DOCSLIB.ORG

Supporting Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supporting Information Supporting Information Wu et al. 10.1073/pnas.0905115106 20 15 10 5 0 10 15 20 25 30 35 40 Fig. S1. HGT cutoff and tree topology. Robinson-Foulds (RF) distance [Robinson DF, Foulds LR (1981) Math Biosci 53:131–147] between viral proteome trees with different horizontal gene transfer (HGT) cutoffs h at feature length 8. Tree distances are between h and h-1. The tree topology remains stable for h in the range 13–31. We use h ϭ 20 in this work. Wu et al. www.pnas.org/cgi/content/short/0905115106 1of6 20 18 16 14 12 10 8 6 0.0/0.5 0.5/0.7 0.7/0.9 0.9/1.1 1.1/1.3 1.3/1.5 Fig. S2. Low complexity features and tree topology. Robinson-Foulds (RF) distance between viral proteome trees with different low-complexity cutoffs K2 for feature length 8 and HGT cutoff 20. The tree topology changes least for K2 ϭ 0.9, 1.1 and 1.3. We choose K2 ϭ 1.1 for this study. Wu et al. www.pnas.org/cgi/content/short/0905115106 2of6 Table S1. Distribution of the 164 inter-viral-family HGT instances bro hr RR2 RR1 IL-10 Ubi TS Photol. Total Baculo 45 1 10 9 11 1 77 Asco 11 7 1 19 Nudi 1 1 1 3 SGHV 1 1 2 Nima 1 1 2 Herpes 48 12 Pox 18 8 2 3 1 3 35 Irido 1 1 2 4 Phyco 2 3 2 1 8 Allo 1 1 2 Total 56 8 35 24 6 17 14 4 164 The HGT cutoff is 20 8-mers. These HGT instances involve 8 gene families: baculovirus repeated ORF (bro), homologous region (hr), ribonucleotide reductase large subunit (RR1) and small subunit (RR2), interleukin 10 (IL-10), ubiquitin (Ubi), thymidylate synthase (TS), DNA photolyase 2 (photol). The involved viral families are: baculoviridae (Baculo), ascoviridae (Asco) nudivirus (Nudi), saliva gland hypertrophy virus (SGHV), nimaviridae (Nima), herpesviridae (Herpes), poxviridae (Pox), iridoviridae (Irido), phycodnaviridae (Phyco), alloherpesviridae (Allo). Wu et al. www.pnas.org/cgi/content/short/0905115106 3of6 Table S2. List of 142 large dsDNA viruses Family Subfamily Genus NCBI Accession Code Virus name Abbreviation Alloherpesviridae Ictalurivirus NC࿝001493.1 Ictalurid herpesvirus 1 IcHV1 Alloherpesviridae unclassified NC࿝008210.1 Ranid herpesvirus 2 RaHV2 Alloherpesviridae unclassified NC࿝008211.1 Ranid herpesvirus 1 RaHV1 Alloherpesviridae unclassified NC࿝009127.1 Cyprinid herpesvirus 3 CyHV3 Ascoviridae Ascovirus NC࿝008361.1 Spodoptera frugiperda ascovirus SfAV-1a 1a Ascoviridae Ascovirus NC࿝008518.1 Trichoplusia ni ascovirus 2c TnAV-2c Ascoviridae Ascovirus NC࿝009233.1 Heliothis virescens ascovirus 3e HvAV-3e Asfarviridae Asfivirus NC࿝001659.1 African swine fever virus ASFV Baculoviridae Alphaabaculovirus NC࿝001623.1 Autographa californica AcMNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝001875.2 Orgyia pseudotsugata MNPV OpMNPV Baculoviridae Alphaabaculovirus NC࿝001962.1 Bombyx mori NPV BmNPV Baculoviridae Alphaabaculovirus NC࿝001973.1 Lymantria dispar MNPV LdMNPV Baculoviridae Alphaabaculovirus NC࿝002169.1 Spodoptera exigua MNPV SeMNPV Baculoviridae Alphaabaculovirus NC࿝002654.2 Helicoverpa armigera HearNPV-G4 nucleopolyhedrovirus G4 Baculoviridae Alphaabaculovirus NC࿝003083.1 Epiphyas postvittana NPV EppoNPV Baculoviridae Alphaabaculovirus NC࿝003094.2 Helicoverpa armigera NPV HearNPV-C1 Baculoviridae Alphaabaculovirus NC࿝003102.1 Spodoptera litura NPV SpltNPV Baculoviridae Alphaabaculovirus NC࿝003349.1 Helicoverpa zea SNPV