DOCSLIB.ORG

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next‑Generation Sequencing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next‑Generation Sequencing Food and Environmental Virology https://doi.org/10.1007/s12560-019-09402-3 ORIGINAL PAPER Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next‑Generation Sequencing Sofa Strubbia1 · My V. T. Phan2 · Julien Schaefer1 · Marion Koopmans2 · Matthew Cotten2,3,4,5 · Françoise S. Le Guyader1 Received: 5 July 2019 / Accepted: 17 August 2019 © The Author(s) 2019 Abstract This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specifc biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses. Keywords Human enteric viruses · Norovirus · Sewage · Metagenomic · Virome Introduction Metcalf et al. 1995; Gerba et al. 2018). Documenting viral prevalence and diversity in sewage may be a useful method Increasing human population leads to increased demand for for monitoring viruses circulating in the community (Smith agricultural products and water, wastewater re-use will be et al. 2016). However, their detection by PCR approaches necessary, which will pose a risk for virus pollution of the requires previously identifed sequences for primer design environment and subsequent afects viral transmission (Sano and will not detect more distant viruses. et al. 2016). More than 100 species of enteric viruses have Metagenomics refer to the description of all nucleic acids been identifed in human feces and in sewage such as astrovi- sequences present in a sample (Forbes et al. 2017). Most of ruses, caliciviruses, enteroviruses, enteric adenoviruses, and human enteric viruses have small RNA genomes making rotaviruses (Fernandez-Cassi et al. 2018; Hoque et al. 2019; their detection difcult. Indeed, their relative abundance if compared to bacteria, phage, parasites present in the envi- * Françoise S. Le Guyader ronment challenge their detection and identifcation (Cot- [email protected] ten and Koopmans 2016; Nieuwenhuijse and Koopmans, 2017; Adriaenssens et al. 2018). Thus, viral metagenomics 1 Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP is generally performed by removing as much host and bac- 21105, 44311 Nantes Cedex 3, France teria as possible followed by nuclease treatment to remove 2 Department of Viroscience, Erasmus MC, University free nucleic acids (Kim et al. 2017; Nieuwenhuijse et al. Medical Center Rotterdam, Rotterdam, The Netherlands 2017). Detection of viruses can be performed after de novo 3 Present Address: London School of Hygiene and Tropical assembly of short-read data into longer sequences (contigs) Medicine, London, UK followed by a variety of computational methods for detecting 4 Present Address: Uganda Virus Research Institute, Entebbe, known and novel viral sequences (Cotten et al. 2014; Cot- Uganda ten et al. 2016; Oakeson et al. 2017). However, each sample 5 Present Address: MRC-Centre for Virus Research, Glasgow, type is unique and methods need to be adapted to account for UK Vol.:(0123456789)1 3 Food and Environmental Virology origin and to address the metagenomic objective. A concrete example was provided by the analysis of samples collected MethodA MethodB Method C 5 stools 1 stool 3 sewages during the Tara oceans expedition (Alberti et al. 2017). The 4 sewages 4 sewages strategy applied allowed generation of data from a variety of organisms, including viruses and plankton from oceanic samples collected worldwide. Their approach showed the Conductivity and acidic conditions importance of using separate processing steps to analyze the diferent compartments of a volume of (sea)water. To identify human enteric viruses in complex samples such as stool or sewage samples, a method able to select these small PEG precipitation particles resistant to acidic conditions, to eliminate bacteria and to decrease as much as possible background genomes such as phage genomes will be useful. Mucine capture The aim of the current study was to evaluate methods for human enteric virus detection using metagenomics with a focus on norovirus. Noroviruses have great genomic diver- Filtration & Omnicleave treatment sity and they are divided into seven genogroups and many genotypes based upon genomic sequence phylogeny (de Graaf et al. 2017). Three of these genogroups (GI, GII and GIV) infect humans, and constitute the principal agent of Nucleicacidextraction acute gastroenteritis worldwide. Importantly for environ- mental research norovirus are excreted at high concentra- Norovirus tions by infected individuals and they are highly persistent RNA enrichment (Atmar et al. 2018). Their concentrations in sewage, that may vary among countries, are usually high and their pres- ence in waters constitutes a major public health issue nowa- Librairies & Miseqsequencing days (Sano et al. 2016; Schaefer et al. 2018). To specifcally enrich our metagenomics libraries in norovirus sequences, Fig. 1 we