Human Adenovirus Removal in Wastewater Treatment and Membrane Process
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Non-Norovirus Viral Gastroenteritis Outbreaks Reported to the National Outbreak Reporting System, USA, 2009–2018 Claire P
Non-Norovirus Viral Gastroenteritis Outbreaks Reported to the National Outbreak Reporting System, USA, 2009–2018 Claire P. Mattison, Molly Dunn, Mary E. Wikswo, Anita Kambhampati, Laura Calderwood, Neha Balachandran, Eleanor Burnett, Aron J. Hall During 2009–2018, four adenovirus, 10 astrovirus, 123 The Study rotavirus, and 107 sapovirus gastroenteritis outbreaks NORS is a dynamic, voluntary outbreak reporting were reported to the US National Outbreak Reporting system. For each reported outbreak, health depart- System (annual median 30 outbreaks). Most were at- ments report the mode of transmission, number of tributable to person-to-person transmission in long-term confirmed and suspected cases, and aggregate epi- care facilities, daycares, and schools. Investigations of demiologic and demographic information as avail- norovirus-negative gastroenteritis outbreaks should in- able. NORS defines outbreaks as >2 cases of similar clude testing for these viruses. illness associated with a common exposure or epi- demiologic link (9). Health departments determine n the United States, ≈179 million cases of acute gas- reported outbreak etiologies on the basis of available troenteritis (AGE) occur annually (1). Norovirus is I laboratory, epidemiologic, and clinical data; specific the leading cause of AGE in the United States; other laboratory testing protocols vary by health depart- viral causes include adenovirus (specifically group F ment. Outbreak etiologies are considered confirmed or types 40 and 41), astrovirus, sapovirus, and rotavi- when >2 laboratory-confirmed cases are reported rus (2,3). These viruses are spread primarily through and considered suspected when <2 laboratory-con- the fecal–oral route through person-to-person contact firmed cases are reported. Outbreaks are considered or through contaminated food, water, or fomites (4–8). -
Package Insert Astrovirus, Sapovirus Open System PCR Reagents 450-052-Series
Package Insert Astrovirus, Sapovirus Open System PCR Reagents 450-052-Series For Research Use Only Research use only reagents are not intended for human or animal diagnostic use. It is the responsibility of the end user to determine the performance of the reagents in an appropriately designed validation study for their intended use. The Astrovirus, Sapovirus real-time PCR-based detection reagent is manufactured and packaged as an open system reagent (OSR) for use with open system platforms and has to be validated by the user. Examples of open system platforms are the Applied Biosystems QuantStudioTM 5 (Design & Analysis software version 1.5.1 or later), Applied Biosystems 7500 Fast Dx (SDS software version 1.4 or later), Bio-Rad CFX96 TouchTM or CFX384 TouchTM (Maestro software version 1.1 or later) real-time PCR platforms. PLEASE READ ENTIRE PACKAGE INSERT BEFORE PROCEEDING TO USE THE OSR. PRODUCT OVERVIEW The BioGX Sample-Ready™ OSR has been formulated in lyophilized format for the multiplex real-time PCR-based detection of RNA from Astrovirus (ORF1a gene1), Sapovirus (polymerase/capsid junction gene1) and a synthetic single stranded RNA [Internal Amplification Control (IAC)/Sample Processing Control (SPC)]. The synthetic single stranded RNA serves as both a sample processing control and an internal amplification control. Two different formats for the lyophilized Sample-Ready OSR kits are available: 1. BD MAXTM System REF 450-052-C-MAX 2. ABI QuantStudioTM 5, ABI 7500 Fast Dx, Bio-Rad CFX96 TouchTM and Bio-Rad CFX384 TouchTMPlatforms REF 450-052-LMP Note: BD MAXTM System OSR (450-052-C-MAX) contains all PCR primers, probes, enzymes, dNTPs, MgCl2, buffers, and other components required for PCR reaction. -
Colaboración Especial
Rev Esp Salud Pública 2005; 79: 253-269 N.º 2 - Marzo-Abril 2005 COLABORACIÓN ESPECIAL EFECTOS SOBRE LA SALUD DE LA CONTAMINACIÓN DE AGUA Y ALIMENTOS POR VIRUS EMERGENTES HUMANOS, (*) Sílvia Bofill-Mas, Pilar Clemente-Casares, Néstor Albiñana-Giménez, Carlos Maluquer de Motes Porta, Ayalkibet Hundesa Gonfa y Rosina Girones Llop Departamento de Microbiología. Facultad de Biología. Universidad de Barcelona. RESUMEN Effects on Health of Water and Food El desarrollo de tecnologías moleculares aplicadas a estudios Contamination by Emergent ambientales ha permitido constatar que incluso en países altamente industrializados existe una alta prevalencia de virus en el medio Human Viruses ambiente, lo que causa un importante impacto en la salud pública e importantes pérdidas económicas, principalmente a través de la The development of molecular technologies applied to environ- transmisión de virus por agua y