HzSNPV Baculoviridae Alphaabaculovirus NC࿝003529.1 Mamestra configurata NPV-A MacoNPV-A Baculoviridae Alphaabaculovirus NC࿝004117.1 Mamestra configurata NPV-B MacoNPV-B Baculoviridae Alphaabaculovirus NC࿝004323.1 Rachiplusia ou MNPV RoMNPV Baculoviridae Alphaabaculovirus NC࿝004690.1 Adoxophyes honmai NPV AdhoNPV Baculoviridae Alphaabaculovirus NC࿝004778.3 Choristoneura fumiferana MNPV CfMNPV Baculoviridae Alphaabaculovirus NC࿝005137.2 Choristoneura fumiferana DEF CfDEFNPV MNPV Baculoviridae Alphaabaculovirus NC࿝007151.1 Chrysodeixis chalcites ChchNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝007383.1 Trichoplusia ni SNPV TnSNPV Baculoviridae Alphaabaculovirus NC࿝007767.1 Hyphantria cunea HycuNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝007921.1 Agrotis segetum AgseNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008035.3 Antheraea pernyi AnpeNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008293.1 Clanis bilineata ClbiNPV nucleopolyhedrosis virus Baculoviridae Alphaabaculovirus NC࿝008348.1 Leucania separata nuclear LeseNPV polyhedrosis virus Baculoviridae Alphaabaculovirus NC࿝008349.1 Plutella xylostella multiple PlxyMNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008520.1 Anticarsia gemmatalis AngeNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008586.1 Ecotropis obliqua NPV EcobNPV Baculoviridae Alphaabaculovirus NC࿝008725.1 Maruca vitrata MNPV MaviMNPV Baculoviridae Alphaabaculovirus NC࿝009011.1 Spodoptera frugiperda MNPV SfMNPV Baculoviridae Alphaabaculovirus NC࿝010276.1 Orgyia leucostigma NPV OrleNPV Baculoviridae Betabaculovirus NC࿝002331.1 Xestia c-nigrum granulovirus XecnGV Baculoviridae Betabaculovirus NC࿝002593.1 Plutella xylostella granulovirus PlxyGV Baculoviridae Betabaculovirus NC࿝002816.1 Cydia pomonella granulovirus CpGV Baculoviridae Betabaculovirus NC࿝004062.1 Phthorimaea operculella PhopGV granulovirus Baculoviridae Betabaculovirus NC࿝005038.1 Adoxophyes orana granulovirus AdorGV Baculoviridae Betabaculovirus NC࿝005068.1 Cryptophlebia leucotreta CrleGV granulovirus Baculoviridae Betabaculovirus NC࿝005839.2 Agrotis segetum granulovirus AgseGV Baculoviridae Betabaculovirus NC࿝008168.1 Choristoneura occidentalis ChocGV granulovirus Baculoviridae Betabaculovirus NC࿝009503.1 Spodoptera litura granulovirus SpltGV Baculoviridae Betabaculovirus NC࿝010240.1 Helicoverpa armigera HearGV granulovirus Baculoviridae Deltabaculovirus NC࿝003084.1 Culex nigripalpus NPV CuniNPV Wu et al. www.pnas.org/cgi/content/short/0905115106 4of6 Family Subfamily Genus NCBI Accession Code Virus name Abbreviation Baculoviridae Gammabaculovirus NC࿝005905.1 Neodiprion sertifer NPV NeseNPV Baculoviridae Gammabaculovirus NC࿝005906.1 Neodiprion lecontii NPV NeleNPV Baculoviridae Gammabaculovirus NC࿝008252.1 Neodiprion abietis NeabNPV nucleopolyhedrovirus Herpesviridae Alphaherpesvirinae Iltovirus NC࿝005264.1 Psittacid herpesvirus 1 PsHV1 Herpesviridae Alphaherpesvirinae Iltovirus NC࿝006623.1 Gallid herpesvirus 1 GaHV1 Herpesviridae Alphaherpesvirinae Mardivirus NC࿝002229.3 Gallid herpesvirus 2 GaHV2 Herpesviridae Alphaherpesvirinae Mardivirus NC࿝002577.1 Gallid herpesvirus 3 GaHV3 Herpesviridae Alphaherpesvirinae Mardivirus NC࿝002641.1 Meleagrid herpesvirus 1 MeHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝001798.1 Human herpesvirus 2 HHV2 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝001806.1 