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1. Intramuscular [18F]F-FDG Administration for Successful PET Imaging of Golden Hamsters in a Maximum Containment Laboratory Setting

Author

Hui Wang, Jurgen Seidel, Christopher Bartos, Russell Byrum, Philip J. Sayre, Kurt Cooper, Yu Cong, Dong-Yun Kim, Claudia Calcagno, Jens H. Kuhn, Anya Crane, Jiro Wada, Reed F. Johnson, Dima A. Hammoud, and Ji Hyun Lee

Subjects
infectious diseases, imaging, [18F]F-FDG PET, administration route, biosafety level 4, intramuscular, Microbiology, QR1-502
Abstract

Positron emission tomography (PET) is becoming an important tool for the investigation of emerging infectious diseases in animal models. Usually, PET imaging is performed after intravenous (IV) radiotracer administration. However, IV injections are difficult to perform in some small animals, such as golden hamsters. This challenge is particularly evident in longitudinal imaging studies, and even more so in maximum containment settings used to study high-consequence pathogens. We propose the use of intramuscular (IM) administration of 2-deoxy-2[18F]fluoro-D-glucose ([18F]F-FDG) for PET imaging of hamsters in a biosafety level 4 (BSL-4) laboratory setting. After [18F]F-FDG administration via IM or IV (through surgically implanted vascular access ports), eight hamsters underwent static or dynamic PET scans. Time–activity curves (TACs) and standardized uptake values (SUVs) in major regions of interest (ROIs) were used to compare the two injection routes. Immediately after injection, TACs differed between the two routes. At 60 min post-injection, [18F]F-FDG activity for both routes reached a plateau in most ROIs except the brain, with higher accumulation in the liver, lungs, brain, and nasal cavities observed in the IM group. IM delivery of [18F]F-FDG is an easy, safe, and reliable alternative for longitudinal PET imaging of hamsters in a BSL-4 laboratory setting.

Published
2022
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2. Duplex One-Step RT-qPCR Assays for Simultaneous Detection of Genomic and Subgenomic RNAs of SARS-CoV-2 Variants

Author

Sushma M. Bhosle, Julie P. Tran, Shuiqing Yu, Jillian Geiger, Jennifer D. Jackson, Ian Crozier, Anya Crane, Jiro Wada, Travis K. Warren, Jens H. Kuhn, and Gabriella Worwa

Subjects
SARS-CoV-2, variant, duplex RT-qPCR, RNA, genomic, subgenomic, Microbiology, QR1-502
Abstract

A hallmark of severe acute respiratory syndrome virus (SARS-CoV-2) replication is the discontinuous transcription of open reading frames (ORFs) encoding structural virus proteins. Real-time reverse transcription PCR (RT-qPCR) assays in previous publications used either single or multiplex assays for SARS-CoV-2 genomic RNA detection and a singleplex approach for subgenomic RNA detection. Although multiplex approaches often target multiple genomic RNA segments, an assay that concurrently detects genomic and subgenomic targets has been lacking. To bridge this gap, we developed two duplex one-step RT-qPCR assays that detect SARS-CoV-2 genomic ORF1a and either subgenomic spike or subgenomic ORF3a RNAs. All primers and probes for our assays were designed to bind to variants of SARS-CoV-2. In this study, our assays successfully detected SARS-CoV-2 Washington strain and delta variant isolates at various time points during the course of live virus infection in vitro. The ability to quantify subgenomic SARS-CoV-2 RNA is important, as it may indicate the presence of active replication, particularly in samples collected longitudinally. Furthermore, specific detection of genomic and subgenomic RNAs simultaneously in a single reaction increases assay efficiency, potentially leading to expedited lucidity about viral replication and pathogenesis of any variant of SARS-CoV-2.

