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The Viral Microbiome

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The viral microbiome Assoc. Prof. Dr. Christoph Steininger Klinik für Innere Medizin I Medizinische Universität Wien Viruses . Size 1/100 of bacteria . Replication only in living cells . High genetic variability (no conserved regions like 16S rRNA) . Genome: RNA & DNA, single- & double-stranded Course of infection . Acute (Rhinovirus, Influenza) . Persistent (Lymphocytic choriomeningitis virus) . Latent, reactivating (Herpesviruses) . Slow virus infection (HIV, Measles SSPE) Discovery of transmissible tumors Francis Peyton Rous 1911: Cancer has to be caused by a virus 1961: Identification of Rous Sarcoma Virus as ssRNA virus Rous Sarcoma Virus 1966: Nobel prize in Physiology/Medicine Cancer associated with human papillomaviruses High-grade cervical lesions in Australian women aged <18 yrs Margaret Stanley, Nature 2012 Brotherton et al. Lancet 2011 Merkel cell carcinoma • Rare, aggressive skin cancer • Merkel cell polyomavirus (MCPyV) DNA detectable in 80% of MCC tumors • Seroprevalence of polyomavirus infections in general population: . BK virus 92% . JC virus 45% . WU polyomavirus 98% . KI polyomavirus 90% . MCPyV 59% Carter et al. J Natl Cancer Inst 2009; Pastrana et al. PlosPathogens 2009 Cancer caused by infectious pathogens (Status 2014) EBV; 5% KSHV; Other; 1% 2% Helicobacter; HBV & HCV; 32,5% 30% HPV; 30% De Martel et al. Lancet Oncology 2012 . 12,7 Mio new cases of cancer in 2008 . 16% of cancer cases attributable to infections . Relevance of infections in carcinogenesis higher in developing countries Estimated burden of chronic viral infections in humans . ~8–12 chronic viral infections per individuum Virgin et al. Cell 2009 Diseases of unknown etiology with suspected viral cause Wylie et al. Curr Opin Microbiol 2013 Virus-host equilibrium in chronic viral infections Chronic infection - Continuous/intermittent Ag presentation - Tissue damage & aberrant repair - Altered homeostasis - Genotoxicity - Proliferative responses Cancer Viral strategies Immune response - Latency - Dampen responses - Immune evasion - Chronic activation - Mutation - Immunopathology - Immunoprivilege - Repertoire contraction Detection of novel oncogenic viruses Method Issues Cell culture • Selection of cells for permissivity • Identification of viral replication Microscopy • Insensitive • Size of viral particles • Differentiation of viruses PCR • Genomes highly variable Serology • Cross-reactivity Adenovirus Virus attachment Virus culture Electron microscope Metagenomics Breitbart et al. Res. Microbiol. (2008); Allander et al. Proc. Natl. Acad. Sci. USA (2005); Breitbart et al. J. Bacteriol. (2003); Breitbart et al. Biotechniques (2005); Bibby et al. Trends in Biotechnology 2013 The human microbiome . Bacteria . Fungi . Parasites & Ova Meiofauna (Eukaryote) . Protozoa . Viruses (109 virus particles/gram feces) 1. Eukaryotic Viruses 2. Prokaryotic Viruses (Bakteriophages) 3. Plantviruses 4. Human endogeneous retroviruses (HERV) ScienceNews Popgeorgiev et al. Journal of Infectious Diseases 2013; Ogilvie et al. Nat Comm 2013 Plasma DNA Source: 1. Eukaryotic intestinal viruses . Rotavirus Documented outbreaks of gastroenteritis in the US . Norovirus Caliciviruses . Sapovirus . Enteric Adenoviruses . Astrovirus . Aichivirus Source: CDC 2014 Discovery of novel eukaryotic viruses Virus Replication Disease Reservoir Ref. Cyclovirus-Vietnam Feces & CSF Encephalitis Pigs, poultry Van Tan et al. Mbio 2013 Burkina Faso Feces Diarrhea ??? Phan et al. J Clin Astrovirus Virol 2014 Virginia Astrovirus Feces Diarrhea Mammals Finkbeiner et al. J Virol 2009 Torque Teno Serum (HIV- ??? ??? Farsani et al. Virology Journal Mimi Virus 13 positiv) 2013 Humanes Respiratory Bronchilitis Bats, civet cat Van der Hoek et Coronavirus NL63 secretions al. Nat Med 2004 Lujovirus Serum & Tissue Hemorrhagic ??? Briese et al. PlosPathogens fever 2009 Picobirnavirus Feces Diarrhea ??? Leeuwen et al. J Clin Microbiol 2011 Human Plasma Fever African Green Scuda et al. J polyomavirus 9 Monkey Virol 2011 (HPyV9). Discovery of novel human viruses Cumulative number of viruses discovered Arboviruses and non-arboviruses discovered annually Woolhouse et al. Proc Biol Sci. 2008; Rosenberg et al. PNAS 2013 Transspecies transfer of viruses Graham et al. Nat Rev Microbiol 2013 . >80 Mio pet cats worldwide . Feline Co-infections common (40% of cats shed >5 viruses in feces) . Novel viruses in asymptomatic cats (Sakobuvirus, Bocavirus, Astroviren, Picobirnavirus) Ng et al. Veterinary Microbiol 2013; Benedictis et al. Infection, Genetics, Evolution 2011 The „silent“ human virome Group Family Species dsDNA Adenoviridae Enteric adenovirus 40, 41 Iridoviridae Lymphocystis disease virus Myoviridae phiBCD7, Bacillus phage G, phiP-SSM4 Podoviridae Enterobacteria phage P22, phage T3 Siphoviridae Listeria phage A118, phiE125 Lactococcus phage bIL285, phiCP39-O, Clostridium Phages Halophage eHP-10 Papillomaviridae Human papillomavirus 6, 18, 66 Polyomaviridae BK virus, JC virus, SV40 virus, Human polyomavirus 9, 12, Merkel cell polyomavirus Herpesviridae Epstein-Barr virus, Human cytomegalovirus ssDNA Anelloviridae TTV Circoviridae Chicken anemia virus, TN9, PK5034, PK5222, NG12 Microviridae Chlamydia phage 1,3,4, Bdellovibrio phage phiMH2K, Chlamydia phage CPG1, Spiroplasma phage 4, Chlamydia phage CPAR39 dsRNA Picobirnaviridae Human picobirnavirus Reoviridae Human rotavirus (+) ssRNA Caliciviridae Norwalk virus Astroviridae Human astrovirus Virgaviridae Pepper mild mottle virus, Tobacco mosaic virus Picornaviridae Cosavirus, Klassevirus/salivirus, Aichi virus, Enterovirus, Parechovirus, Saffold cardiovirus, Echovirus, Coxsackievirus, Poliovirus Popgeorgiev et al. Intervirology 2013; Wylie et al. BMC Biology 2014; Foulongne et al. PlosOne 2012 The human megavirome . Mimi-, Mega-, Pandoravirus – infect Acanthamoeba . Human, intestinale Megaviridae . Iridoviridae Acanthamoeba Pithovirus polyphaga sibericum . Poxvirus-related genomic sequences Mimivirus . Senegalvirus . Marseillevirus . Human, Plasma-Megaviridae Poxvirus . Giant Blood Marseillevirus (infects T-cells) E. coli Sputnik Virophage . Discovery of Virophages Parvovirus Myovirus Bacteriophage Mimi- Legendre et al. PNAS 2013; virus Popgeorgiev et al. Intervirology 2013; Popgeorgiev et al. J Infect Dis 2013 Raoult, The Scientist 2014 2. Intestinal Bacteriophages . ~10x more viral particles than bacteria in feces . High level of genetic diversity . Source of transfer of genes between bacteria . Bactericidal due to lytic replication Norman et al. Gastroenterology 2014; Barr et al. PNAS 2013 Phages protect from pathogenic bacteria Barr et al. PNAS 2013 crAssphage . 6x more abundant in feces than all other known phages together . 90% of all reads in virus-like particle (VLP)-derived metagenomes . 22% of total community metagenomes . 1.68% of all human fecal metagenomic sequencing reads in the public databases . Year of discovery: 2014 . Majority of crAssphage-encoded proteins match no known sequences in the database discarded as data junk Dutilh et al. Nat Comm 2014 3. Intestinal plant viruses Pepper mild mottle virus Zhang et al. Plos Biology 2006; Colson Plos ONE 2010 4. Human endogenous retroviruses (HERV) . 8%–9% of the human genome EBV infects T-cells . HERVs are mostly replication defective (no virus generated) . Defective HERVs may still IFN-α↑ . express viral proteins . regulate cellular gene expression Activation of silent . modulate host immune response HERV-K18 element . participate in mutagenic events Env overexpressed (superantigen activity) Inflammatory cascade Feschotte & Gilbert, Nat Rev Genetics 2012 initiated Role of HERV-W env (syncytin-1) in human cancer . Overexpressed in 76% of urothelial cell carcinoma tissues (controls, 6%) . Overexpression increases proliferation and viability of immortalized human uroepithelial cells . Involved in mediating cancer-endothelial cell fusions in vitro . Syncytin-1 expression = positive Urogenital cancer tissue prognostic factor in breast cancer . Syncytin-1 expression in 38% of all breast cancer samples . Upregulated in endometrial carcinoma Yu et al. Oncogene 2014; Blesa et al. Cancer Therapy 2008; Larsson et al. Placenta 2002 Physiologic functions of syncytins . Inserted in human-prehominoids chromosome 7q21, 40-45 millions years ago . Absolute requirement for placenta development and embryo survival . Positive selective Syncytin gene advantage – switch from capture events egg to uterus . Induction of maternal immune tolerance to fetus? . Cellular resistance against infection by retroviruses of family spleen necrosis virus Lavialle et al. Phil. Trans. R. Soc. B 2013; Blesa et al. Cancer Therapy 2008 Endogenous viral elements (EVE) Family or Taxa Number per haploid . Chromosomal genus genome integration of viral Baculovirus Insects Unknown Herpesviridae Humans 1 DNA (or DNA Nudivirus Parasitic wasps Several Phycodnaviridae Brown algae 1 copies of viral RNA) Circoviridae Mammals 1 to 2 in the host germ Geminiviridae Tomentosae 5 to 120 Parvoviridae Mammals; shrimp 1 to 3 cells Partitiviridae Plants; arthropods; Protozoa 1 to 4 Reovirus Aedes spp. mosquitoes 1 . All major types of Totiviridae Fungi; plants; ticks 1 to 6 Dicistroviridae Honeybees 1 eukaryotic viruses Flaviviridae Medaka fish; mosquitoes 1 to 4 can give rise to Potyviridae Grapes Several Bornaviridae Vertebrates 1 to 17 EVEs Bunyaviridae Ticks 14 Filoviridae Mammals 1 to 13 Nyavirus Zebrafish 6 Orthomyxoviridae Ticks 1 Rhabdoviridae Insects (ticks and mosquitoes) 1 to 28 Retroviridae Vertebrates Several hundreds to several hundreds
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  • Persistent Virus and Addiction Modules: an Engine of Symbiosis

    Persistent Virus and Addiction Modules: an Engine of Symbiosis

    UC Irvine UC Irvine Previously Published Works Title Persistent virus and addiction modules: an engine of symbiosis. Permalink https://escholarship.org/uc/item/5ck1g026 Journal Current opinion in microbiology, 31 ISSN 1369-5274 Author Villarreal, Luis P Publication Date 2016-06-01 DOI 10.1016/j.mib.2016.03.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Available online at www.sciencedirect.com ScienceDirect Persistent virus and addiction modules: an engine of symbiosis Luis P Villarreal The giant DNA viruses are highly prevalent and have a particular host would occasionally survive but still retain a bit of affinity for the lytic infection of unicellular eukaryotic host. The the selfish virus DNA. Thus although parasitic selfish giant viruses can also be infected by inhibitory virophage which (virus-like) information is common in the genomes of all can provide lysis protection to their host. The combined life forms, its presence was explained as mostly defective protective and destructive action of such viruses can define a remnants of past plague sweeps that provides no func- general model (PD) of virus-mediated host survival. Here, I tional benefit to the host (e.g. junk). Until recently, this present a general model for role such viruses play in the explanation seemed satisfactory. In the last twenty years, evolution of host symbiosis. By considering how virus mixtures however, various observation-based developments have can participate in addiction modules, I provide a functional compelled us to re-evaluate this stance. Both comparative explanation for persistence of virus derived genetic ‘junk’ in genomics and metagenomics (sequencing habitats) has their host genomic habitats.