Genome Sequencing by Random Priming Methods for Viral Identification

Total Page:16

File Type:pdf, Size:1020Kb

Genome Sequencing by Random Priming Methods for Viral Identification Genome sequencing by random priming methods for viral identification Rosseel Toon Dissertation submitted in fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Veterinary Sciences, Faculty of Veterinary Medicine, Ghent University, 2015 Promotors: Dr. Steven Van Borm Prof. Dr. Hans Nauwynck “The real voyage of discovery consist not in seeking new landscapes, but in having new eyes” Marcel Proust, French writer, 1923 Table of contents Table of contents ....................................................................................................................... 1 List of abbreviations ................................................................................................................. 3 Chapter 1 General introduction ................................................................................................ 5 1. Viral diagnostics and genomics ....................................................................................... 7 2. The DNA sequencing revolution ................................................................................... 12 2.1. Classical Sanger sequencing .................................................................................. 12 2.2. Next-generation sequencing ................................................................................... 16 3. The viral metagenomic workflow ................................................................................. 24 3.1. Sample preparation ................................................................................................ 25 3.2. Sequence independent amplification ..................................................................... 27 3.3. DNA sequencing .................................................................................................... 51 3.4. Bioinformatic data analysis .................................................................................... 52 3.5. Follow-up ............................................................................................................... 55 4. The challenges ............................................................................................................... 56 Chapter 2 Aims of the thesis ................................................................................................... 69 Chapter 3 Implementation and Case studies ........................................................................... 73 Chapter 3.1 Implementation of a viral metagenomic workflow ......................................... 75 Chapter 3.2 Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos) using random access amplification and next generation sequencing technologies .................................................................................... 81 Chapter 3.3 Phylogeographic analysis of avian influenza viruses isolated from Charadriiformes in Belgium confirms intercontinental reassortment in gulls .................. 105 Chapter 3.4 What's in a strain? Viral metagenomics identifies genetic variation and contaminating circoviruses in laboratory isolates of pigeon paramyxovirus type 1 ......... 127 Chapter 3.5 DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe ..................................... 147 1 Chapter 3.6 False-positive results in metagenomic virus discovery, a strong case for follow-up diagnosis ........................................................................................................... 161 Chapter 4 Fine-tuning of methodology ................................................................................. 175 Chapter 4.1 The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing ........................ 177 Chapter 4.2 Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples ............................................................................................... 203 Chapter 5 General discussion ............................................................................................... 229 Summary ............................................................................................................................... 261 Samenvatting ........................................................................................................................ 267 Bibliography ......................................................................................................................... 275 Curriculum Vitae ................................................................................................................. 281 Dankwoord ............................................................................................................................ 285 2 List of abbreviations A Adenine aa Amino acids AFLP Amplified fragment length polymorphism AI(V) Avian influenza A (virus) APMV Avian paramyxovirus BLAST Basic Local Alignment Search Tool bp Bases or base pairs BVDV Bovine viral diarrhea virus C Cytosine CCD Charge-coupled device cDNA Complementary DNA CDS Coding sequence Contigs Contiguous overlapping sets of sequences Cp Crossing point value CPE Cytopathic effect Ct Threshold cycle value Da Dalton (molecular weight unit) ddNTP 2’,3’-dideoxynucleotides (ddATP, ddGTP, ddCTP, ddTTP) DNA Deoxyribonucleic acid DNase Deoxyribonuclease dNTP Deoxynucleoside triphosphates (dATP, dGTP, dCTP, dTTP) DOP-PCR Degenerate-oligonucleotide primer PCR dsDNA Double stranded DNA dsRNA Double stranded RNA EDTA Ethylenediaminetetraacetic acid EID50 50 percent embryo infectious dose ELISA Enzyme-linked immunosorbent assay emPCR Emulsion PCR G Guanine HA Hemagglutination or hemagglutinin gene