Published
2022
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3. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry

Author

Yíngyún Caì, Shuǐqìng Yú, Rohit K. Jangra, Elena N. Postnikova, Jiro Wada, Robert B. Tesh, Sean P. J. Whelan, Michael Lauck, Michael R. Wiley, Courtney L. Finch, Sheli R. Radoshitzky, David H. O’Connor, Gustavo Palacios, Kartik Chandran, Charles Y. Chiu, and Jens H. Kuhn

Subjects
Bas-Congo virus, Mononegavirales, mononegavirus, Rhabdoviridae, rhabdovirus, tibrovirus, Microbiology, QR1-502
Abstract

In 2012, the genome of a novel rhabdovirus, Bas-Congo virus (BASV), was discovered in the acute-phase serum of a Congolese patient with presumed viral hemorrhagic fever. In the absence of a replicating virus isolate, fulfilling Koch’s postulates to determine whether BASV is indeed a human virus and/or pathogen has been impossible. However, experiments with vesiculoviral particles pseudotyped with Bas-Congo glycoprotein suggested that BASV particles can enter cells from multiple animals, including humans. In 2015, genomes of two related viruses, Ekpoma virus 1 (EKV-1) and Ekpoma virus 2 (EKV-2), were detected in human sera in Nigeria. Isolates could not be obtained. Phylogenetic analyses led to the classification of BASV, EKV-1, and EKV-2 in the same genus, Tibrovirus, together with five biting midge-borne rhabdoviruses [i.e., Beatrice Hill virus (BHV), Bivens Arm virus (BAV), Coastal Plains virus (CPV), Sweetwater Branch virus (SWBV), and Tibrogargan virus (TIBV)] not known to infect humans. Using individual recombinant vesiculoviruses expressing the glycoproteins of all eight known tibroviruses and more than 75 cell lines representing different animal species, we demonstrate that the glycoproteins of all tibroviruses can mediate vesiculovirus particle entry into human, bat, nonhuman primate, cotton rat, boa constrictor, and Asian tiger mosquito cells. Using four of five isolated authentic tibroviruses (i.e., BAV, CPV, SWBV, and TIBV), our experiments indicate that many cell types may be partially resistant to tibrovirus replication after virion cell entry. Consequently, experimental data solely obtained from experiments using tibrovirus surrogate systems (e.g., vesiculoviral pseudotypes, recombinant vesiculoviruses) cannot be used to predict whether BASV, or any other tibrovirus, infects humans.

Published
2019
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4. MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells.

Author

Yu Cong, Brit J Hart, Robin Gross, Huanying Zhou, Matthew Frieman, Laura Bollinger, Jiro Wada, Lisa E Hensley, Peter B Jahrling, Julie Dyall, and Michael R Holbrook

Subjects
Medicine, Science
Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) presents an emerging threat to public health worldwide by causing severe respiratory disease in humans with high virulence and case fatality rate (about 35%) since 2012. Little is known about the pathogenesis and innate antiviral response in primary human monocyte-derived macrophages (MDMs) and dendritic cells (MDDCs) upon MERS-CoV infection. In this study, we assessed MERS-CoV replication as well as induction of inflammatory cytokines and chemokines in MDMs and immature and mature MDDCs. Immature MDDCs and MDMs were permissive for MERS-CoV infection, while mature MDDCs were not, with stimulation of proinflammatory cytokine and chemokine upregulation in MDMs, but not in MDDCs. To further evaluate the antiviral activity of well-defined drugs in primary antigen presenting cells (APCs), three compounds (chloroquine, chlorpromazine and toremifine), each with broad-spectrum antiviral activity in immortalized cell lines, were evaluated in MDMs and MDDCs to determine their antiviral effect on MERS-CoV infection. While chloroquine was not active in these primary cells, chlorpromazine showed strong anti-MERS-CoV activity, but it was associated with high cytotoxicity narrowing the potential window for drug utilization. Unlike in established cells, toremifene had marginal activity when tested in antigen presenting cells, with high apparent cytotoxicity, also limiting its potential as a therapeutic option. These results demonstrate the value of testing drugs in primary cells, in addition to established cell lines, before initiating preclinical or clinical studies for MERS treatment and the importance of carefully assessing cytotoxicity in drug screen assays. Furthermore, these studies also highlight the role of APCs in stimulating a robust protective immune response to MERS-CoV infection.