Human herpesvirus 1 HHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝004812.1 Macacine herpesvirus 1 MaHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝006560.1 Cercopithecine herpesvirus 2 CeHV2 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝007653.1 Papiine herpesvirus 2 PaHV2 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001348.1 Human herpesvirus 3 HHV3 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001491.2 Equid herpesvirus 1 EHV1 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001844.1 Equid herpesvirus 4 EHV4 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001847.1 Bovine herpesvirus 1 BHV1 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝002686.2 Cercopithecine herpesvirus 9 CeHV9 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝005261.2 Bovine herpesvirus 5 BHV5 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝006151.1 Suid herpesvirus 1 SuHV1 Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝001347.3 Human herpesvirus 5 strain HHV5-AD169 AD169 Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝003521.1 Panine herpesvirus 2 CCMV Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝006150.1 Macacine herpesvirus 8 MaHV8 Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝006273.2 Human herpesvirus 5 HHV5 Herpesviridae Betaherpesvirinae Muromegalovirus NC࿝002512.2 Murid herpesvirus 2 MHV2 Herpesviridae Betaherpesvirinae Muromegalovirus NC࿝004065.1 Murid herpesvirus 1 MHV1 Herpesviridae Betaherpesvirinae Roseolovirus NC࿝000898.1 Human herpesvirus 6B HHV6B Herpesviridae Betaherpesvirinae Roseolovirus NC࿝001664.1 Human herpesvirus 6A HHV6A Herpesviridae Betaherpesvirinae Roseolovirus NC࿝001716.2 Human herpesvirus 7 HHV7 Herpesviridae Betaherpesvirinae unclassified NC࿝002794.1 Tupaiid herpesvirus 1 TuHV1 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝004367.1 Callitrichine herpesvirus 3 CalHV3 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝006146.1 Macacine herpesvirus 4 MaHV4 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝007605.1 Human herpesvirus 4 type 1 HHV4–1 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝009334.1 Human herpesvirus 4 type 2 HHV4–2 Herpesviridae Gammaherpesvirinae Macavirus NC࿝002531.1 Alcelaphine herpesvirus 1 AHV1 Herpesviridae Gammaherpesvirinae Macavirus NC࿝007646.1 Ovine herpesvirus 2 OHV2 Herpesviridae Gammaherpesvirinae Percavirus NC࿝001650.1 Equid herpesvirus 2 EHV2 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝001350.1 Saimiriine herpesvirus 2 SaHV2 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝001826.2 Murid herpesvirus 4 MHV4 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝001987.1 Ateline herpesvirus 3 AtHV3 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝002665.1 Bovine herpesvirus 4 BHV4 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝003401.1 Macacine herpesvirus 5 MaHV5 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝003409.1 Human herpesvirus
Load more

Recommended publications
  • Identification of Two Major Virion Protein Genes of White Spot Syndrome Virus of Shrimp