alimentos. Concentraciones signifi- mental studies has shown that even in highly industrialized countries cativas de virus son detectadas en las aguas vertidas al ambiente y en there is a high prevalence of viruses in the environment that repre- los biosólidos generados en plantas de tratamiento de agua residual. sents an important impact on public health and substantial economic En este trabajo se describen las características generales de la conta- losses mainly related to the transmission of viruses through water minación ambiental por virus, principalmente por virus emergentes, and food. Significant concentrations of viruses are detected in the analizándose con mayor profundidad los virus de la hepatitis E water flowed to the environment and in the biosolids generated in (VHE) y los poliomavirus humanos como los virus contaminantes wastewater treatment plants. -
Detection and Characterization of a Novel Norovirus in Bats, China
Virologica Sinica (2018) 33:100–103 www.virosin.org https://doi.org/10.1007/s12250-018-0010-9 www.springer.com/12250 (0123456789().,-volV)(0123456789().,-volV) LETTER Detection and Characterization of a Novel Norovirus in Bats, China Ling’en Yang1,2 · Quanxi Wang1 · Lin Xu2 · Changchun Tu1,2,3 · Xiaohong Huang1 · Biao He2,3 Received: 7 November 2017 / Accepted: 21 December 2017 © Wuhan Institute of Virology, CAS and Springer Nature Singapore Pte Ltd. 2018. This article is an open access publication Dear Editor, found in GI, GII and GIV, while porcine NoVs group in distinct genotypes within GII, bovine and ovine viruses Noroviruses (NoVs) are second only to the rotaviruses as belong exclusively to GIII, murine NoVs are grouped in etiologic agents of acute fulminant gastroenteritis in infants GV, canine NoVs are in GIV and GVI, and lion viruses and young children worldwide, with an estimated 200,000 have been found only in GIV (Green 2013). deaths per year in children younger than 5 years of age in As one of the most widely distributed mammals, bats are developing countries (Patel et al. 2008). NoVs are classi- important natural reservoirs of viruses, of which more than fied within the genus Norovirus of the family Caliciviridae 137 have been discovered (Luis et al. 2013), including with Norwalk virus as its prototype member (ICTV 2017). many highly pathogenic agents such as Hendra and Nipah The virions are small (38–40 nm in diameter) nonen- viruses (Yob et al. 2001), SARS-related coronaviruses (Ge veloped, with an icosahedral capsidanda linear, positive- et al. -
Epidemiology and Molecular Characterization of Sapovirus and Astrovirus in Japan, 20082009
Jpn. J. Infect. Dis., 63, 2010 Laboratory and Epidemiology Communications Epidemiology and Molecular Characterization of Sapovirus and Astrovirus in Japan, 20082009 Wisoot Chanit, Aksara Thongprachum, Shoko Okitsu1, Masashi Mizuguchi, and Hiroshi Ushijima1* Department of Developmental Medical Sciences, Institute of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo 1130033; and 1Aino Health Science Center, Aino University, Tokyo 1500002, Japan Communicated by Takaji Wakita (Accepted June 3, 2010) Sapovirus (SaV) and human astrovirus (HAstV) are known to cause acute gastroenteritis in infants and young children (1,2). As a member of the family Caliciviridae, SaVs have a singlestranded positive sense RNA genome and are divided into five genogroups (GIGV). At least 13 genotypes can be distinguished within GI and GII (3). HAstVs belonging to the family Astroviridae have been classified into eight serotypes HAstV1HAstV8. In general, HAstV1 is the most prevalent whereas type 3, 4, 7, and 8 are rare (4,5). A total of 662 fecal specimens were collected from nonhospitalized children with acute gastroenteritis in pediatric clinics in six localities in Japan (Tokyo, Sapporo, Saga, Osaka, Shizuoka, and Maizuru) during July 2008June 2009. RNA was extracted and purified using the QIAamp Viral RNA Mini kit (Qiagen, Hilden, Germany). Multiplex RTPCR with specific primers re sulted in the identification of SaV and HAstV (6). Nu cleotide sequences of SaV and HAstVpositive PCR products were determined using BigDye terminator cy cle sequencing kit and ABI Prism 310 Genetic Analyzer (Applied Biosystems, Foster City, Calif., USA). Phylo genetic trees were generated using the MEGA version 4 (7). -
HUMAN ADENOVIRUS Credibility of Association with Recreational Water: Strongly Associated