HI Hemagglutination inhibition HIV Human immunodeficiency virus HPAI High-pathogenic avian influenza virus ICPI Intracerebral pathogenicity index IQR Interquartile range LASL Linker Amplified Shotgun Library LPAI Low-pathogenic avian influenza virus MDA Multiple displacement amplification 3 MID Multiplex identifier N Random nucleotide (A, C, G or T) NA Neuraminidase ND(V) Newcastle disease (virus) NGS Next-generation DNA sequencing nt Nucleotides ORF Open reading frame PBS Phosphate buffered saline PCR Polymerase chain reaction PEG Polyethylene glycol PGM Personal Genome Machine PHV Parvovirus-like hybrid virus PiCV Pigeon circovirus PPMV1 Pigeon type 1 paramyxoviruses (q)[RT]-PCR (quantitative real-time) [reverse transcription] PCR reaction pWGA Primase-based whole genome amplification QV Quality score RACE Rapid Amplification of cDNA Ends RCA Rolling circle amplification RNA Ribonucleic acid RNase Ribonuclease rPCR Random PCR rRNA Ribosomal RNA RT Reverse transcription SARS Severe Acute Respiratory Syndrome SBV Schmallenberg virus SE southeast SISPA Sequence independent single primer amplification SMRT Single molecule real time sequencing SPF Specific-pathogen-free SPIA Single primer isothermal amplification ssDNA Single stranded DNA ssRNA Single stranded RNA T Thymine TCID Tissue culture infective dose U Units of polymerase v/v Volume concentration (% volume/volume) VIDISCA Virus-Discovery-cDNA-Amplified fragment length polymorphism VIDISCA-454 VIDISCA combined with 454 pyrosequencing WGA Whole genome amplification WTA Whole transcriptome amplification 4 CHAPTER 1 General introduction Chapter 1 General introduction 6 Chapter 1 General introduction 1. Viral diagnostics and genomics We live in a globalized society where people move increasingly between countries and continents, and livestock animals are farmed and traded extensively. Emerging and reemerging infectious diseases are a constant threat to livestock and the human population. A recent example is the current Ebola virus disease epidemic in West Africa which started in March 2014. This virus has already affected more than 22,000 people, and killed over 9,000 (according to data from World Health Organization on 8 February 2015). Furthermore, recent reviews indicate that the majority of emerging human infections are zoonotic. Therefore, contact with livestock or wildlife increases the probability of infections threatening human populations and individuals lacking immunity. About 15 million (>25 %) of 57 million annual human deaths worldwide are estimated to be linked to infectious diseases [1]. Moreover, livestock diseases may result in significant economic losses and socio-economic consequences. Viral diseases are often spread and transmitted by vectors such as bloodsucking mosquitoes, ticks and wildlife animals. Sometimes, an intermediate host like a domestic animal is the link between viral circulations in wildlife and humans. For instance, some human infections originating from bats, such as Nipah, Hendra, SARS and Ebola viral infections, may involve intermediate amplification in pigs, horses, civets and primates respectively [2]. Complex pathogen lifecycles complicate the control of diseases. Rapid diagnosis of infectious diseases is essential in order to take appropriate action to control livestock and human diseases. Characterization of new pathogens will help to understand diseases and is an important step in the development of vaccines and better diagnostic tests. Viruses are the most abundant infectious agents on the planet. In an apparently sterile environment like sea water, the number of virus particles is estimated at 106 to 109 particles per milliliter [3].
Recommended publications
  • 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]
  • Nucleotide Amino Acid Size (Nt) #Orfs Marnavirus Heterosigma Akashiwo Heterosigma Akashiwo RNA Heterosigma Lang Et Al
    Supplementary Table 1: Summary of information for all viruses falling within the seven Marnaviridae genera in our analyses. Accession Genome Genus Species Virus name Strain Abbreviation Source Country Reference Nucleotide Amino acid Size (nt) #ORFs Marnavirus Heterosigma akashiwo Heterosigma akashiwo RNA Heterosigma Lang et al. , 2004; HaRNAV AY337486 AAP97137 8587 One Canada RNA virus 1 virus akashiwo Tai et al. , 2003 Marine single- ASG92540 Moniruzzaman et Classification pending Q sR OV 020 KY286100 9290 Two celled USA ASG92541 al ., 2017 eukaryotes Marine single- Moniruzzaman et Classification pending Q sR OV 041 KY286101 ASG92542 9328 One celled USA al ., 2017 eukaryotes APG78557 Classification pending Wenzhou picorna-like virus 13 WZSBei69459 KX884360 9458 One Bivalve China Shi et al ., 2016 APG78557 Classification pending Changjiang picorna-like virus 2 CJLX30436 KX884547 APG79001 7171 One Crayfish China Shi et al ., 2016 Beihai picorna-like virus 57 BHHQ57630 KX883356 APG76773 8518 One Tunicate China Shi et al ., 2016 Classification pending Beihai picorna-like virus 57 BHJP51916 KX883380 APG76812 8518 One Tunicate China Shi et al ., 2016 Marine single- ASG92530 Moniruzzaman et Classification pending N OV 137 KY130494 7746 Two celled USA ASG92531 al ., 2017 eukaryotes Hubei picorna-like virus 7 WHSF7327 KX884284 APG78434 9614 One Pill worm China Shi et al ., 2016 Classification pending Hubei picorna-like virus 7 WHCC111241 KX884268 APG78407 7945 One Insect China Shi et al ., 2016 Sanxia atyid shrimp virus 2 WHCCII13331 KX884278 APG78424 10445 One Insect China Shi et al ., 2016 Classification pending Freshwater atyid Sanxia atyid shrimp virus 2 SXXX37884 KX883708 APG77465 10400 One China Shi et al ., 2016 shrimp Labyrnavirus Aurantiochytrium single Aurantiochytrium single stranded BAE47143 Aurantiochytriu AuRNAV AB193726 9035 Three4 Japan Takao et al.
