Comparative Viral Metagenomics from Chicken Feces and Farm Dust in the Netherlands
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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. -
The Viruses of Wild Pigeon Droppings
The Viruses of Wild Pigeon Droppings Tung Gia Phan1,2, Nguyen Phung Vo1,3,A´ kos Boros4,Pe´ter Pankovics4,Ga´bor Reuter4, Olive T. W. Li6, Chunling Wang5, Xutao Deng1, Leo L. M. Poon6, Eric Delwart1,2* 1 Blood Systems Research Institute, San Francisco, California, United States of America, 2 Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America, 3 Pharmacology Department, School of Pharmacy, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh, Vietnam, 4 Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, A´ NTSZ Regional Institute of State Public Health Service, Pe´cs, Hungary, 5 Stanford Genome Technology Center, Stanford, California, United States of America, 6 Centre of Influenza Research and School of Public Health, University of Hong Kong, Hong Kong SAR Abstract Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. -
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 -
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. -
The Intestinal Virome of Malabsorption Syndrome-Affected and Unaffected
Virus Research 261 (2019) 9–20 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics T ⁎ Diane A. Limaa, , Samuel P. Cibulskib, Caroline Tochettoa, Ana Paula M. Varelaa, Fabrine Finklera, Thais F. Teixeiraa, Márcia R. Loikoa, Cristine Cervac, Dennis M. Junqueirad, Fabiana Q. Mayerc, Paulo M. Roehea a Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil b Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil c Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil d Centro Universitário Ritter dos Reis - UniRitter, Health Science Department, Porto Alegre, RS, Brazil ARTICLE INFO ABSTRACT Keywords: Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, Enteric disorders characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have Virome been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric Broiler chickens viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) High-throughput sequencing chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. -
The Foot-And-Mouth Disease Virus Replication Complex
The Foot-and-Mouth Disease Virus Replication Complex: Dissecting the Role of the Viral Polymerase (3Dpol) and Investigating Interactions with Phosphatidylinositol-4-kinase (PI4K) Eleni-Anna Loundras Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Molecular and Cellular Biology August 2017 The candidate confirms that the work submitted is her own, except where work which has formed part of jointly authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. The work appearing in Chapter 3 and Chapter 4 of the thesis has appeared in publications as follow: • Employing transposon mutagenesis in investigate foot-and-mouth disease virus replication. Journal of Virology (2015), 96 (12), pp 3507-3518., DOI: 10.1099/jgv.0.000306. Morgan R. Herod (MRH), Eleni-Anna Loundras (EAL), Joseph C. Ward, Fiona Tulloch, David J. Rowlands (DJR), Nicola J. Stonehouse (NJS). The author (EAL) was responsible for assisting with preparation of experiments and production of experimental data. MRH, as primary author drafted the manuscript and designed the experiments. NJS and DJR conceived the idea, supervised the project, and edited the manuscript. • Both cis and trans activities of foot-and-mouth disease virus 3D polymerase are essential for viral replication. Journal of Virology (2016), 90 (15), pp 6864-688., DOI: 10.1128/JVI.00469-16. Morgan R. Herod, Cristina Ferrer-Orta, Eleni-Anna Loundras, Joseph C. -
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 ....................................................... -
Identification and Genome Characterization of the First Sicinivirus Isolate from Chickens in Mainland China by Using Viral Metagenomics
RESEARCH ARTICLE Identification and Genome Characterization of the First Sicinivirus Isolate from Chickens in Mainland China by Using Viral Metagenomics Hongzhuan Zhou1, Shanshan Zhu1, Rong Quan1, Jing Wang1, Li Wei1, Bing Yang1, Fuzhou Xu1, Jinluo Wang1, Fuyong Chen2, Jue Liu1* 1 Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Garden Middle Road, Haidian District, Beijing, 100097, People’s Republic of China, 2 College of a11111 Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100197, People’s Republic of China * [email protected] Abstract OPEN ACCESS Unlike traditional virus isolation and sequencing approaches, sequence-independent ampli- Citation: Zhou H, Zhu S, Quan R, Wang J, Wei L, Yang B, et al. (2015) Identification and Genome fication based viral metagenomics technique allows one to discover unexpected or novel Characterization of the First Sicinivirus Isolate from viruses efficiently while bypassing culturing step. Here we report the discovery of the first Chickens in Mainland China by Using Viral Sicinivirus isolate (designated as strain JSY) of picornaviruses from commercial layer chick- Metagenomics. PLoS ONE 10(10): e0139668. ens in mainland China by using a viral metagenomics technique. This Sicinivirus isolate, doi:10.1371/journal.pone.0139668 which contains a whole genome of 9,797 nucleotides (nt) excluding the poly(A) tail, pos- Editor: Luis Menéndez-Arias, Centro de Biología sesses one of the largest picornavirus genome so far reported, but only shares 88.83% and Molecular Severo Ochoa (CSIC-UAM), SPAIN 82.78% of amino acid sequence identity to that of ChPV1 100C (KF979332) and Sicinivirus Received: March 26, 2015 1 strain UCC001 (NC_023861), respectively. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person -
Sustained RNA Virome Diversity in Antarctic Penguins and Their Ticks
The ISME Journal (2020) 14:1768–1782 https://doi.org/10.1038/s41396-020-0643-1 ARTICLE Sustained RNA virome diversity in Antarctic penguins and their ticks 1 2 2 3 2 1 Michelle Wille ● Erin Harvey ● Mang Shi ● Daniel Gonzalez-Acuña ● Edward C. Holmes ● Aeron C. Hurt Received: 11 December 2019 / Revised: 16 March 2020 / Accepted: 20 March 2020 / Published online: 14 April 2020 © The Author(s) 2020. This article is published with open access Abstract Despite its isolation and extreme climate, Antarctica is home to diverse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome diversity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To assess whether penguins have limited microbial diversity we determined the RNA viromes of three species of penguins and their ticks sampled on the Antarctic peninsula. Using total RNA sequencing we identified 107 viral species, comprising likely penguin associated viruses (n = 13), penguin diet and microbiome associated viruses (n = 82), and tick viruses (n = 8), two of which may have the potential to infect penguins. Notably, the level of virome diversity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data run counter to the idea that penguins are subject 1234567890();,: 1234567890();,: to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs. -
Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model
RESEARCH ARTICLE Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model Susanna K. P. Lau1,2,3,4☯, Patrick C. Y. Woo1,2,3,4☯, Kenneth S. M. Li4☯, Hao-Ji Zhang5☯, Rachel Y. Y. Fan4, Anna J. X. Zhang4, Brandon C. C. Chan4, Carol S. F. Lam4, Cyril C. Y. Yip4, Ming-Chi Yuen6, Kwok-Hung Chan4, Zhi-Wei Chen1,2,3,4, Kwok-Yung Yuen1,2,3,4* a11111 1 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China, 2 Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China, 3 Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China, 4 Department of Microbiology, The University of Hong Kong, Hong Kong, China, 5 Department of Veterinary Medicine, Foshan University, Foshan, China, 6 Food and Environmental Hygiene Department, Hong Kong, China ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Lau SKP, Woo PCY, Li KSM, Zhang H-J, Fan RYY, Zhang AJX, et al. (2016) Identification of Novel Rosavirus Species That Infects Diverse Abstract Rodent Species and Causes Multisystemic Dissemination in Mouse Model. PLoS Pathog 12 While novel picornaviruses are being discovered in rodents, their host range and pathoge- (10): e1005911. doi:10.1371/journal.ppat.1005911 nicity are largely unknown. We identified two novel picornaviruses, rosavirus B from the Editor: Eric L Delwart, Blood Systems Research street rat, Norway rat, and rosavirus C from five different wild rat species (chestnut spiny Institute, UNITED STATES rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) in Received: May 19, 2016 China. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID- 19 Pandemic: A
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID- 19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. March 2021 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Raphael Freitas de Souza, Faculty of Dentistry, McGill University Paul Allison, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University March 31, 2021 1 Contents Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. .................................................................................................................................. 1 Foreword to the second update ............................................................................................. 4 Introduction ............................................................................................................................. 5 Project goal............................................................................................................................. 5 Specific objectives .................................................................................................................. 6 Methods used to identify and include relevant literature ......................................................