    Virology 266, 227–236 (2000) doi:10.1006/viro.1999.0088, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Identification of Two Major Virion Protein Genes of White Spot Syndrome Virus of Shrimp Marie¨lle C. W. van Hulten, Marcel Westenberg, Stephen D. Goodall, and Just M. Vlak1 Laboratory of Virology, Wageningen Agricultural University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands Received August 25, 1999; returned to author for revision October 28, 1999; accepted November 8, 1999 White Spot Syndrome Virus (WSSV) is an invertebrate virus, causing considerable mortality in shrimp. Two structural proteins of WSSV were identified. WSSV virions are enveloped nucleocapsids with a bacilliform morphology with an approximate size of 275 ϫ 120 nm, and a tail-like extension at one end. The double-stranded viral DNA has an approximate size 290 kb. WSSV virions, isolated from infected shrimps, contained four major proteins: 28 kDa (VP28), 26 kDa (VP26), 24 kDa (VP24), and 19 kDa (VP19) in size, respectively. VP26 and VP24 were found associated with nucleocapsids; the others were associated with the envelope. N-terminal amino acid sequences of nucleocapsid protein VP26 and the envelope protein VP28 were obtained by protein sequencing and used to identify the respective genes (vp26 and vp28) in the WSSV genome. To confirm that the open reading frames of WSSV vp26 (612) and vp28 (612) are coding for the putative major virion proteins, they were expressed in insect cells using baculovirus vectors and analyzed by Western analysis.
    [Show full text]
  • Development of Biotehcnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses
    JYVÄSKYLÄ STUDIES IN BIOLOGICAL AND ENVIRONMENTAL SCIENCE 154 Leona Gilbert Development of Biotehcnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses JYVÄSKYLÄN YLIOPISTO JYVÄSKYLÄ STUDIES IN BIOLOGICAL AND ENVIRONMENTAL SCIENCE 154 Leona Gilbert Development of Biotechnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses Esitetään Jyväskylän yliopiston matemaattis-luonnontieteellisen tiedekunnan suostumuksella julkisesti tarkastettavaksi yliopiston Ambiotica-rakennuksen salissa (YAA303) kesäkuun 18. päivänä 2005 kello 12. Academic dissertation to be publicly discussed, by permission of the Faculty of Mathematics and Science of the University of Jyväskylä, in the Building Ambiotica, Auditorium YAA303, on June 18th, 2005 at 12 o'clock noon. UNIVERSITY OF JYVÄSKYLÄ JYVÄSKYLÄ 2005 Development of Biotechnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses JYVÄSKYLÄ STUDIES IN BIOLOGICAL AND ENVIRONMENTAL SCIENCE 154 Leona Gilbert Development of Biotechnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses UNIVERSITY OF JYVÄSKYLÄ JYVÄSKYLÄ 2005 Editors Jukka Särkkä Department of Biological and Environmental Science, University of Jyväskylä Pekka Olsbo, Irene Ylönen Publishing Unit, University Library of Jyväskylä Cover picture: Molecular models of the fluorescent biotechnological tools for CPV and B19. Picture by Leona Gilbert. ISBN 951-39-2134-4 (nid.) ISSN 1456-9701 Copyright © 2005, by University of Jyväskylä Jyväskylä University Printing House, Jyväskylä 2005 ABSTRACT Gilbert, Leona Development of biotechnological tools for studying infectious pathways of canine and human parvoviruses. Jyväskylä, University of Jyväskylä, 2005, 104 p. (Jyväskylä Studies in Biological and Environmental Science, ISSN 1456-9701; 154) ISBN 951-39-2182-4 Parvoviruses are among the smallest vertebrate DNA viruses known to date. The production of parvovirus-like particles (parvo-VLPs) has been successfully exploited for parvovirus vaccine development.