selected three protocols that take advantage of known Schematic of sample processing and sequencing used in this study. The three main frames on the top contain the method names properties of these viruses. The frst method uses SureSelect (A, B and C), the number and the type of sample treated with each target enrichment (Agilent) with probes matching human protocol. Key steps common to all protocols are represented in gray norovirus sequences. The second method comprises pH vari- rectangle ations, based on norovirus capsids isoelectric point and on their resistance to both high and low pH. The third method is based on norovirus binding to glycans structures that are and the remaining four samples (sample 1887, 1919, 1920, present in human but also pig mucins. 1927) were analyzed using method B and C. Method A: Polyethylene Glycol Precipitation Materials and Methods and Norovirus SureSelect Target Samples Sewage samples were concentrated using a polyethylene glycol precipitation method (PEG) as previously described Five human stool samples (sample 570, 287, 5, 581, 582) (Lewis et al. 1988; Schaefer et al. 2018). Briefy, 40 mL of positive for norovirus collected between January 2008 and sample were mixed with 10 mL of a 50% PEG 6000 solution October 2016 were used as a 10% suspension in water. Four (Sigma-Aldrich, St Quentin France) (Fig. 1). After gentle samples were analyzed following method B and one sample agitation overnight at 4 °C, the mixture was centrifuged for following method B and C (stool sample 570) (Fig. 1). Seven 1.5 h at 13,500 × g and the pellet was suspended in 3 mL of raw sewage samples were collected from a gathering point 0.05 M glycine bufer (pH 9). After nucleic acid extraction upstream of any process between January 2014 and February as described below, norovirus RNA sequence were enriched 2017 from diferent sewage treatment plants located in the using the SureSelect target enrichment specifc array dur- southern part of Brittany (France). Three sewage samples ing the library preparation (details in the library preparation (sample 1777, 1797, 1854) were analyzed using method A paragraph) (Brown et al., 2016). 1 3 Food and Environmental Virology Method B: Acidic Treatment and PEG Precipitation at 37 °C with 5 Units of Turbo DNAse, (Ambion, Ther- moFisher Scientifc, France) (method B and C). To optimize human enteric viruses recovery, viruses were acid adsorbed to organic or inorganic particles present in Norovirus Quantifcation the samples by increasing the conductivity of stool sus- pension or sewage samples to 2000 µS by addition of 5 M A microfuidic-based digital one-step RT-PCR, that allow sodium chloride at pH 3 (Mullendore et al. 2001), and quantifcation without external calibration curves was per- then concentrated using PEG precipitation as described formed using primers and probes targeting the ORF1-2 above (Fig. 1). After centrifugation, the pellet was sus- region (Polo et al. 2016). Positive and negative controls were pended in 3 mL of 0.05 M glycine bufer (pH 9), and fl- included in each series, and quantifcation was calculated tered through 5, 1.2, 0.45 and 0.22 µM flters (Minisart using the Poisson distribution (QuantStudio™ 3D Analysis NML 17594, NML17593, PES16533, PES16532). Then, Suite™ Cloud Software, version 3.0.3; ThermoFisher). The the fltrate was incubated with 2000 Units of OmniCleave fnal result was expressed as RNA copies/µl. Endonuclease (Epicentre, Madison, USA) for one hour at 37 °C to eliminate free nucleic acids, followed by nucleic Library and Sequencing acid extraction. For method A, cDNA were synthesized using Superscripts II and random primers according to the manufacturer protocol Method C: Porcine Gastric Mucin (PGM) Capture (Life Technologies).
Load more

Recommended publications
  • Survival of Human Norovirus Surrogates in Juices and Their Inactivation Using Novel Methods
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 5-2011 Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods Katie Marie Horm [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Recommended Citation Horm, Katie Marie, "Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods. " Master's Thesis, University of Tennessee, 2011. https://trace.tennessee.edu/utk_gradthes/882 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Katie Marie Horm entitled "Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Master of Science, with a major in Food Science and Technology. Doris H. D'Souza, Major Professor We have read this thesis and recommend its acceptance: Federico M. Harte, Gina M. Pighetti Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Survival of Human Norovirus Surrogates In Juices and their Inactivation Using Novel Methods A Thesis Presented for the Master of Science Degree The University of Tennessee, Knoxville Katie Marie Horm May 2011 Acknowledgments I would like to think my major professor/advisor Dr.
    [Show full text]
  • Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats
    viruses Article Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats Laura M. Bergner 1,2,* , Nardus Mollentze 1,2 , Richard J. Orton 2 , Carlos Tello 3,4, Alice Broos 2, Roman Biek 1 and Daniel G. Streicker 1,2 1 Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; [email protected] (N.M.); [email protected] (R.B.); [email protected] (D.G.S.) 2 MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; [email protected] (R.J.O.); [email protected] (A.B.) 3 Association for the Conservation and Development of Natural Resources, Lima 15037, Peru; [email protected] 4 Yunkawasi, Lima 15049, Peru * Correspondence: [email protected] Abstract: The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely Citation: Bergner, L.M.; Mollentze, applied to viruses at the time of their discovery. Here, we characterized viral genomes detected N.; Orton, R.J.; Tello, C.; Broos, A.; through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) Biek, R.; Streicker, D.G. and used these data as a case study in evaluating zoonotic potential using molecular sequencing Characterizing and Evaluating the data.
    [Show full text]
  • Opportunistic Intruders: How Viruses Orchestrate ER Functions to Infect Cells
    REVIEWS Opportunistic intruders: how viruses orchestrate ER functions to infect cells Madhu Sudhan Ravindran*, Parikshit Bagchi*, Corey Nathaniel Cunningham and Billy Tsai Abstract | Viruses subvert the functions of their host cells to replicate and form new viral progeny. The endoplasmic reticulum (ER) has been identified as a central organelle that governs the intracellular interplay between viruses and hosts. In this Review, we analyse how viruses from vastly different families converge on this unique intracellular organelle during infection, co‑opting some of the endogenous functions of the ER to promote distinct steps of the viral life cycle from entry and replication to assembly and egress. The ER can act as the common denominator during infection for diverse virus families, thereby providing a shared principle that underlies the apparent complexity of relationships between viruses and host cells. As a plethora of information illuminating the molecular and cellular basis of virus–ER interactions has become available, these insights may lead to the development of crucial therapeutic agents. Morphogenesis Viruses have evolved sophisticated strategies to establish The ER is a membranous system consisting of the The process by which a virus infection. Some viruses bind to cellular receptors and outer nuclear envelope that is contiguous with an intri‑ particle changes its shape and initiate entry, whereas others hijack cellular factors that cate network of tubules and sheets1, which are shaped by structure. disassemble the virus particle to facilitate entry. After resident factors in the ER2–4. The morphology of the ER SEC61 translocation delivering the viral genetic material into the host cell and is highly dynamic and experiences constant structural channel the translation of the viral genes, the resulting proteins rearrangements, enabling the ER to carry out a myriad An endoplasmic reticulum either become part of a new virus particle (or particles) of functions5.
    [Show full text]
  • Cellular Entry and Uncoating of Naked and Quasi-Enveloped Human
    RESEARCH ARTICLE Cellular entry and uncoating of naked and quasi-enveloped human hepatoviruses Efraı´nE Rivera-Serrano1,2, Olga Gonza´ lez-Lo´ pez1,2, Anshuman Das2, Stanley M Lemon2,3* 1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 2Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, United States; 3Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, United States Abstract Many ‘non-enveloped’ viruses, including hepatitis A virus (HAV), are released non- lytically from infected cells as infectious, quasi-enveloped virions cloaked in host membranes. Quasi-enveloped HAV (eHAV) mediates stealthy cell-to-cell spread within the liver, whereas stable naked virions shed in feces are optimized for environmental transmission. eHAV lacks virus- encoded surface proteins, and how it enters cells is unknown. We show both virion types enter by clathrin- and dynamin-dependent endocytosis, facilitated by integrin b1, and traffic through early and late endosomes. Uncoating of naked virions occurs in late endosomes, whereas eHAV undergoes ALIX-dependent trafficking to lysosomes where the quasi-envelope is enzymatically degraded and uncoating ensues coincident with breaching of endolysosomal membranes. Neither virion requires PLA2G16, a phospholipase essential for entry of other picornaviruses. Thus naked and quasi-enveloped virions enter via similar endocytic pathways, but uncoat in different compartments and release their genomes to the cytosol in a manner mechanistically distinct from other Picornaviridae. DOI: https://doi.org/10.7554/eLife.43983.001 *For correspondence: [email protected] Competing interests: The Introduction authors declare that no The presence or absence of an external lipid envelope has featured strongly in the systematic classi- competing interests exist.
    [Show full text]
  • Origins and Evolution of the Global RNA Virome
    bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Origins and Evolution of the Global RNA Virome 2 Yuri I. Wolfa, Darius Kazlauskasb,c, Jaime Iranzoa, Adriana Lucía-Sanza,d, Jens H. 3 Kuhne, Mart Krupovicc, Valerian V. Doljaf,#, Eugene V. Koonina 4 aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA 5 b Vilniaus universitetas biotechnologijos institutas, Vilnius, Lithuania 6 c Département de Microbiologie, Institut Pasteur, Paris, France 7 dCentro Nacional de Biotecnología, Madrid, Spain 8 eIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious 9 Diseases, National Institutes of Health, Frederick, Maryland, USA 10 fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA 11 12 #Address correspondence to Valerian V. Dolja, [email protected] 13 14 Running title: Global RNA Virome 15 16 KEYWORDS 17 virus evolution, RNA virome, RNA-dependent RNA polymerase, phylogenomics, horizontal 18 virus transfer, virus classification, virus taxonomy 1 bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 ABSTRACT 20 Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in 21 animals and plants. The recent advances of metaviromics prompted us to perform a detailed 22 phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome.
    [Show full text]
  • Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
    Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280
    [Show full text]
  • High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage
    Edinburgh Research Explorer High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage Citation for published version: Ng, TF, Marine, R, Wang, C, Simmonds, P, Kapusinszky, B, Bodhidatta, L, Oderinde, BS, Wommack, KE & Delwart, E 2012, 'High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage', Journal of Virology, vol. 86, no. 22, pp. 12161-12175. https://doi.org/10.1128/jvi.00869-12 Digital Object Identifier (DOI): 10.1128/jvi.00869-12 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Journal of Virology Publisher Rights Statement: Copyright © 2012, American Society for Microbiology. All Rights Reserved. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage Terry Fei Fan Ng,a,b Rachel Marine,c Chunlin Wang,d Peter Simmonds,e Beatrix Kapusinszky,a,b Ladaporn Bodhidatta,f Bamidele Soji Oderinde,g K.
    [Show full text]
  • First Insight Into the Viral Community of the Cnidarian Model Metaorganism Aiptasia Using RNA-Seq Data
    First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data Jan D. Brüwer and Christian R. Voolstra Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia ABSTRACT Current research posits that all multicellular organisms live in symbioses with asso- ciated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes.
    [Show full text]
  • Ancient Recombination Events and the Origins of Hepatitis E Virus Andrew G
    Kelly et al. BMC Evolutionary Biology (2016) 16:210 DOI 10.1186/s12862-016-0785-y RESEARCH ARTICLE Open Access Ancient recombination events and the origins of hepatitis E virus Andrew G. Kelly, Natalie E. Netzler and Peter A. White* Abstract Background: Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. Results: To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the “Alpha-like” super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the “Picorna-like” supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family.
    [Show full text]
  • Detection and Characterization of Three Zoonotic Viruses in Wild Rodents and Shrews from Shenzhen City, China
    VIROLOGICA SINICA 2017, 32 (4): 290–297 DOI: 10.1007/s12250-017-3973-z RESEARCH ARTICLE Detection and characterization of three zoonotic viruses in wild rodents and shrews from Shenzhen city, China Bo Wang1#, Chun-Lin Cai2#, Bei Li1, Wei Zhang1, Yan Zhu1, Wei-Hong Chen2, Fei Zhuo2, Zheng-Li Shi1, Xing-Lou Yang1* 1. CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan 430071, China 2. Luohu Center for Disease Control and Prevention, Shenzhen 518020, China Diverse species of rodents and shrews, which are abundant worldwide, harbor a variety of viruses; some of these are closely related to human viruses and possess zoonotic potential. Previously studies have demonstrated that the mammarenavirus and hantavirus carried by rodents or shrews could cause diseases in human population. To determine the distribution of zoonotic viruses in Shenzhen city, the major city in southern China with a high population density, we analyzed 225 rodents (Rattus norvegicus and Rattus flavipectus) and 196 shrews (Suncus murinus) from urban and rural districts for the presence of mammarenavirus, hantavirus, and hepatitis E virus (HEV) by RT-PCR targeting the conserved regions. The infection rates for mammarenavirus, hantaviruses, and HEV in rodents and shrews were 3.56%, 6.89%, and 1.66%, respectively. Partial genome fragment analysis indicated that mammarenavirus and hantavirus strains had more than 90% and 99% nucleic acid identity with Cardamones virus and Seoul virus, respectively, which cause diseases in humans. Although the present HEV strains identified are typically found worldwide, phylogenetic analysis demonstrated a divergence of 16%. To our knowledge, the present work is the first report of the prevalence of mammarenavirus, hantaviruses, and rat HEV strains in rodents and shrews from Shenzhen city, China.
    [Show full text]
  • Viral Hepatitis Transmission and Prevention
    Training workshop on screening, diagnosis and treatment of hepatitis B and C 1 Session 5 Viral hepatitis transmission and prevention 2 Learning objectives At the end of this sessions, participants will understand the following: • Modes of transmission of the various hepatitis viruses (hepatitis A to hepatitis E) • Strategies for prevention of transmission of these viruses At the end of this sessions, participants should be able to understand the following: • Modes of transmission of various hepatitis viruses (hepatitis A to hepatitis E) • Strategies for prevention of transmission of these viruses 3 Main features of the hepatitis viruses HAV HBV HCV HDV HEV Virus family Picornaviridae Hepadnaviridae Flaviviridae Deltaviridae Hepeviridae Chronicity rate No 5% of adults ~75% Co-infection of Very rare 90% of infants HBV; modifies course Hepatocellular No Yes Yes Yes No carcinoma Route of Person-to Perinatal Bloodborne Bloodborne Waterborne transmission person Bloodborne (perinatal) Sexual Foodborne Foodborne Sexual (sexual) (perinatal) Person-to- Waterborne person Vaccine Yes Yes No HBV vaccine Not generally (licensed in China) Treatment None Available - Available - No treatment, if None options lifelong CURE HBV–HDV treatment coinfected, treat as for HBV This slide summarizes the several clinical features of the hepatitis viruses from HAV to HEV in general. There are some differences among these viruses regarding chronicity rate, complication of hepatocellular carcinoma and routes of transmission. We shall see that only hepatitis B is a DNA virus; the rest are all RNA viruses. Hence, hepatitis B virus, akin to other DNA viruses such as CMV, HSV, etc. if it enters the human body, its DNA gets integrated with human DNA and remains inside the host body for the rest of his/her life.
    [Show full text]
  • Diversification of Mammalian Deltaviruses by Host Shifting
    Diversification of mammalian deltaviruses by host shifting Laura M. Bergnera,b,1, Richard J. Ortonb, Alice Broosb, Carlos Telloc,d, Daniel J. Beckere, Jorge E. Carreraf,g, Arvind H. Patelb, Roman Bieka, and Daniel G. Streickera,b,1 aInstitute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland; bMedical Research Center–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland; cAssociation for the Conservation and Development of Natural Resources, 15037 Lima, Perú; dYunkawasi, 15049 Lima, Perú; eDepartment of Biology, University of Oklahoma, Norman, OK 73019; fDepartamento de Mastozoología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú; and gPrograma de Conservación de Murciélagos de Perú, Piura 20001, Perú Edited by Paul E. Turner, Yale University, New Haven, CT, and approved November 25, 2020 (received for review September 22, 2020) Hepatitis delta virus (HDV) is an unusual RNA agent that replicates satellites either cospeciated with their hosts over ancient time- using host machinery but exploits hepatitis B virus (HBV) to scales or possess an unrecognized capacity for host shifting, mobilize its spread within and between hosts. In doing so, HDV which would imply their potential to emerge in novel species. enhances the virulence of HBV. How this seemingly improbable The latter scenario has been presumed unlikely since either both hyperparasitic lifestyle emerged is unknown, but it underpins the satellite and helper would need to be compatible with the novel likelihood that HDV and related deltaviruses may alter other host or deltaviruses would need to simultaneously switch host host–virus interactions.
    [Show full text]