information from RNA to DNA. Retrovirus: A retrovirus is a lysogenic virus with an RNA genome that uses reverse transcriptase to make DNA for insertion into the host genome. Retroviruses • RNA viruses • single stranded, positive sense, enveloped, icosahedral. • Distinguished from all other RNA viruses by presence of an unusual enzyme, reverse transcriptase. Retroviruses • Retro = reversal • RNA is serving as a template for DNA synthesis. • One genera of veterinary interest • Alpharetrovirus • • Family - Retroviridae • Subfamily - Orthoretrovirinae [Ortho: from Greek orthos"straight" • Genus -. Alpharetrovirus • Genus - Betaretrovirus Family- • Genus - Gammaretrovirus • Genus - Deltaretrovirus Retroviridae • Genus - Lentivirus [ Lenti: from Latin lentus, "slow“ ]. • Genus - Epsilonretrovirus • Subfamily - Spumaretrovirinae • Genus - Spumavirus Retroviridae • Subfamily • Orthoretrovirinae • Genus • Alpharetrovirus Alpharetrovirus • Species • Avian leukosis virus(ALV) • Rous sarcoma virus (RSV) • Avian myeloblastosis virus (AMV) • Fujinami sarcoma virus (FuSV) • ALVs have been divided into 10 envelope subgroups - A , B, C, D, E, F, G, H, I & J based on • host range Avian • receptor interference patterns • neutralization by antibodies leukosis- • subgroup A to E viruses have been divided into two groups sarcoma • Noncytopathic (A, C, and E) • Cytopathic (B and D) virus (ALV) • Cytopathic ALVs can cause a transient cytotoxicity in 30- 40% of the infected cells 1. The viral envelope formed from host cell membrane; contains 72 spiked knobs. 2. These consist of a transmembrane protein TM (gp 41), which is linked to surface protein SU (gp 120) that binds to a cell receptor during infection.