    [Show full text]
  • Trunkloads of Viruses
    COMMENTARY Trunkloads of Viruses Philip E. Pellett Department of Immunology and Microbiology, Wayne State University School of Medicine, Detroit, Michigan, USA Elephant populations are under intense pressure internationally from habitat destruction and poaching for ivory and meat. They also face pressure from infectious agents, including elephant endotheliotropic herpesvirus 1 (EEHV1), which kills ϳ20% of Asian elephants (Elephas maximus) born in zoos and causes disease in the wild. EEHV1 is one of at least six distinct EEHV in a phylogenetic lineage that appears to represent an ancient but newly recognized subfamily (the Deltaherpesvirinae) in the family Herpesviridae. lephant endotheliotropic herpesvirus 1 (EEHV1) causes a rap- the Herpesviridae (the current complete list of approved virus tax- Downloaded from Eidly progressing and usually fatal hemorrhagic disease that ons is available at http://ictvonline.org/). In addition, approxi- occurs in the wild in Asia and affects ϳ20% of Asian elephant mately 200 additional viruses detected using methods such as (Elephas maximus) calves born in zoos in the United States and those described above await formal consideration (V. Lacoste, Europe (1). About 60% of juvenile deaths of captive elephants are personal communication). With very few exceptions, the amino attributed to such infections. Development of control measures acid sequence of a small conserved segment of the viral DNA poly- has been hampered by the lack of systems for culture of the virus in merase (ϳ150 amino acids) is sufficient to not only reliably iden- laboratories. Its genetic study has been restricted to analysis of tify a virus as belonging to the evolutionary lineage represented by blood, trunk wash fluid, and tissue samples collected during nec- the Herpesviridae, but also their subfamily, and in most cases a http://jvi.asm.org/ ropsies.
    [Show full text]
  • Changes to Virus Taxonomy 2004
    Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales
    [Show full text]
  • Lack of Viral Mirna Expression in an Experimental Infection
    Núñez-Hernández et al. Veterinary Research (2015) 46:48 DOI 10.1186/s13567-015-0181-4 VETERINARY RESEARCH SHORT REPORT Open Access Evaluation of the capability of the PCV2 genome to encode miRNAs: lack of viral miRNA expression in an experimental infection Fernando Núñez-Hernández1, Lester J Pérez2, Gonzalo Vera3, Sarai Córdoba3, Joaquim Segalés1,4, Armand Sánchez3,5 and José I Núñez1* Abstract Porcine circovirus type 2 (PCV2) is a ssDNA virus causing PCV2-systemic disease (PCV2-SD), one of the most important diseases in swine. MicroRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. Viral miRNAs have recently been described and the number of viral miRNAs has been increasing in the past few years. In this study, small RNA libraries were constructed from two tissues of subclinically PCV2 infected pigs to explore if PCV2 can encode viral miRNAs. The deep sequencing data revealed that PCV2 does not express miRNAs in an in vivo subclinical infection. Introduction, methods, and results family with the highest miRNAs encoding capacity Porcine circovirus type 2-systemic disease (PCV2-SD) is [6,7]. Other viruses belonging to the families Polyoma- a devastating disease that causes important economic viridae, Adenoviridae, Papillomaviridae, Baculoviridae losses [1]. The disease is essentially caused by PCV2, a and Ascoviridae encode miRNAs in low numbers single stranded DNA, non enveloped virus belonging to [8-12]. Recently, a Human Torque Teno virus, a small, the Circoviridae family [2]. The PCV2 genome encodes ssDNA virus from the Anelloviridae family, that en- four ORFs. ORF1 encodes for two proteins (Rep and codes a miRNA involved in interferon modulation has Rep’) which are involved in replication.