6 Viruses This chapter summarises the evidence for viral illnesses acquired through ingestion or inhalation of water or contact with water during water-based recreation. The organisms that will be described are: adenovirus; coxsackievirus; echovirus; hepatitis A virus; and hepatitis E virus. The following information for each organism is presented: general description, health aspects, evidence for association with recreational waters and a conclusion summarising the weight of evidence. © World Health Organization (WHO). Water Recreation and Disease. Plausibility of Associated Infections: Acute Effects, Sequelae and Mortality by Kathy Pond. Published by IWA Publishing, London, UK. ISBN: 1843390663 192 Water Recreation and Disease HUMAN ADENOVIRUS Credibility of association with recreational water: Strongly associated I Organism Pathogen Human adenovirus Taxonomy Adenoviruses belong to the family Adenoviridae. There are four genera: Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus. At present 51 antigenic types of human adenoviruses have been described. Human adenoviruses have been classified into six groups (A–F) on the basis of their physical, chemical and biological properties (WHO 2004). Reservoir Humans. Adenoviruses are ubiquitous in the environment where contamination by human faeces or sewage has occurred. Distribution Adenoviruses have worldwide distribution. Characteristics An important feature of the adenovirus is that it has a DNA rather than an RNA genome. Portions of this viral DNA persist in host cells after viral replication has stopped as either a circular extra chromosome or by integration into the host DNA (Hogg 2000). This persistence may be important in the pathogenesis of the known sequelae of adenoviral infection that include Swyer-James syndrome, permanent airways obstruction, bronchiectasis, bronchiolitis obliterans, and steroid-resistant asthma (Becroft 1971; Tan et al. -
Discovery of Novel Virus Sequences in an Isolated and Threatened Bat Species, the New Zealand Lesser Short-Tailed Bat (Mystacina Tuberculata) Jing Wang,1 Nicole E
Journal of General Virology (2015), 96, 2442–2452 DOI 10.1099/vir.0.000158 Discovery of novel virus sequences in an isolated and threatened bat species, the New Zealand lesser short-tailed bat (Mystacina tuberculata) Jing Wang,1 Nicole E. Moore,1 Zak L. Murray,1 Kate McInnes,2 Daniel J. White,3 Daniel M. Tompkins3 and Richard J. Hall1 Correspondence 1Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Richard J. Hall Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand [email protected] 2Department of Conservation, 18–32 Manners Street, PO Box 6011, Wellington, New Zealand 3Landcare Research, Private Bag 1930, Dunedin, New Zealand Bats harbour a diverse array of viruses, including significant human pathogens. Extensive metagenomic studies of material from bats, in particular guano, have revealed a large number of novel or divergent viral taxa that were previously unknown. New Zealand has only two extant indigenous terrestrial mammals, which are both bats, Mystacina tuberculata (the lesser short- tailed bat) and Chalinolobus tuberculatus (the long-tailed bat). Until the human introduction of exotic mammals, these species had been isolated from all other terrestrial mammals for over 1 million years (potentially over 16 million years for M. tuberculata). Four bat guano samples were collected from M. tuberculata roosts on the isolated offshore island of Whenua hou (Codfish Island) in New Zealand. Metagenomic analysis revealed that this species still hosts a plethora of divergent viruses. Whilst the majority of viruses detected were likely to be of dietary origin, some putative vertebrate virus sequences were identified. -
Enteric Viruses and Inflammatory Bowel Disease
viruses Review Enteric Viruses and Inflammatory Bowel Disease Georges Tarris 1,2, Alexis de Rougemont 2 , Maëva Charkaoui 3, Christophe Michiels 3, Laurent Martin 1 and Gaël Belliot 2,* 1 Department of Pathology, University Hospital of Dijon, F 21000 Dijon, France; [email protected] (G.T.); [email protected] (L.M.) 2 National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, F 21000 Dijon, France; [email protected] 3 Department of Hepatogastroenterology, University Hospital of Dijon, F 21000 Dijon, France; [email protected] (M.C.); [email protected] (C.M.) * Correspondence: [email protected]; Tel.: +33-380-293-171; Fax: +33-380-293-280 Abstract: Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is a multifactorial disease in which dietary, genetic, immunological, and microbial factors are at play. The role of enteric viruses in IBD remains only partially explored. To date, epidemiological studies have not fully described the role of enteric viruses in inflammatory flare-ups, especially that of human noroviruses and rotaviruses, which are the main causative agents of viral gastroenteritis. Genome-wide association studies have demonstrated the association between IBD, polymorphisms of the FUT2 and FUT3 genes (which drive the synthesis of histo-blood group antigens), and ligands for norovirus and rotavirus in the intestine. The role of autophagy in defensin-deficient Paneth cells and the perturbations of cytokine secretion in T-helper 1 and T-helper 17 inflammatory pathways following enteric virus infections have been demonstrated as well. -