    [Show full text]
  • Computational Exploration of Virus Diversity on Transcriptomic Datasets
    Computational Exploration of Virus Diversity on Transcriptomic Datasets Digitaler Anhang der Dissertation zur Erlangung des Doktorgrades (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Simon Käfer aus Andernach Bonn 2019 Table of Contents 1 Table of Contents 1 Preliminary Work - Phylogenetic Tree Reconstruction 3 1.1 Non-segmented RNA Viruses ........................... 3 1.2 Segmented RNA Viruses ............................. 4 1.3 Flavivirus-like Superfamily ............................ 5 1.4 Picornavirus-like Viruses ............................. 6 1.5 Togavirus-like Superfamily ............................ 7 1.6 Nidovirales-like Viruses .............................. 8 2 TRAVIS - True Positive Details 9 2.1 INSnfrTABRAAPEI-14 .............................. 9 2.2 INSnfrTADRAAPEI-16 .............................. 10 2.3 INSnfrTAIRAAPEI-21 ............................... 11 2.4 INSnfrTAORAAPEI-35 .............................. 13 2.5 INSnfrTATRAAPEI-43 .............................. 14 2.6 INSnfrTBERAAPEI-19 .............................. 15 2.7 INSytvTABRAAPEI-11 .............................. 16 2.8 INSytvTALRAAPEI-35 .............................. 17 2.9 INSytvTBORAAPEI-47 .............................. 18 2.10 INSswpTBBRAAPEI-21 .............................. 19 2.11 INSeqtTAHRAAPEI-88 .............................. 20 2.12 INShkeTCLRAAPEI-44 .............................. 22 2.13 INSeqtTBNRAAPEI-11 .............................. 23 2.14 INSeqtTCJRAAPEI-20
    [Show full text]
  • Viral Diversity in Tree Species
    Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Biologia Microbiana Doctoral Thesis Viral diversity in tree species FLÁVIA MILENE BARROS NERY Brasília - DF, 2020 FLÁVIA MILENE BARROS NERY Viral diversity in tree species Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Microbiology by the Post - Graduate Program in Microbiology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Fernando Lucas Melo BRASÍLIA, DF - BRAZIL FICHA CATALOGRÁFICA NERY, F.M.B Viral diversity in tree species Flávia Milene Barros Nery Brasília, 2025 Pages number: 126 Doctoral Thesis - Programa de Pós-Graduação em Biologia Microbiana, Universidade de Brasília, DF. I - Virus, tree species, metagenomics, High-throughput sequencing II - Universidade de Brasília, PPBM/ IB III - Viral diversity in tree species A minha mãe Ruth Ao meu noivo Neil Dedico Agradecimentos A Deus, gratidão por tudo e por ter me dado uma família e amigos que me amam e me apoiam em todas as minhas escolhas. Minha mãe Ruth e meu noivo Neil por todo o apoio e cuidado durante os momentos mais difíceis que enfrentei durante minha jornada. Aos meus irmãos André, Diego e meu sobrinho Bruno Kawai, gratidão. Aos meus amigos de longa data Rafaelle, Evanessa, Chênia, Tati, Leo, Suzi, Camilets, Ricardito, Jorgito e Diego, saudade da nossa amizade e dos bons tempos. Amo vocês com todo o meu coração! Minha orientadora e grande amiga Profa Rita de Cássia Pereira Carvalho, a quem escolhi e fui escolhida para amar e fazer parte da família.