    [Show full text]
  • Protein Composition of the Occlusion Bodies of Epinotia Aporema Granulovirus
    bioRxiv preprint doi: https://doi.org/10.1101/465021; this version posted November 7, 2018. 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 4.0 International license. 1 Protein composition of the occlusion bodies of Epinotia aporema 2 granulovirus 3 4 Tomás Masson, María Laura Fabre, María Leticia Ferrelli, Matías Luis Pidre, Víctor 5 Romanowski. 6 1 Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de 7 Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina. 8 9 Abstract 10 Within family Baculoviridae, members of the Betabaculovirus genus are employed as 11 biocontrol agents against lepidopteran pests, either alone or in combination with 12 selected members of the Alphabaculovirus genus. Epinotia aporema granulovirus 13 (EpapGV) is a fast killing betabaculovirus that infects the bean shoot borer (E. 14 aporema) and is a promising biopesticide. Because occlusion bodies (OBs) play a key 15 role in baculovirus horizontal transmission, we investigated the composition of 16 EpapGV OBs. Using mass spectrometry-based proteomics we could identify 56 proteins 17 that are included in the OBs during the final stages of larval infection. Our data 18 provides experimental validation of several annotated hypothetical coding sequences. 19 Proteogenomic mapping against genomic sequence detected a previously unannotated 20 ac110-like core gene and a putative translation fusion product of ORFs epap48 and 21 epap49. Comparative studies of the proteomes available for the family Baculoviridae 22 highlight the conservation of core gene products as parts of the occluded virion.
    [Show full text]
  • Recombinant and Chimeric Viruses
    Recombinant and chimeric viruses: Evaluation of risks associated with changes in tropism Ben P.H. Peeters Animal Sciences Group, Wageningen University and Research Centre, Division of Infectious Diseases, P.O. Box 65, 8200 AB Lelystad, The Netherlands. May 2005 This report represents the personal opinion of the author. The interpretation of the data presented in this report is the sole responsibility of the author and does not necessarily represent the opinion of COGEM or the Animal Sciences Group. Dit rapport is op persoonlijke titel door de auteur samengesteld. De interpretatie van de gepresenteerde gegevens komt geheel voor rekening van de auteur en representeert niet de mening van de COGEM, noch die van de Animal Sciences Group. Advisory Committee Prof. dr. R.C. Hoeben (Chairman) Leiden University Medical Centre Dr. D. van Zaane Wageningen University and Research Centre Dr. C. van Maanen Animal Health Service Drs. D. Louz Bureau Genetically Modified Organisms Ing. A.M.P van Beurden Commission on Genetic Modification Recombinant and chimeric viruses 2 INHOUDSOPGAVE RECOMBINANT AND CHIMERIC VIRUSES: EVALUATION OF RISKS ASSOCIATED WITH CHANGES IN TROPISM Executive summary............................................................................................................................... 5 Introduction............................................................................................................................................ 7 1. Genetic modification of viruses .................................................................................................9
    [Show full text]
  • Microtubule-Dependent Trafficking of Alphaherpesviruses in the Nervous
    viruses Review Microtubule-Dependent Trafficking of Alphaherpesviruses in the Nervous System: The Ins and Outs Drishya Diwaker 1 and Duncan W. Wilson 1,2,* 1 Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; [email protected] 2 Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA * Correspondence: [email protected]; Tel.: +1-(718)-430-2305 Received: 29 November 2019; Accepted: 15 December 2019; Published: 17 December 2019 Abstract: The Alphaherpesvirinae include the neurotropic pathogens herpes simplex virus and varicella zoster virus of humans and pseudorabies virus of swine. These viruses establish lifelong latency in the nuclei of peripheral ganglia, but utilize the peripheral tissues those neurons innervate for productive replication, spread, and transmission. Delivery of virions from replicative pools to the sites of latency requires microtubule-directed retrograde axonal transport from the nerve terminus to the cell body of the sensory neuron. As a corollary, during reactivation newly assembled virions must travel along axonal microtubules in the anterograde direction to return to the nerve terminus and infect peripheral tissues, completing the cycle. Neurotropic alphaherpesviruses can therefore exploit neuronal microtubules and motors for long distance axonal transport, and alternate between periods of sustained plus end- and minus end-directed motion at different stages of their infectious cycle. This review summarizes our current understanding of the molecular details by which this is achieved. Keywords: herpes simplex virus; pseudorabies virus; neurons; anterograde axonal transport; retrograde axonal transport; microtubules; motors 1.
