Screening for Potential Viral Pathogens in Wastewater Effluent
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Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
ORIGINAL RESEARCH published: 10 March 2017 doi: 10.3389/fmicb.2017.00380 Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification Arshan Nasir 1, 2 and Gustavo Caetano-Anollés 1* 1 Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA, 2 Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new Edited by: additions, suggesting it could be a useful supplement to experimental approaches and Ricardo Flores, to aid qualitative assessment of viral diversity in metagenome samples. Polytechnic University of Valencia, Spain Keywords: capsid, virion, protein structure, virus taxonomy, SCOP, fold superfamily Reviewed by: Mario A. Fares, Consejo Superior de Investigaciones INTRODUCTION Científicas(CSIC), Spain Janne J. Ravantti, The last few years have dramatically increased our knowledge about viral systematics and University of Helsinki, Finland evolution. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
On the Biological Success of Viruses
MI67CH25-Turner ARI 19 June 2013 8:14 V I E E W R S Review in Advance first posted online on June 28, 2013. (Changes may still occur before final publication E online and in print.) I N C N A D V A On the Biological Success of Viruses Brian R. Wasik and Paul E. Turner Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106; email: [email protected], [email protected] Annu. Rev. Microbiol. 2013. 67:519–41 Keywords The Annual Review of Microbiology is online at adaptation, biodiversity, environmental change, evolvability, extinction, micro.annualreviews.org robustness This article’s doi: 10.1146/annurev-micro-090110-102833 Abstract Copyright c 2013 by Annual Reviews. Are viruses more biologically successful than cellular life? Here we exam- All rights reserved ine many ways of gauging biological success, including numerical abun- dance, environmental tolerance, type biodiversity, reproductive potential, and widespread impact on other organisms. We especially focus on suc- cessful ability to evolutionarily adapt in the face of environmental change. Viruses are often challenged by dynamic environments, such as host immune function and evolved resistance as well as abiotic fluctuations in temperature, moisture, and other stressors that reduce virion stability. Despite these chal- lenges, our experimental evolution studies show that viruses can often readily adapt, and novel virus emergence in humans and other hosts is increasingly problematic. We additionally consider whether viruses are advantaged in evolvability—the capacity to evolve—and in avoidance of extinction. On the basis of these different ways of gauging biological success, we conclude that viruses are the most successful inhabitants of the biosphere. -
Viruses in a 14Th-Century Coprolite
AEM Accepts, published online ahead of print on 7 February 2014 Appl. Environ. Microbiol. doi:10.1128/AEM.03242-13 Copyright © 2014, American Society for Microbiology. All Rights Reserved. 1 Title: Viruses in a 14th-century coprolite 2 Running title: Viruses in a 14th-century coprolite 3 4 Sandra Appelt1,*, Laura Fancello1,*, Matthieu Le Bailly2, Didier Raoult1, Michel Drancourt1, 5 Christelle Desnues†,1 6 7 1 Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13385 8 Marseille, France. 9 2 Franche-Comté University, CNRS UMR 6249 Chrono-Environment, 25 030 Besançon, France. 10 * These authors have contributed equally to this work 11 † Corresponding author: 12 Christelle Desnues, Unité de recherche sur les maladies infectieuses et tropicales émergentes 13 (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Faculté de médecine, Aix Marseille 14 Université, 27 Bd Jean Moulin, 13385 Marseille, France. Tel: (+33) 4 91 38 46 30, Fax: (+33) 4 15 91 38 77 72. 16 Email: [email protected] 17 Number of words in Abstract: 133 words 18 Number of words in Main Text: 2538 words 19 Number of words in Methods: 954 words 20 Figures: 4, Supplementary Figures: 3 21 Tables: 0, Supplementary Tables: 6 22 Keywords: coprolite, paleomicrobiology, metagenomics, bacteriophages, viruses, ancient DNA 1 23 Abstract 24 Coprolites are fossilized fecal material that can reveal information about ancient intestinal and 25 environmental microbiota. Viral metagenomics has allowed systematic characterization of viral 26 diversity in environmental and human-associated specimens, but little is known about the viral 27 diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite 28 from a closed barrel in a Middle Age site in Belgium using electron microscopy and 29 metagenomics. -
Viruses of Hyperthermophilic Archaea: Entry and Egress from the Host Cell
Viruses of hyperthermophilic archaea : entry and egress from the host cell Emmanuelle Quemin To cite this version: Emmanuelle Quemin. Viruses of hyperthermophilic archaea : entry and egress from the host cell. Microbiology and Parasitology. Université Pierre et Marie Curie - Paris VI, 2015. English. NNT : 2015PA066329. tel-01374196 HAL Id: tel-01374196 https://tel.archives-ouvertes.fr/tel-01374196 Submitted on 30 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie – Paris VI Unité de Biologie Moléculaire du Gène chez les Extrêmophiles Ecole doctorale Complexité du Vivant ED515 Département de Microbiologie - Institut Pasteur 7, quai Saint-Bernard, case 32 25, rue du Dr. Roux 75252 Paris Cedex 05 75015 Paris THESE DE DOCTORAT DE L’UNIVERSITE PIERRE ET MARIE CURIE Spécialité : Microbiologie Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE PIERRE ET MARIE CURIE VIRUSES OF HYPERTHERMOPHILIC ARCHAEA: ENTRY INTO AND EGRESS FROM THE HOST CELL Présentée par M. Emmanuelle Quemin Soutenue le 28 Septembre 2015 devant le jury composé de : Prof. Guennadi Sezonov Président du jury Prof. Christa Schleper Rapporteur de thèse Dr. Paulo Tavares Rapporteur de thèse Dr. -
WO 2015/061752 Al 30 April 2015 (30.04.2015) P O P CT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/061752 Al 30 April 2015 (30.04.2015) P O P CT (51) International Patent Classification: Idit; 816 Fremont Street, Apt. D, Menlo Park, CA 94025 A61K 39/395 (2006.01) A61P 35/00 (2006.01) (US). A61K 31/519 (2006.01) (74) Agent: HOSTETLER, Michael, J.; Wilson Sonsini (21) International Application Number: Goodrich & Rosati, 650 Page Mill Road, Palo Alto, CA PCT/US20 14/062278 94304 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 24 October 2014 (24.10.2014) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 61/895,988 25 October 2013 (25. 10.2013) US MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, 61/899,764 4 November 2013 (04. 11.2013) US PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 61/91 1,953 4 December 2013 (04. 12.2013) us SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 61/937,392 7 February 2014 (07.02.2014) us TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Possible Insights Into the Use of Silver Nanoparticles in Targeting SARS-Cov-2 (COVID-19)
Review Article Possible Insights into the Use of Silver Nanoparticles in Targeting SARS-CoV-2 (COVID-19) Abhinav Raj Ghosh, Bhooshitha AN, Chandan HM, KL Krishna* Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, Karnataka, INDIA. ABSTRACT Aim: The aims of this review are to assess the anti-viral and targeting strategies using nano materials and the possibility of using Silver nanoparticles for combating the SARS-CoV-2. Background: The novel Coronavirus (SARS-CoV-2) has become a global pandemic and has spread rapidly worldwide. Researchers have successfully identified the molecular structure of the novel coronavirus however significant success has not yet been observed with the therapies currently in clinical trials and exhaustive studies are yet to be carried out in the long road to discovery of a vaccine or a possible cure. Another hurdle associated with the discovery of a cure is the mutation of this virus which may occur at any point in time. Hypothesis: Previous studies have identified a wide number of strains of Coronaviruses with differences in virulent properties. Silver nanoparticles have been used extensively in anti-viral research with promising results in-vitro. However, it has not yet been tested for the same in clinical subjects. It has also been tested on two variants of coronavirus in-vitro with significant data to understand the pathogenesis and which may be implemented in further research possibly in other variants of coronavirus. Another interesting targeting approach would be to test the effect of Silver Nanoparticles on TNF-α as well as Interleukins in SARS-CoV-2 patients. -
Mosquito-Borne Viruses, Insect-Specific
FULL PAPER Virology Mosquito-borne viruses, insect-specific flaviviruses (family Flaviviridae, genus Flavivirus), Banna virus (family Reoviridae, genus Seadornavirus), Bogor virus (unassigned member of family Permutotetraviridae), and alphamesoniviruses 2 and 3 (family Mesoniviridae, genus Alphamesonivirus) isolated from Indonesian mosquitoes SUPRIYONO1), Ryusei KUWATA1,2), Shun TORII1), Hiroshi SHIMODA1), Keita ISHIJIMA3), Kenzo YONEMITSU1), Shohei MINAMI1), Yudai KURODA3), Kango TATEMOTO3), Ngo Thuy Bao TRAN1), Ai TAKANO1), Tsutomu OMATSU4), Tetsuya MIZUTANI4), Kentaro ITOKAWA5), Haruhiko ISAWA6), Kyoko SAWABE6), Tomohiko TAKASAKI7), Dewi Maria YULIANI8), Dimas ABIYOGA9), Upik Kesumawati HADI10), Agus SETIYONO10), Eiichi HONDO11), Srihadi AGUNGPRIYONO10) and Ken MAEDA1,3)* 1)Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan 2)Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime 794-8555, Japan 3)Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan 4)Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8508, Japan 5)Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan 6)Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 -
Mesoniviridae: a Proposed New Family in the Order Nidovirales Formed by a Title Single Species of Mosquito-Borne Viruses
NAOSITE: Nagasaki University's Academic Output SITE Mesoniviridae: a proposed new family in the order Nidovirales formed by a Title single species of mosquito-borne viruses Lauber, Chris; Ziebuhr, John; Junglen, Sandra; Drosten, Christian; Zirkel, Author(s) Florian; Nga, Phan Thi; Morita, Kouichi; Snijder, Eric J.; Gorbalenya, Alexander E. Citation Archives of Virology, 157(8), pp.1623-1628; 2012 Issue Date 2012-08 URL http://hdl.handle.net/10069/30101 ©The Author(s) 2012. This article is published with open access at Right Springerlink.com This document is downloaded at: 2020-09-18T09:28:45Z http://naosite.lb.nagasaki-u.ac.jp Arch Virol (2012) 157:1623–1628 DOI 10.1007/s00705-012-1295-x VIROLOGY DIVISION NEWS Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses Chris Lauber • John Ziebuhr • Sandra Junglen • Christian Drosten • Florian Zirkel • Phan Thi Nga • Kouichi Morita • Eric J. Snijder • Alexander E. Gorbalenya Received: 20 January 2012 / Accepted: 27 February 2012 / Published online: 24 April 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Recently, two independent surveillance studies insect nidoviruses, which is intermediate between that of in Coˆte d’Ivoire and Vietnam, respectively, led to the the families Arteriviridae and Coronaviridae, while ni is an discovery of two mosquito-borne viruses, Cavally virus abbreviation for ‘‘nido’’. A taxonomic proposal to establish and Nam Dinh virus, with genome and proteome properties the new family Mesoniviridae, genus Alphamesonivirus, typical for viruses of the order Nidovirales. Using a state- and species Alphamesonivirus 1 has been approved for of-the-art approach, we show that the two insect nidovi- consideration by the Executive Committee of the ICTV. -
Spindle Shaped Virus (SSV) : Mutants and Their Infectivity
Portland State University PDXScholar University Honors Theses University Honors College 2014 Spindle Shaped Virus (SSV) : Mutants and Their Infectivity Thien Hoang Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/honorstheses Let us know how access to this document benefits ou.y Recommended Citation Hoang, Thien, "Spindle Shaped Virus (SSV) : Mutants and Their Infectivity" (2014). University Honors Theses. Paper 231. https://doi.org/10.15760/honors.56 This Thesis is brought to you for free and open access. It has been accepted for inclusion in University Honors Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Spindle Shaped Virus (SSV): Mutants and Their Infectivity by Thien Hoang An undergraduate honors thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in University Honors and Biology: Micro/molecular biology Thesis Adviser Dr. Kenneth Stedman Portland State University 2014 Abstract: SSV1 is an archaeal virus that infects the thermoacidophile Sulfolobus residing in hot springs. The lemon shaped/spindle-shaped fuselloviruses (SSV) that infect Sulfolobus solfataricus is quite morphologically different from almost all other viruses. Because these archaeal viruses live in hot springs with high temperatures and low pH, their genomes and structures have adapted to withstand such harsh conditions. Little research has been done on these extreme viruses, and of the little research, SSV has been the most prominent. Not much is known about the genes that the genome encodes and so I have inserted transposons randomly into genome to determine functionality. -
A Systematic Review of the Natural Virome of Anopheles Mosquitoes
Review A Systematic Review of the Natural Virome of Anopheles Mosquitoes Ferdinand Nanfack Minkeu 1,2,3 and Kenneth D. Vernick 1,2,* 1 Institut Pasteur, Unit of Genetics and Genomics of Insect Vectors, Department of Parasites and Insect Vectors, 28 rue du Docteur Roux, 75015 Paris, France; [email protected] 2 CNRS, Unit of Evolutionary Genomics, Modeling and Health (UMR2000), 28 rue du Docteur Roux, 75015 Paris, France 3 Graduate School of Life Sciences ED515, Sorbonne Universities, UPMC Paris VI, 75252 Paris, France * Correspondence: [email protected]; Tel.: +33-1-4061-3642 Received: 7 April 2018; Accepted: 21 April 2018; Published: 25 April 2018 Abstract: Anopheles mosquitoes are vectors of human malaria, but they also harbor viruses, collectively termed the virome. The Anopheles virome is relatively poorly studied, and the number and function of viruses are unknown. Only the o’nyong-nyong arbovirus (ONNV) is known to be consistently transmitted to vertebrates by Anopheles mosquitoes. A systematic literature review searched four databases: PubMed, Web of Science, Scopus, and Lissa. In addition, online and print resources were searched manually. The searches yielded 259 records. After screening for eligibility criteria, we found at least 51 viruses reported in Anopheles, including viruses with potential to cause febrile disease if transmitted to humans or other vertebrates. Studies to date have not provided evidence that Anopheles consistently transmit and maintain arboviruses other than ONNV. However, anthropophilic Anopheles vectors of malaria are constantly exposed to arboviruses in human bloodmeals. It is possible that in malaria-endemic zones, febrile symptoms may be commonly misdiagnosed. -
Virology Is That the Study of Viruses ? Submicroscopic, Parasitic Particles
Current research in Virology & Retrovirology 2021, Vol.4, Issue 3 Editorial Bahman Khalilidehkordi Shahrekord University of Medical Sciences, Iran mobile genetic elements of cells (such as transposons, Editorial retrotransposons or plasmids) that became encapsulated in protein capsids, acquired the power to “break free” from Virology is that the study of viruses – submicroscopic, the host cell and infect other cells. Of particular interest parasitic particles of genetic material contained during a here is mimivirus, a huge virus that infects amoebae and protein coat – and virus-like agents. It focuses on the sub- encodes much of the molecular machinery traditionally sequent aspects of viruses: their structure, classification associated with bacteria. Two possibilities are that it’s a and evolution, their ways to infect and exploit host cells for simplified version of a parasitic prokaryote or it originated copy , their interaction with host organism physiology and as an easier virus that acquired genes from its host. The immunity, the diseases they cause, the techniques to iso- evolution of viruses, which frequently occurs together with late and culture them, and their use in research and ther- the evolution of their hosts, is studied within the field of apy. Virology is a subfield of microbiology.Structure and viral evolution. While viruses reproduce and evolve, they’re classification of Virus: A major branch of virology is virus doing not engage in metabolism, don’t move, and depend classification. Viruses are often classified consistent with on variety cell for copy . The often-debated question of the host cell they infect: animal viruses, plant viruses, fun- whether or not they’re alive or not could also be a matter gal viruses, and bacteriophages (viruses infecting bacte- of definition that does not affect the biological reality of vi- ria, which include the foremost complex viruses).