    [Show full text]
  • Viruses in Transplantation - Not Always Enemies
    Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause
    [Show full text]
  • Diversity and Classification of Reoviruses in Crustaceans: a Proposal
    Journal of Invertebrate Pathology 182 (2021) 107568 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity and classification of reoviruses in crustaceans: A proposal Mingli Zhao a, Camila Prestes dos Santos Tavares b, Eric J. Schott c,* a Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA b Integrated Group of Aquaculture and Environmental Studies, Federal University of Parana,´ Rua dos Funcionarios´ 1540, Curitiba, PR 80035-050, Brazil c Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA ARTICLE INFO ABSTRACT Keywords: A variety of reoviruses have been described in crustacean hosts, including shrimp, crayfish,prawn, and especially P virus in crabs. However, only one genus of crustacean reovirus - Cardoreovirus - has been formally recognized by ICTV CsRV1 (International Committee on Taxonomy of Viruses) and most crustacean reoviruses remain unclassified. This Cardoreovirus arises in part from ambiguous or incomplete information on which to categorize them. In recent years, increased Crabreovirus availability of crustacean reovirus genomic sequences is making the discovery and classification of crustacean Brachyuran Phylogenetic analysis reoviruses faster and more certain. This minireview describes the properties of the reoviruses infecting crusta­ ceans and suggests an overall classification of brachyuran crustacean reoviruses based on a combination of morphology, host, genome organization pattern and phylogenetic sequence analysis. 1. Introduction fish, crustaceans, marine protists, insects, ticks, arachnids, plants and fungi (Attoui et al., 2005; Shields et al., 2015). Host range and disease 1.1. Genera of Reoviridae family symptoms are also important indicators that help to identify viruses of different genera (Attoui et al., 2012).
    [Show full text]
  • Origin and Evolution of Emerging Liaoning Virus(Genus Seadornavirus, Family Reoviridae)
    Origin and Evolution of Emerging Liaoning Virusgenus Seadornavirus, family Reoviridae) Jun Zhang Shandong University of Technology Hong Liu ( [email protected] ) Shandong University of Technology https://orcid.org/0000-0002-5182-4750 Jiahui Wang Shandong University of Technology Jiheng Wang Shandong University of Technology Jianming Zhang Shandong University of Technology Jiayue Wang Shandong University of Technology Xin Zhang Shandong University of Technology Hongfang Ji Shandong University of Technology Zhongfen Ding Shandong University of Technology Han Xia Chinese Academy of Sciences Chunyang Zhang Shandong University of Technology Qian Zhao Shandong University of Technology Guodong Liang Chinese Center for Disease Control and Prevention Research Keywords: Liaoning virus, LNV, Seadornavirus, Evolution, Migration Posted Date: January 15th, 2020 DOI: https://doi.org/10.21203/rs.2.20915/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract Background:Liaoning virus(LNV) is a member of the genus Seadornavirus, family Reoviridae and has been isolated from kinds of sucking insects in Asia and Australia. However, there are no systematic studies describe the molecular genetic evolution and migration of LNVs isolated from different time, regions and vectors. Methods:Here, a phylogenetic analysis using Bayesian Markov chain Monte Carlo simulations was conducted on the LNVs isolated from a variety of vectors during 1990-2014,worldwide. Results:The phylogenetic analysis demonstrated that the LNV could be divided into 3 genotypes, of which genotype 1 mainly composed of LNVs isolated from Australia during 1990 to 2014 as well as the original LNV strain(LNV-NE97-31) isolated from Liaoning province in northern China in 1997,genotype 2 comprised of the isolates all from Xinjiang province in western China and genotype 3 consisted the isolates from Qinghai and Shanxi province of central China.
    [Show full text]
  • WO 2018/183889 Al 04 October 2018 (04.10.2018) W ! P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2018/183889 Al 04 October 2018 (04.10.2018) W ! P O PCT (51) International Patent Classification: bridge, MA 02139 (US). HICKLIN, Daniel; c/o Potenza C07K 16/22 (2006.01) A61K 39/00 (2006.01) Therapeutics, Inc., 1030 Massachusetts Avenue, Suite 210, C07K 16/28 (2006.01) Cambridge, MA 02139 (US). SEIDEL-DUGAN, Cyn¬ thia; c/o Potenza Therapeutics, Inc., 1030 Massachusetts (21) International Application Number: Avenue, Suite 210, Cambridge, MA 02139 (US). WINS¬ PCT/US20 18/025460 TON, William; c/o Potenza Therapeutics, Inc., 1030 Mass (22) International Filing Date: achusetts Avenue, Suite 210, Cambridge, MA 02139 (US). 30 March 2018 (30.03.2018) BRODKIN, Heather; c/o Potenza Therapeutics, Inc., 1030 Massachusetts Avenue, Suite 210, Cambridge, MA 02139 (25) Filing Language: English (US). SALMERON-GARCIA, Jose-Andres; c/o Poten (26) Publication Language: English za Therapeutics, Inc., 1030 Massachusetts Avenue, Suite 210, Cambridge, MA 02139 (US). NIRSCHL, Christo¬ (30) Priority Data: pher, James; c/o Potenza Therapeutics, Inc., 1030 Massa 62/479,042 30 March 2017 (30.03.2017) US chusetts Avenue, Suite 210, Cambridge, MA 02139 (US). (71) Applicant: POTENZA THERAPEUTICS, INC. (74) Agent: KABLER, Kevin et al; Fenwick & West LLP, 801 [US/US]; 1030 Massachusetts Avenue, Suite 210, Cam Calfornia Street, Mountain View, CA 94041 (US). bridge, MA 02139 (US). (81) Designated States (unless otherwise indicated, for every (72) Inventor; and kind of national protection available): AE, AG, AL, AM, (71) Applicant: STEINER, Philipp [CH/US]; c/o Potenza AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, Therapeutics, Inc., 1030 Massachusetts Avenue, Suite 210, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, Cambridge, MA 02139 (US).
    [Show full text]
  • Annual Conference 2018 Abstract Book
    Annual Conference 2018 POSTER ABSTRACT BOOK 10–13 April, ICC Birmingham, UK @MicrobioSoc #Microbio18 Virology Workshop: Clinical Virology Zone A Presentations: Wednesday and Thursday evening P001 Rare and Imported Pathogens Lab (RIPL) turn around time (TAT) for the telephoned communication of positive Zika virus (ZIKV) PCR and serology results. Zaneeta Dhesi, Emma Aarons Rare and Imported Pathogens Lab, Public Health England, Salisbury, United Kingdom Abstract Background: RIPL introduced developmental assays for ZIKV PCR and serology on 18/01/16 and 10/03/16 respectively. The published ZIKV test TATs were 5 days for PCR and 7 days for serology. Methods: All ZIKV RNA positive, seroconversion and “probable” cases diagnosed at RIPL up until 31/05/17 were identified. For each case, the date on which the relevant positive sample was received, and the date on which it was telephoned out to the requestor was ascertained. The number of working days between these two dates was calculated. Results: ZIKV PCR - 151 ZIKV PCR positive results were identified, of which 4 samples were excluded because no TAT could be calculated. The mean TAT for the remaining 147 samples was 1.7 working days. Ninety percent of these results were telephoned within 3 or fewer days of the sample having been received. There was 1 sample where the TAT was above the 90th centile. ZIKV Serology - 147 seroconversion or “Probable” ZIKV cases diagnosed serologically were identified. The mean TAT for these samples was 2.5 working days. Ninety percent of these results were telephoned within 4 or fewer days of the sample having been received.
    [Show full text]
  • Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda Africana Bat Flies in South Africa
    viruses Article Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa Petrus Jansen van Vuren 1,2, Michael Wiley 3, Gustavo Palacios 3, Nadia Storm 1,2, Stewart McCulloch 2, Wanda Markotter 2, Monica Birkhead 1, Alan Kemp 1 and Janusz T. Paweska 1,2,4,* 1 Centre for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham 2131, South Africa; [email protected] (P.J.v.V.); [email protected] (N.S.); [email protected] (M.B.); [email protected] (A.K.) 2 Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria 0028, South Africa; [email protected] (S.M.); [email protected] (W.K.) 3 Center for Genomic Science, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; [email protected] (M.W.); [email protected] (G.P.) 4 Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa * Correspondence: [email protected]; Tel.: +27-11-3866382 Academic Editor: Andrew Mehle Received: 27 November 2015; Accepted: 23 February 2016; Published: 29 February 2016 Abstract: We report on the isolation of a novel fusogenic orthoreovirus from bat flies (Eucampsipoda africana) associated with Egyptian fruit bats (Rousettus aegyptiacus) collected in South Africa. Complete sequences of the ten dsRNA genome segments of the virus, tentatively named Mahlapitsi virus (MAHLV), were determined. Phylogenetic analysis places this virus into a distinct clade with Baboon orthoreovirus, Bush viper reovirus and the bat-associated Broome virus.
    [Show full text]
  • Arenaviridae Astroviridae Filoviridae Flaviviridae Hantaviridae
    Hantaviridae 0.7 Filoviridae 0.6 Picornaviridae 0.3 Wenling red spikefish hantavirus Rhinovirus C Ahab virus * Possum enterovirus * Aronnax virus * * Wenling minipizza batfish hantavirus Wenling filefish filovirus Norway rat hunnivirus * Wenling yellow goosefish hantavirus Starbuck virus * * Porcine teschovirus European mole nova virus Human Marburg marburgvirus Mosavirus Asturias virus * * * Tortoise picornavirus Egyptian fruit bat Marburg marburgvirus Banded bullfrog picornavirus * Spanish mole uluguru virus Human Sudan ebolavirus * Black spectacled toad picornavirus * Kilimanjaro virus * * * Crab-eating macaque reston ebolavirus Equine rhinitis A virus Imjin virus * Foot and mouth disease virus Dode virus * Angolan free-tailed bat bombali ebolavirus * * Human cosavirus E Seoul orthohantavirus Little free-tailed bat bombali ebolavirus * African bat icavirus A Tigray hantavirus Human Zaire ebolavirus * Saffold virus * Human choclo virus *Little collared fruit bat ebolavirus Peleg virus * Eastern red scorpionfish picornavirus * Reed vole hantavirus Human bundibugyo ebolavirus * * Isla vista hantavirus * Seal picornavirus Human Tai forest ebolavirus Chicken orivirus Paramyxoviridae 0.4 * Duck picornavirus Hepadnaviridae 0.4 Bildad virus Ned virus Tiger rockfish hepatitis B virus Western African lungfish picornavirus * Pacific spadenose shark paramyxovirus * European eel hepatitis B virus Bluegill picornavirus Nemo virus * Carp picornavirus * African cichlid hepatitis B virus Triplecross lizardfish paramyxovirus * * Fathead minnow picornavirus
    [Show full text]
  • Desenvolvimento E Avaliação De Uma Plataforma De Diagnóstico Para Meningoencefalites Virais Por Pcr Em Tempo Real
    DANILO BRETAS DE OLIVEIRA DESENVOLVIMENTO E AVALIAÇÃO DE UMA PLATAFORMA DE DIAGNÓSTICO PARA MENINGOENCEFALITES VIRAIS POR PCR EM TEMPO REAL Orientadora: Profa. Dra. Erna Geessien Kroon Co-orientador: Dr. Gabriel Magno de Freitas Almeida Co-orientador: Prof. Dr. Jônatas Santos Abrahão Belo Horizonte Janeiro de 2015 DANILO BRETAS DE OLIVEIRA DESENVOLVIMENTO E AVALIAÇÃO DE UMA PLATAFORMA DE DIAGNÓSTICO PARA MENINGOENCEFALITES VIRAIS POR PCR EM TEMPO REAL Tese de doutorado apresentada ao Programa de Pós-Graduação em Microbiologia do Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, como requisito à obtenção do título de doutor em Microbiologia. Orientadora: Profa. Dra. Erna Geessien Kroon Co-orientador: Dr. Gabriel Magno de Freitas Almeida Co-orientador: Prof. Dr. Jônatas Santos Abrahão Belo Horizonte Janeiro de 2015 SUMÁRIO LISTA DE FIGURAS .......................................................................................... 7 LISTA DE TABELAS ........................................................................................ 10 LISTA DE ABREVIATURAS ............................................................................. 11 I. INTRODUÇÃO .............................................................................................. 17 1.1. INFECÇÕES VIRAIS NO SISTEMA NERVOSO CENTRAL (SNC) ....... 18 1.2. AGENTES VIRAIS CAUSADORES DE MENINGOENCEFALITES .......... 22 1.2.1. VÍRUS DA FAMÍLIA Picornaviridae ........................................................ 22 1.2.1.1.VÍRUS DO GÊNERO Enterovirus .......................................................
    [Show full text]