    [Show full text]
  • Where Do We Stand After Decades of Studying Human Cytomegalovirus?
    microorganisms Review Where do we Stand after Decades of Studying Human Cytomegalovirus? 1, 2, 1 1 Francesca Gugliesi y, Alessandra Coscia y, Gloria Griffante , Ganna Galitska , Selina Pasquero 1, Camilla Albano 1 and Matteo Biolatti 1,* 1 Laboratory of Pathogenesis of Viral Infections, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; [email protected] (F.G.); gloria.griff[email protected] (G.G.); [email protected] (G.G.); [email protected] (S.P.); [email protected] (C.A.) 2 Complex Structure Neonatology Unit, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; [email protected] * Correspondence: [email protected] These authors contributed equally to this work. y Received: 19 March 2020; Accepted: 5 May 2020; Published: 8 May 2020 Abstract: Human cytomegalovirus (HCMV), a linear double-stranded DNA betaherpesvirus belonging to the family of Herpesviridae, is characterized by widespread seroprevalence, ranging between 56% and 94%, strictly dependent on the socioeconomic background of the country being considered. Typically, HCMV causes asymptomatic infection in the immunocompetent population, while in immunocompromised individuals or when transmitted vertically from the mother to the fetus it leads to systemic disease with severe complications and high mortality rate. Following primary infection, HCMV establishes a state of latency primarily in myeloid cells, from which it can be reactivated by various inflammatory stimuli. Several studies have shown that HCMV, despite being a DNA virus, is highly prone to genetic variability that strongly influences its replication and dissemination rates as well as cellular tropism. In this scenario, the few currently available drugs for the treatment of HCMV infections are characterized by high toxicity, poor oral bioavailability, and emerging resistance.
    [Show full text]
  • Virus–Host Interactions and Their Roles in Coral Reef Health and Disease
    !"#$"%& Virus–host interactions and their roles in coral reef health and disease Rebecca Vega Thurber1, Jérôme P. Payet1,2, Andrew R. Thurber1,2 and Adrienne M. S. Correa3 !"#$%&'$()(*+%&,(%--.#(+''/%!01(1/$%0-1$23++%(#4&,,+5(5&$-%#6('+1#$0$/$-("0+708-%#0$9(&17( 3%+7/'$080$9(4+$#3+$#6(&17(&%-($4%-&$-1-7("9(&1$4%+3+:-10'(70#$/%"&1'-;(<40#(=-80-5(3%+807-#( &1(01$%+7/'$0+1($+('+%&,(%--.(80%+,+:9(&17(->34&#0?-#($4-(,01@#("-$5--1(80%/#-#6('+%&,(>+%$&,0$9( &17(%--.(-'+#9#$->(7-',01-;(A-(7-#'%0"-($4-(70#$01'$08-("-1$40'2&##+'0&$-7(&17(5&$-%2'+,/>12( &##+'0&$-7(80%+>-#($4&$(&%-(/10B/-($+('+%&,(%--.#6(540'4(4&8-(%-'-08-7(,-##(&$$-1$0+1($4&1( 80%/#-#(01(+3-12+'-&1(#9#$->#;(A-(493+$4-#0?-($4&$(80%/#-#(+.("&'$-%0&(&17(-/@&%9+$-#( 791&>0'&,,9(01$-%&'$(50$4($4-0%(4+#$#(01($4-(5&$-%('+,/>1(&17(50$4(#',-%&'$010&1(C#$+19D('+%&,#($+( 01.,/-1'-(>0'%+"0&,('+>>/10$9(791&>0'#6('+%&,(",-&'401:(&17(70#-&#-6(&17(%--.("0+:-+'4->0'&,( cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest $4&$($4-(01.,/-1'-(+.(80%/#-#(+1(%--.(./1'$0+1(0#(&1(-##-1$0&,('+>3+1-1$(+.($4-#-(:,+"&,,9( 0>3+%$&1$(-180%+1>-1$#; To p - d ow n e f f e c t s Viruses infect all cellular life, including bacteria and evidence that macroorganisms play important parts in The ecological concept that eukaryotes, and contain ~200 megatonnes of carbon the dynamics of viroplankton; for example, sponges can organismal growth and globally1 — thus, they are integral parts of marine eco- filter and consume viruses6,7.
    [Show full text]
  • Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Yellow-Eyed Penguin (Megadyptes Antipodes)
    viruses Article Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Yellow-Eyed Penguin (Megadyptes antipodes) Subir Sarker 1,* , Ajani Athukorala 1, Timothy R. Bowden 2,† and David B. Boyle 2 1 Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia; [email protected] 2 CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia; [email protected] (T.R.B.); [email protected] (D.B.B.) * Correspondence: [email protected]; Tel.: +61-3-9479-2317; Fax: +61-3-9479-1222 † Present address: CSIRO Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia. Abstract: Emerging viral diseases have become a significant concern due to their potential con- sequences for animal and environmental health. Over the past few decades, it has become clear that viruses emerging in wildlife may pose a major threat to vulnerable or endangered species. Diphtheritic stomatitis, likely to be caused by an avipoxvirus, has been recognised as a signifi- cant cause of mortality for the endangered yellow-eyed penguin (Megadyptes antipodes) in New Zealand. However, the avipoxvirus that infects yellow-eyed penguins has remained uncharacterised. Here, we report the complete genome of a novel avipoxvirus, penguinpox virus 2 (PEPV2), which was derived from a virus isolate obtained from a skin lesion of a yellow-eyed penguin. The PEPV2 genome is 349.8 kbp in length and contains 327 predicted genes; five of these genes were found to be unique, while a further two genes were absent compared to shearwaterpox virus 2 (SWPV2).
    [Show full text]
  • 25 May 7, 2014
    Joint Pathology Center Veterinary Pathology Services Wednesday Slide Conference 2013-2014 Conference 25 May 7, 2014 ______________________________________________________________________________ CASE I: 3121206023 (JPC 4035610). Signalment: 5-week-old mixed breed piglet, (Sus domesticus). History: Two piglets from the faculty farm were found dead, and another piglet was weak and ataxic and, therefore, euthanized. Gross Pathology: The submitted piglet was in good body condition. It was icteric and had a diffusely pale liver. Additionally, petechial hemorrhages were found on the kidneys, and some fibrin was present covering the abdominal organs. Laboratory Results: The intestine was PCR positive for porcine circovirus (>9170000). Histopathologic Description: Mesenteric lymph node: Diffusely, there is severe lymphoid depletion with scattered karyorrhectic debris (necrosis). Also scattered throughout the section are large numbers of macrophages and eosinophils. The macrophages often contain botryoid basophilic glassy intracytoplasmic inclusion bodies. In fewer macrophages, intranuclear basophilic inclusions can be found. Liver: There is massive loss of hepatocytes, leaving disrupted liver lobules and dilated sinusoids engorged with erythrocytes. The remaining hepatocytes show severe swelling, with micro- and macrovesiculation of the cytoplasm and karyomegaly. Some swollen hepatocytes have basophilic intranuclear, irregular inclusions (degeneration). Throughout all parts of the liver there are scattered moderate to large numbers of macrophages (without inclusions). Within portal areas there is multifocally mild to moderate fibrosis and bile duct hyperplasia. Some bile duct epithelial cells show degeneration and necrosis, and there is infiltration of neutrophils within the lumen. The limiting plate is often obscured mainly by infiltrating macrophages and eosinophils, and fewer neutrophils, extending into the adjacent parenchyma. Scattered are small areas with extra medullary hematopoiesis.
    [Show full text]