Enteric Hepatitis Viruses
3B2v8:07f=w PMVI À V017 : 17003 Prod:Type: ED: XML:ver:5:0:1 pp:39270ðcol:fig::NILÞ PAGN: SCAN: 1 Human Viruses in Water 39 Albert Bosch (Editor) r 2007 Elsevier B.V. All rights reserved 3 DOI 10.1016/S0168-7069(07)17003-8 5 7 Chapter 3 9 11 Enteric Hepatitis Viruses 13 Rosa M. Pinto´ a, Juan-Carlos Saizb 15 aEnteric Virus Laboratory, Department of Microbiology, School of Biology, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain 17 bLaboratory of Zoonotic and Environmental Virology, Department of Biotechnology, Instituto Nacional de Investigacio´n Agraria y Alimentaria (INIA). Ctra. Corun˜a km. 19 7.5, 28040 Madrid, Spain 21 23 Background 25 The term ‘‘jaundice’’ was used as early as in the ancient Greece when Hippocrates 27 described an illness probably corresponding to a viral hepatitis. However, it was not until the beginning of the twentieth century when a form of hepatitis was AU :1 29 associated to an infectious disease occurring in epidemics and the term ‘‘infectious hepatitis’’ was established. Later on in the early 1940s two separate entities were 31 defined: ‘‘infectious’’ and ‘‘serum’’ hepatitis, and from 1965 to nowadays the different etiological agents of viral hepatitis have been identified. Although all viral 33 hepatitis are infectious the aforementioned terms refer to the mode of transmission, corresponding the ‘‘infectious’’ entity to those hepatitis transmitted through the 35 fecal-oral route and the ‘‘serum’’ hepatitis to those transmitted parenterally. Thus, the infectious or enteric hepatitis include two types: hepatitis A and hepatitis E, 37 which will be reviewed here. -
Molecular Study of Sapovirus in Acute Gastroenteritis in Children: a Cross-Sectional Study [Version 2; Peer Review: 2 Approved with Reservations]
F1000Research 2021, 10:123 Last updated: 14 SEP 2021 RESEARCH ARTICLE Molecular study of sapovirus in acute gastroenteritis in children: a cross-sectional study [version 2; peer review: 2 approved with reservations] Maysaa El Sayed Zaki 1, Raghdaa Shrief2, Rasha H. Hassan3 1Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt 2Medical Microbioogy and Immunology Department, Faculty of Medicine, Damietta University, New Damietta, 34511, Egypt 3Pediatrics Department, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt v2 First published: 17 Feb 2021, 10:123 Open Peer Review https://doi.org/10.12688/f1000research.29991.1 Latest published: 24 May 2021, 10:123 https://doi.org/10.12688/f1000research.29991.2 Reviewer Status Invited Reviewers Abstract Background: Sapovirus has emerged as a viral cause of acute 1 2 gastroenteritis. However, there are insufficient data about the presence of this virus among children with acute gastroenteritis. The version 2 present study aimed to evaluate the presence of sapovirus in children (revision) report with acute gastroenteritis by reverse transcriptase-polymerase chain 24 May 2021 reaction (RT-PCR). Methods: A cross-sectional study enrolled 100 children patients with version 1 acute gastroenteritis from outpatient clinics with excluded bacterial 17 Feb 2021 report pathogens and parasitic infestation. A stool sample was collected from each child for laboratory examination. Each stool sample was 1. Marta Diez Valcarce , Centers for Disease subjected to study by direct microscopic examination, study for rotavirus by enzyme-linked immunoassay (ELISA) and the remaining Control and Prevention, Atlanta, USA sample was subjected to RNA extraction and RT- PCR for sapovirus. Results: The most frequently detected virus was rotavirus by ELISA 2. -
Structure Unveils Relationships Between RNA Virus Polymerases
viruses Article Structure Unveils Relationships between RNA Virus Polymerases Heli A. M. Mönttinen † , Janne J. Ravantti * and Minna M. Poranen * Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland; heli.monttinen@helsinki.fi * Correspondence: janne.ravantti@helsinki.fi (J.J.R.); minna.poranen@helsinki.fi (M.M.P.); Tel.: +358-2941-59110 (M.M.P.) † Present address: Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), 00014 Helsinki, Finland. Abstract: RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure- based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. -
Discovery of New Mycoviral Genomes Within Publicly Available Fungal Transcriptomic Datasets
bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets 1 1 1,2 1 Kerrigan B. Gilbert , Emily E. Holcomb , Robyn L. Allscheid , James C. Carrington * 1 Donald Danforth Plant Science Center, Saint Louis, Missouri, USA 2 Current address: National Corn Growers Association, Chesterfield, Missouri, USA * Address correspondence to James C. Carrington E-mail: [email protected] Short title: Virus discovery from RNA-seq data bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina.