Phylogenetic Factorization of Mammalian Viruses Complements Trait- Based Analyses and Guides Surveillance Efforts
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Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris Spelaea)
viruses Article Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris spelaea) Ian H Mendenhall 1,* , Dolyce Low Hong Wen 1,2, Jayanthi Jayakumar 1, Vithiagaran Gunalan 3, Linfa Wang 1 , Sebastian Mauer-Stroh 3,4 , Yvonne C.F. Su 1 and Gavin J.D. Smith 1,5,6 1 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; [email protected] (D.L.H.W.); [email protected] (J.J.); [email protected] (L.W.); [email protected] (Y.C.F.S.) [email protected] (G.J.D.S.) 2 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore 3 Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore; [email protected] (V.G.); [email protected] (S.M.-S.) 4 Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore 5 SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore 6 Duke Global Health Institute, Duke University, Durham, NC 27710, USA * Correspondence: [email protected] Received: 30 January 2019; Accepted: 7 March 2019; Published: 12 March 2019 Abstract: Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission. -
Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection?
viruses Review Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection? Solène Grayo Institut Pasteur de Guinée, BP 4416 Conakry, Guinea; [email protected] or [email protected] Abstract: The emergence of the Zika virus (ZIKV) mirrors its evolutionary nature and, thus, its ability to grow in diversity or complexity (i.e., related to genome, host response, environment changes, tropism, and pathogenicity), leading to it recently joining the circle of closed congenital pathogens. The causal relation of ZIKV to microcephaly is still a much-debated issue. The identification of outbreak foci being in certain endemic urban areas characterized by a high-density population emphasizes that mixed infections might spearhead the recent appearance of a wide range of diseases that were initially attributed to ZIKV. Globally, such coinfections may have both positive and negative effects on viral replication, tropism, host response, and the viral genome. In other words, the possibility of coinfection may necessitate revisiting what is considered to be known regarding the pathogenesis and epidemiology of ZIKV diseases. ZIKV viral coinfections are already being reported with other arboviruses (e.g., chikungunya virus (CHIKV) and dengue virus (DENV)) as well as congenital pathogens (e.g., human immunodeficiency virus (HIV) and cytomegalovirus (HCMV)). However, descriptions of human latent viruses and their impacts on ZIKV disease outcomes in hosts are currently lacking. This review proposes to select some interesting human latent viruses (i.e., herpes simplex virus 2 (HSV-2), Epstein–Barr virus (EBV), human herpesvirus 6 (HHV-6), human parvovirus B19 (B19V), and human papillomavirus (HPV)), whose virological features and Citation: Grayo, S. -
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 -
Chronic Viral Infections Vs. Our Immune System: Revisiting Our View of Viruses As Pathogens
Chronic Viral Infections vs. Our Immune System: Revisiting our view of viruses as pathogens Tiffany A. Reese Assistant Professor Departments of Immunology and Microbiology Challenge your idea of classic viral infection and disease • Define the microbiome and the virome • Brief background on persistent viruses • Illustrate how viruses change disease susceptibility – mutualistic symbiosis – gene + virus = disease phenotype – virome in immune responses Bacteria-centric view of the microbiome The microbiome defined Definition of microbiome – Merriam-Webster 1 :a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body 2 :the collective genomes of microorganisms inhabiting a particular environment and especially the human body Virome Ø Viral component of the microbiome Ø Includes both commensal and pathogenic viruses Ø Viruses that infect host cells Ø Virus-derived elements in host chromosomes Ø Viruses that infect other organisms in the body e.g. phage/bacteria Viruses are everywhere! • “intracellular parasites with nucleic acids that are capable of directing their own replication and are not cells” – Roossinck, Nature Reviews Microbiology 2011. • Viruses infect all living things. • We are constantly eating and breathing viruses from our environment • Only a small subset of viruses cause disease. • We even carry viral genomes as part of our own genetic material! Diverse viruses all over the body Adenoviridae Picornaviridae -
Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: a Complex Story
viruses Review Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story Mauricio Comas-Garcia 1,2 1 Research Center for Health Sciences and Biomedicine (CICSaB), Universidad Autónoma de San Luis Potosí (UASLP), Av. Sierra Leona 550 Lomas 2da Seccion, 72810 San Luis Potosi, Mexico; [email protected] 2 Department of Sciences, Universidad Autónoma de San Luis Potosí (UASLP), Av. Chapultepec 1570, Privadas del Pedregal, 78295 San Luis Potosi, Mexico Received: 14 February 2019; Accepted: 8 March 2019; Published: 13 March 2019 Abstract: The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle. Keywords: (+)ssRNA viruses; RNA packaging; virion assembly; packaging signals; RNA replication 1. Introduction Nucleocapsid assembly and the RNA replication of positive-sense single-stranded RNA [(+)ssRNA] viruses occur in the cytoplasm. -
Coevolution of Persistently Infecting Small DNA Viruses and Their Hosts
Proc. Natl. Acad. Sci. USA Vol. 90, pp. 4117-4121, May 1993 Evolution Coevolution of persistently infecting small DNA viruses and their hosts linked to host-interactive regulatory domains (polyomavirus/papillomavirus/parvovirus/retinoblastoma protein/p53 protein) F. F. SHADAN AND Luis P. VILLARREAL Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92717 Communicated by Francisco J. Ayala, January 8, 1993 ABSTRACT Although most RNA viral genomes (and re- transcriptase-mediated, vertically transmitted transposable el- lated cellular retroposons) can evolve at rates a millionfold ements (cellular retroposons) appear to result in a dislinkage greater than that of their host genomes, some of the small DNA from the much slower rates of host species evolution (for viruses (polyomaviruses and papillomaviruses) appear to evolve review see ref. 5). Yet high rates of evolution and adaptation at much slower rates. These DNA viruses generally cause host to cause disease may not be a characteristic ofall viral families. species-specific inapparent primary infections followed by life- Some virus families (especially the small DNA viruses, long, benign persistent infections. Using global progressive including the Polyomaviridae, Papillomaviridae, and some sequence alignments for kidney-specific Polyomaviridae (mouse, Parvoviridae), however, appear to be relatively stable genet- hamster, primate, human), we have constructed parsimonious ically and also may not fit a predator-prey population model. evolutionary trees for the viral capsid proteins (VP1, VP2/VP3) In contrast to many RNA and some other viruses, the small and the large tumor (T) antigen. We show that these three coding DNA viruses generally cause inapparent primary infections sequences can yield phylogenetic trees similar to each other and followed by lifelong persistent infection with little disease to that of their host species. -
ICTV Virus Taxonomy Profile: Papillomaviridae
ICTV VIRUS TAXONOMY PROFILES Van Doorslaer et al., Journal of General Virology 2018;99:989–990 DOI 10.1099/jgv.0.001105 ICTV ICTV Virus Taxonomy Profile: Papillomaviridae Koenraad Van Doorslaer,1,* Zigui Chen,2 Hans-Ulrich Bernard,3 Paul K. S. Chan,2 Rob DeSalle,4 Joakim Dillner,5 Ola Forslund,6 Takeshi Haga,7 Alison A. McBride,8 Luisa L. Villa,9 Robert D. Burk10 and ICTV Report Consortium Abstract The Papillomaviridae is a family of small, non-enveloped viruses with double-stranded DNA genomes of 5 748 to 8 607 bp. Their classification is based on pairwise nucleotide sequence identity across the L1 open reading frame. Members of the Papillomaviridae primarily infect mucosal and keratinised epithelia, and have been isolated from fish, reptiles, birds and mammals. Despite a long co-evolutionary history with their hosts, some papillomaviruses are pathogens of their natural host species. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Papillomaviridae, which is available at http://www.ictv.global/report/papillomaviridae. Table 1. Characteristics of the family Papillomaviridae Typical member: human papillomavirus 16 (K02718), species Alphapapillomavirus 9, genus Alphapapillomavirus, subfamily Firstpapillomavirinae Virion Non-enveloped, 55 nm, icosahedral Genome Circular dsDNA genome of 5 748 to 8 607 bp Replication Bidirectional (theta) replication Translation Early and late transcripts, alternative splicing, alternative open reading frames Host Range Mammals, birds, reptiles and fish Taxonomy Two subfamilies include >50 genera and >130 species VIRION the capsid proteins L1 and L2. The upstream regulatory region, located between the L1 and E6 open reading frames, The non-enveloped viral capsid is ~600 Å in diameter and contains the origin of replication as well as binding sites for consists of 72 pentamers of the major capsid protein, L1, viral and cellular transcription factors (Fig. -
Sexually Transmitted Viral Infections
FOCUS: SEXUALLY TRANSMITTED DISEASES Sexually Transmitted Viral Infections BETHANY N. KENT LEARNING OBJECTIVES: INTRODUCTION 1. Explain the different disease signs and Sexually transmitted viral infections are widespread, symptoms of viral sexually transmitted diverse, and generally incurable. The variance in viral diseases. types that cause sexually transmitted viral infections show 2. Illustrate the connection between advances in an equal diversity in transmission mechanisms, diagnostics and better treatment outcomes. symptoms, and treatment options. Hepatitis B, which Downloaded from 3. Describe the link between appropriate HIV causes liver damage, and Zika virus, which causes mild treatment and HIV viral mutations. flu-like symptoms and congenital birth defects, are members of the Flaviviridae family. Herpes simplex virus ABSTRACT (HSV), a nerve-cell infecting virus that causes skin Sexually transmitted diseases (STD) of viral origin lesions, and Cytomegalovirus, which is typically comprise the most prevalent STDs on earth. The impact symptomless in healthy adults, but can cause congenital http://hwmaint.clsjournal.ascls.org/ of viral STDs is compounded because, while they are birth defects, are members of the Herpesviridae family. treatable, they are not curable. Symptoms of infection are Human Papillomavirus, or HPV, is the cause of genital dependent on the type of infecting virus and can range warts and some types of cancer; it is a member of the from immune deficiency to skin lesions, warts, and dsDNA Papillomaviridae family. Human cancer. Because of advances in antiviral therapies and Immunodeficiency Virus (HIV), which infects white rapid molecular diagnostics, patients harbor long-term, blood cells and suppresses the immune system, is a single- yet manageable conditions with this group of STDs. -
Morphology of Skin Disease Found in Common Fruits & Vegetables
Morphology of Skin Disease Found in Common Fruits & Vegetables Sophia Chen ARTDES 401 FA 20 Table of Contents Blisters and Pomegranate---------------------1. -Introduction -Development -Virology and Pathogenesis Pus and Banana--------------------------------7. -Introduction -Development -Bacteriology and Pathogenesis Maculopapular Rash and Apple--------------13. -Introduction -Development -Virology and Pathogenesis Filiform Warts and Broccoli------------------19. -Introduction -Development -Virology and Pathogenesis 1. Blisters An area of skin covered by a raised, fluid-filled bubble. Common Cause: Shingles Can have other causes such as burns, trauma, and certain autoim- mune diseases. Shingles is caused by the Varicella Zoster virus, the same virus that causes chickenpox. The sacs are filled with serum, the liquid in blood which separates from blood cells and clotting factors. 2. Shingles (Herpes Zoster) The blisters caused by shingles often pres- ent in clusters that form a stripe that wrap around the torso. Other symptoms include fatigue and itching. Pomegranate (Punica Granatum) Pomegranate is a fruit that has edi- ble seeds inside named arils which are filled with juice and have a red- dish, translucent apperance, similar to blisters cuased by shingles. 3. Onset of Symptoms for Shingles Stage one There are four stages to the devel- opment of shingles, it usually starts with itching and tingling pain for the first few days. Some people may also experience headache and fever. Stage Two Stage Four After the tingling pain, a flat red rash develops on the skin. Around one week later, the Stage Three blisters pop, the content drains, and they scab over. A few days later, the rash will develop into fluid-filled painful blisters. -
A Review of Marine Viruses in Coral Ecosystem
Journal of Marine Science and Engineering Review A Review of Marine Viruses in Coral Ecosystem Logajothiswaran Ambalavanan 1 , Shumpei Iehata 1, Rosanne Fletcher 1, Emylia H. Stevens 1 and Sandra C. Zainathan 1,2,* 1 Faculty of Fisheries and Food Sciences, University Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia; [email protected] (L.A.); [email protected] (S.I.); rosannefl[email protected] (R.F.); [email protected] (E.H.S.) 2 Institute of Marine Biotechnology, University Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia * Correspondence: [email protected]; Tel.: +60-179261392 Abstract: Coral reefs are among the most biodiverse biological systems on earth. Corals are classified as marine invertebrates and filter the surrounding food and other particles in seawater, including pathogens such as viruses. Viruses act as both pathogen and symbiont for metazoans. Marine viruses that are abundant in the ocean are mostly single-, double stranded DNA and single-, double stranded RNA viruses. These discoveries were made via advanced identification methods which have detected their presence in coral reef ecosystems including PCR analyses, metagenomic analyses, transcriptomic analyses and electron microscopy. This review discusses the discovery of viruses in the marine environment and their hosts, viral diversity in corals, presence of virus in corallivorous fish communities in reef ecosystems, detection methods, and occurrence of marine viral communities in marine sponges. Keywords: coral ecosystem; viral communities; corals; corallivorous fish; marine sponges; detec- tion method Citation: Ambalavanan, L.; Iehata, S.; Fletcher, R.; Stevens, E.H.; Zainathan, S.C. A Review of Marine Viruses in Coral Ecosystem. J. Mar. Sci. Eng. 1. -
Swine Papillomavirus (SPV) Is a Non-Enveloped DNA Virus That Causes Transmissible Genital Papilloma in Swine
SWINE PAPILLOMAVIRUS Prepared for the Swine Health Information Center By the Center for Food Security and Public Health, College of Veterinary Medicine, Iowa State University August 2015 SUMMARY Etiology • Swine papillomavirus (SPV) is a non-enveloped DNA virus that causes transmissible genital papilloma in swine. • Two SPV variants have been described (Sus scrofa papillomaviruses type 1 variants a and b [SsPV-1a/b]). Cleaning and Disinfection • Papillomaviruses survive well in the environment and remain infective following exposure to lipid solvents and detergents, low pH, and high temperatures. • No disinfection protocols specific to SPV are available; however, as a non-enveloped virus, SPV may be susceptible to hypochlorite and aldehydes such as formaldehyde and glutaraldehyde. • A human papilloma virus, HPV16, was found to be susceptible to hypochlorite (0.525%) after 45 minutes. Glutaraldehyde had no ability to render HPV16 inactive. HPV16 was also susceptible to disinfection with a silver-based, 1.2% peracetic acid. Epidemiology • Papillomaviruses infect many species including humans, bovines, canines, equines, lagomorphs, and birds; the virus seems to be highly species-specific. SPV has only been documented in pigs. • Humans are not at risk for infection with SPV. • The geographic distribution of SPV is unclear. The few published reports that exist document SPV in England and Belgium. • There is no information available on SPV-induced morbidity or mortality. Transmission • Transmission of SPV is sexual and occurs through natural servicing or artificial insemination of a gilt/sow by an infected boar. Infection in Swine/Pathogenesis • Infection with SPV results in small to moderately sized (1–3 cm), firm, papular to papillary lesions in the genital tract of pigs. -
Papillomaviruses Likelihood of Secondary Transmission
APPENDIX 2 Papillomaviruses Likelihood of Secondary Transmission: • High by direct contact, especially in older children Disease Agent: and young adults • Human papillomavirus (HPV) • High by sexual contact Disease Agent Characteristics: At-Risk Populations: • Family: Papillomaviridae; Genus: Alpha-Papilloma- • Older children and young adults (nongenital skin virus warts) • Virion morphology and size: Nonenveloped, icosahe- • Persons who are sexually active with multiple dral nucleocapsid symmetry, spherical particles, partners 52-55 nm in diameter • Adult patients with Fanconi anemia • Nucleic acid: Circular, double-stranded DNA, 7.9 kb • HPV-infected persons exposed to sun or UV light in length with unidirectional transcription • Increased susceptibility in immune suppressed • Physicochemical properties: Sparse information; pre- patients sumably susceptible to 0.3% povidone-iodine, to polysulfated and polysulfanated compounds, and to Vector and Reservoir Involved: dilute solutions of sodium dodecyl sulfate; ether- resistant, acid-stable, and heat-stable • None Disease Name: Blood Phase: • Nongenital skin warts • One study found HPV DNA in PBMCs, serum, and • Epidermodysplasia verruciformis plasma of patients with cervical and neck cancers and • Anogenital warts (condylomas) in 3 of 19 (15%) PBMCs from healthy blood donors. • Nonmelanoma skin cancer • Cervical cancer Survival/Persistence in Blood Products: • Anogenital cancer, penile cancer • Unknown • Papillomas of respiratory tract, larynx, mouth, or con- junctiva that includes oral and laryngeal cancers Transmission by Blood Transfusion: Priority Level: • In a recent study of 57 HIV-infected children, seven of • Scientific/Epidemiologic evidence regarding blood eight who were HPV DNA positive had a history of safety: Theoretical blood and/or plasma derivative transfusion as the • Public perception and/or regulatory concern regard- cause of their HIV infection.