Published
2018
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5. Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014

Author

Jens H. Kuhn, Kristian G. Andersen, Sylvain Baize, Yīmíng Bào, Sina Bavari, Nicolas Berthet, Olga Blinkova, J. Rodney Brister, Anna N. Clawson, Joseph Fair, Martin Gabriel, Robert F. Garry, Stephen K. Gire, Augustine Goba, Jean-Paul Gonzalez, Stephan Günther, Christian T. Happi, Peter B. Jahrling, Jimmy Kapetshi, Gary Kobinger, Jeffrey R. Kugelman, Eric M. Leroy, Gael Darren Maganga, Placide K. Mbala, Lina M. Moses, Jean-Jacques Muyembe-Tamfum, Magassouba N'Faly, Stuart T. Nichol, Sunday A. Omilabu, Gustavo Palacios, Daniel J. Park, Janusz T. Paweska, Sheli R. Radoshitzky, Cynthia A. Rossi, Pardis C. Sabeti, John S. Schieffelin, Randal J. Schoepp, Rachel Sealfon, Robert Swanepoel, Jonathan S. Towner, Jiro Wada, Nadia Wauquier, Nathan L. Yozwiak, and Pierre Formenty

Subjects
Ebola, Ebola virus, ebolavirus, filovirid, Filoviridae, filovirus, genome annotation, Lomela, Lokolia, Makona, mononegavirad, Mononegavirales, mononegavirus, virus classification, virus isolate, virus nomenclature, virus strain, virus taxonomy, virus variant, Microbiology, QR1-502
Abstract

In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.

Published
2014
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6. ABSL-4 Aerobiology Biosafety and Technology at the NIH/NIAID Integrated Research Facility at Fort Detrick

Author

Matthew G. Lackemeyer, Fabian de Kok-Mercado, Jiro Wada, Laura Bollinger, Jason Kindrachuk, Victoria Wahl-Jensen, Jens H. Kuhn, and Peter B. Jahrling

Subjects
ABSL-4, aerobiology, biosafety level 4, class III biosafety cabinet, BSL-4, high-consequence viral pathogens, medical countermeasure, viral hemorrhagic fever, Microbiology, QR1-502
Abstract

The overall threat of a viral pathogen to human populations is largely determined by the modus operandi and velocity of the pathogen that is transmitted among humans. Microorganisms that can spread by aerosol are considered a more challenging enemy than those that require direct body-to-body contact for transmission, due to the potential for infection of numerous people rather than a single individual. Additionally, disease containment is much more difficult to achieve for aerosolized viral pathogens than for pathogens that spread solely via direct person-to-person contact. Thus, aerobiology has become an increasingly necessary component for studying viral pathogens that are naturally or intentionally transmitted by aerosol. The goal of studying aerosol viral pathogens is to improve public health preparedness and medical countermeasure development. Here, we provide a brief overview of the animal biosafety level 4 Aerobiology Core at the NIH/NIAID Integrated Research Facility at Fort Detrick, Maryland, USA.

Published
2014
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7. Informing the Historical Record of Experimental Nonhuman Primate Infections with Ebola Virus: Genomic Characterization of USAMRIID Ebola Virus/H.sapiens-tc/COD/1995/Kikwit-9510621 Challenge Stock 'R4368' and Its Replacement 'R4415'.

Author

Jeffrey R Kugelman, Cynthia A Rossi, Michael R Wiley, Jason T Ladner, Elyse R Nagle, Bradley P Pfeffer, Karla Garcia, Karla Prieto, Jiro Wada, Jens H Kuhn, and Gustavo Palacios

Subjects
Medicine, Science
Abstract

The creation of licensed medical countermeasures against Select Agents such as Ebola virus (EBOV) is critically dependent on the use of standardized reagents, assays, and animal models. We performed full genome reconstruction, population genomics, contaminant analysis, and characterization of the glycoprotein gene editing site of historical United States Army Medical Research Institute of Infectious Diseases (USAMRIID) nonhuman-primate challenge stock Ebola virus Kikwit "R4368" and its 2014 replacement "R4415." We also provide characterization of the master stock used to create "R4415." The obtained data are essential to understanding the quality of the seed stock reagents used in pivotal animal studies that have been used to inform medical countermeasure development. Furthermore, these data might add to the understanding of the influence of EBOV variant populations on pathogenesis and disease outcome and inform attempts to avoid the evolution of EBOV escape mutants in response to current therapeutics. Finally, as the primary challenge stocks have changed over time, these data will provide a baseline for understanding and correlating past and future animal study results.

Published
2016
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8. Genomic Characterization of the Genus Nairovirus (Family Bunyaviridae)

Author

Jens H. Kuhn, Michael R. Wiley, Sergio E. Rodriguez, Yīmíng Bào, Karla Prieto, Amelia P. A. Travassos da Rosa, Hilda Guzman, Nazir Savji, Jason T. Ladner, Robert B. Tesh, Jiro Wada, Peter B. Jahrling, Dennis A. Bente, and Gustavo Palacios

Subjects
Bunyaviridae, bunyavirus, nairovirus, Dera Ghazi Khan virus, Erve virus, Ganjam virus, Hughes virus, Qalyub virus, Sakhalin virus, Tunis virus, virus classification, virus taxonomy, Microbiology, QR1-502
Abstract

Nairovirus, one of five bunyaviral genera, includes seven species. Genomic sequence information is limited for members of the Dera Ghazi Khan, Hughes, Qalyub, Sakhalin, and Thiafora nairovirus species. We used next-generation sequencing and historical virus-culture samples to determine 14 complete and nine coding-complete nairoviral genome sequences to further characterize these species. Previously unsequenced viruses include Abu Mina, Clo Mor, Great Saltee, Hughes, Raza, Sakhalin, Soldado, and Tillamook viruses. In addition, we present genomic sequence information on additional isolates of previously sequenced Avalon, Dugbe, Sapphire II, and Zirqa viruses. Finally, we identify Tunis virus, previously thought to be a phlebovirus, as an isolate of Abu Hammad virus. Phylogenetic analyses indicate the need for reassignment of Sapphire II virus to Dera Ghazi Khan nairovirus and reassignment of Hazara, Tofla, and Nairobi sheep disease viruses to novel species. We also propose new species for the Kasokero group (Kasokero, Leopards Hill, Yogue viruses), the Ketarah group (Gossas, Issyk-kul, Keterah/soft tick viruses) and the Burana group (Wēnzhōu tick virus, Huángpí tick virus 1, Tǎchéng tick virus 1). Our analyses emphasize the sister relationship of nairoviruses and arenaviruses, and indicate that several nairo-like viruses (Shāyáng spider virus 1, Xīnzhōu spider virus, Sānxiá water strider virus 1, South Bay virus, Wǔhàn millipede virus 2) require establishment of novel genera in a larger nairovirus-arenavirus supergroup.

Published
2016
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9. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Jens H. Kuhn, Scott Adkins, Sergey V. Alkhovsky, Tatjana Avšič-Županc, María A. Ayllón, Justin Bahl, Anne Balkema-Buschmann, Matthew J. Ballinger, Martina Bandte, Martin Beer, Nicolas Bejerman, Éric Bergeron, Nadine Biedenkopf, Laurent Bigarré, Carol D. Blair, Kim R. Blasdell, Steven B. Bradfute, Thomas Briese, Paul A. Brown, Rémy Bruggmann, Ursula J. Buchholz, Michael J. Buchmeier, Alexander Bukreyev, Felicity Burt, Carmen Büttner, Charles H. Calisher, Thierry Candresse, Jeremy Carson, Inmaculada Casas, Kartik Chandran, Rémi N. Charrel, Yuya Chiaki, Anya Crane, Mark Crane, Laurent Dacheux, Elena Dal Bó, Juan Carlos de la Torre, Xavier de Lamballerie, William M. de Souza, Rik L. de Swart, Nolwenn M. Dheilly, Nicholas Di Paola, Francesco Di Serio, Ralf G. Dietzgen, Michele Digiaro, J. Felix Drexler, W. Paul Duprex, Ralf Dürrwald, Andrew J. Easton, Toufic Elbeaino, Koray Ergünay, Guozhong Feng, Claudette Feuvrier, Andrew E. Firth, Anthony R. Fooks, Pierre B. H. Formenty, Juliana Freitas-Astúa, Selma Gago-Zachert, María Laura García, Adolfo García-Sastre, Aura R. Garrison, Scott E. Godwin, Jean-Paul J. Gonzalez, Joëlle Goüy de Bellocq, Anthony Griffiths, Martin H. Groschup, Stephan Günther, John Hammond, Jussi Hepojoki, Melanie M. Hierweger, Seiji Hongō, Masayuki Horie, Hidenori Horikawa, Holly R. Hughes, Adam J. Hume, Timothy H. Hyndman, Dàohóng Jiāng, Gilda B. Jonson, Sandra Junglen, Fujio Kadono, David G. Karlin, Boris Klempa, Jonas Klingström, Michel C. Koch, Hideki Kondō, Eugene V. Koonin, Jarmila Krásová, Mart Krupovic, Kenji Kubota, Ivan V. Kuzmin, Lies Laenen, Amy J. Lambert, Jiànróng Lǐ, Jun-Min Li, François Lieffrig, Igor S. Lukashevich, Dongsheng Luo, Piet Maes, Marco Marklewitz, Sergio H. Marshall, Shin-Yi L. Marzano, John W. McCauley, Ali Mirazimi, Peter G. Mohr, Nick J. G. Moody, Yasuaki Morita, Richard N. Morrison, Elke Mühlberger, Rayapati Naidu, Tomohide Natsuaki, José A. Navarro, Yutaro Neriya, Sergey V. Netesov, Gabriele Neumann, Norbert Nowotny, Francisco M. Ochoa-Corona, Gustavo Palacios, Laurane Pallandre, Vicente Pallás, Anna Papa, Sofia Paraskevopoulou, Colin R. Parrish, Alex Pauvolid-Corrêa, Janusz T. Pawęska, Daniel R. Pérez, Florian Pfaff, Richard K. Plemper, Thomas S. Postler, Françoise Pozet, Sheli R. Radoshitzky, Pedro L. Ramos-González, Marius Rehanek, Renato O. Resende, Carina A. Reyes, Víctor Romanowski, Dennis Rubbenstroth, Luisa Rubino, Artemis Rumbou, Jonathan A. Runstadler, Melanie Rupp, Sead Sabanadzovic, Takahide Sasaya, Heike Schmidt-Posthaus, Martin Schwemmle, Torsten Seuberlich, Stephen R. Sharpe, Mang Shi, Manuela Sironi, Sophie Smither, Jin-Won Song, Kirsten M. Spann, Jessica R. Spengler, Mark D. Stenglein, Ayato Takada, Robert B. Tesh, Jana Těšíková, Natalie J. Thornburg, Nicole D. Tischler, Yasuhiro Tomitaka, Keizō Tomonaga, Noël Tordo, Kenta Tsunekawa, Massimo Turina, Ioannis E. Tzanetakis, Anna Maria Vaira, Bernadette van den Hoogen, Bert Vanmechelen, Nikos Vasilakis, Martin Verbeek, Susanne von Bargen, Jiro Wada, Victoria Wahl, Peter J. Walker, Anna E. Whitfield, John V. Williams, Yuri I. Wolf, Junki Yamasaki, Hironobu Yanagisawa, Gongyin Ye, Yong-Zhen Zhang, Arnfinn Lodden Økland, Virology, NIH - National Institute of Allergy and Infectious Diseases (NIAID) (Estados Unidos), Battelle National Biodefense Institute, Mississippi Agricultural and Forestry Experiment Station (MAFES) (Estados Unidos), United States Department of Agriculture. National Institute of Food and Agriculture, Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), U.S. Horticultural Research Laboratory ( Fort Pierce, USA), United States Department of Agriculture (USDA), N.F. Gamaleya Federal Research Centre N.F. Gamaleya Federal Research Centre of Epidemiology and Microbiology (Gamaleya), University of Ljubljana, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lyssavirus, épidémiologie et neuropathologie - Lyssavirus Epidemiology and Neuropathology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Centre National de Référence de la Rage - National Reference Center Rabies (CNR), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Départemental d’Analyses du Jura (LDA39), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Chinese Center for Disease Control and Prevention, Pharmaq Analytiq, This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This work was also funded in part by Contract No. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of The National Biodefense Analysis and Countermeasures Center, a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.), and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project, under Accession Number 1021494., Ayllón, María A., Casas, I., Navarro Bohigues, J.A., and Pallas, V.

Subjects
Biointeractions and Plant Health, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, Life Science, Humans, 630 Landwirtschaft, General Medicine, Mononegavirales, Phylogeny, Virology & Molecular Biology, Virologie & Moleculaire Biologie
Abstract

50 Pág., In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratifcation vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV, This work was supported in part through Laulima Govern ment Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Gov ernment Solutions, LLC under Contract No. HHSN272201800013C. This work was also funded in part by Contract No. HSHQDC 15-C-00064 awarded by DHS S&T for the management and operation of The National Biodefense Analysis and Countermeasures Center, a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges support from the Mississippi Agri cultural and Forestry Experiment Station (MAFES), USDA-ARS pro ject 58-6066-9-033 and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project, under Accession Num ber 1021494.

Published
2022
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10. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Martin Schwemmle, S. V. Alkhovsky, Mark D. Stenglein, Jinguo Zhang, Shaohua Wen, Víctor Romanowski, Massimo Turina, Peter J. Walker, Baldwyn Torto, Paul A. Rota, Xavier de Lamballerie, Stuart G. Siddell, Noël Tordo, John M. Dye, Inmaculada Casas, Andrew J. Easton, Yasuhiro Tomitaka, Eugene V. Koonin, J. Christopher S. Clegg, Judith K. Brown, Kartik Chandran, Carol D. Blair, Shinya Tsuda, Tony L. Goldberg, Andrew J. Bennett, Ralf G. Dietzgen, Koray Ergünay, Aura R. Garrison, Jiang Hong, Kim R. Blasdell, Matthew J. Ballinger, Zuokun Yang, Manuela Sironi, Florian Hüttner, Timothy H. Hyndman, D. A. Patterson, Roy A. Hall, Eric M. Leroy, Liying Qi, Risto Jalkanen, Gary P. Kobinger, Yanxiang Wang, Michael A. Drebot, Emiliano Di Cicco, Martin H. Groschup, Amy K. Teffer, Thomas S. Postler, Sophie J. Smither, Ni Hong, Sina Bavari, Jamie Bojko, Amy Tabata, Michael J. Buchmeier, Sébastien Massart, Daniel R. Perez, Hironobu Yanagisawa, Janice Uchida, Xiǎohóng Shí, Marina Ciuffo, Jean-Paul Gonzalez, Brian H. Bird, Alejandro Olmedo-Velarde, Justin Bahl, Tao Hu, J. Felix Drexler, Gaya K. Amarasinghe, Jens H. Kuhn, Shaorong Li, Taiyun Wei, Sandra Junglen, José A. Navarro, Sofia Paraskevopoulou, Hans Peter Mühlbach, Nicholas Di Paola, Toufic Elbeaino, Guoping Wang, Song Zhang, Tong Han, Yukio Shirako, Pierre Formenty, Anthony R. Fooks, Lifeng Zhai, Benhur Lee, María Laura García, Dag-Ragnar Blystad, Bertus K. Rima, William G. Dundon, Hideki Ebihara, Jiangxiang Wu, John S. Hu, Gabriel Robles Luna, Jana Fránová, Maria S. Salvato, Norbert Nowotny, Carina Andrea Reyes, Kristina M. Miller, Eric Bergeron, Renato O. Resende, Holly R. Hughes, Victoria Wahl, Changchun Tu, Anna Papa, Roger Hewson, Anna Maria Vaira, Nicolás Bejerman, Alex Pauvolid-Corrêa, Seiji Hongo, Igor S. Lukashevich, Michael Kawate, Bernard R. Agwanda, Sead Sabanadzovic, Gideon J. Mordecai, Piet Maes, Steven B. Bradfute, Stephan Günther, Michele Digiaro, Tomio Usugi, Zhe Zhang, Adam C. Park, Guy Smagghe, Shin-Yi Lee Marzano, Kenji Kubota, Ioannis E. Tzanetakis, Christopher F. Basler, Rik L. de Swart, Yong-Zhen Zhang, Felicity J. Burt, Curtis A. Suttle, Mart Krupovic, Jussi Hepojoki, John W. McCauley, Jonathan S. Towner, Charles H. Calisher, Lei Xu, George Fú Gāo, Jonathan A. Runstadler, David M. Stone, Karia H. Kaukinen, Rachel Breyta, Masayuki Horie, Gael Kurath, Carmen Büttner, Lin-Fa Wang, Jessica R. Spengler, Olga Dolnik, Yuya Chiaki, Nicole Mielke-Ehret, Robert B. Tesh, Gustavo Palacios, Marco Chiapello, Tatjana Avšič-Županc, Martin Verbeek, Qi Cheng, Scott Adkins, Elena Dal Bó, Fujio Kadono, Selma Gago-Zachert, Sergio H. Marshall, Marta Vallino, Gilda B. Jonson, Jingjing Fu, Rosemary Sang, Takahide Sasaya, Amy J. Lambert, Paul Brown, Dennis Rubbenstroth, Dennis A. Bente, Colin R. Parrish, Jin Won Song, María A. Ayllón, Shigeharu Takeuchi, Arvind Varsani, Dàohóng Jiāng, Natalie J. Thornburg, Michael J. Melzer, Stanley L. Langevin, Igor Koloniuk, Mang Shi, John Hammond, Vicente Pallás, Thomas Briese, Amadou A. Sall, Jari Sugano, Sergey V. Netesov, Zhengli Shi, M. Ilyas, Yoshifumi Shimomoto, Wayne B. Borth, Anna E. Whitfield, Ayato Takada, Kirsten Spann, W. Paul Duprex, Marco Forgia, Jiro Wada, Susanne von Bargen, Rim Al Kubrusli, Tobi J. Ming, Gabriele Neumann, Rémi N. Charrel, Caixia Yang, Rayapati A. Naidu, Ralf Dürrwald, David P. Tchouassi, Ursula J. Buchholz, Carlotta Peracchio, Tomohide Natsuaki, Anthony Griffiths, Sheli R. Radoshitzky, Márcio Roberto Teixeira Nunes, Juliana Freitas-Astúa, Janusz T. Paweska, Humberto Debat, Francesco Di Serio, Stephanie Fürl, Susan Payne, Hugh W. Ferguson, Juan Carlos de la Torre, Keizō Tomonaga, Muhammad Waqas, Longhui Li, Elke Mühlberger, Bernadett Pályi, Lies Laenen, Ian Crozier, Yuri I. Wolf, Bernadette G. van den Hoogen, Martin Beer, Jiànróng Lǐ, Thomas Gaskin, Mengji Cao, Ali Mirazimi, F. Murilo Zerbini, Peter Simmonds, Anne Balkema-Buschmann, Adolfo García-Sastre, Hideki Kondō, William Marciel de Souza, Huazhen Liu, John V. Williams, Marco Marklewitz, Alexander Bukreyev, Luisa Rubino, Angela D. Schulze, Nolwenn M. Dheilly, Xueping Zhou, Nikos Vasilakis, Elliot J. Lefkowitz, Boris Klempa, Il-Ryong Choi, Yaqin Wang, and Jonas Klingström

Subjects
Biointeractions and Plant Health, biology, Phylum, Virology, Life Science, Bunyavirales, General Medicine, Mononegavirales, biology.organism_classification, Virology & Molecular Biology, Virologie & Moleculaire Biologie
Abstract

Unfortunately, the inclusion of original names (in non-Latin script) of the following authors caused problems with author name indexing in PubMed. Therefore, these original names were removed from XML data to correct the PubMed record. Mengji Cao, Yuya Chiaki, Hideki Ebihara, Jingjing Fu, George Fú Gāo, Tong Han, Jiang Hong, Ni Hong, Seiji Hongo, Masayuki Horie, Dàohóng Jiāng, Fujio Kadono, Hideki Kondō, Kenji Kubota, Shaorong Li, Longhui Li, Jiànróng Lǐ, Huazhen Liu, Tomohide Natsuaki, Sergey V. Netesov, Anna Papa, Sofia Paraskevopoulou, Liying Qi, Takahide Sasaya, Mang Shi, Xiǎohóng Shí, Zhènglì Shí, Yoshifumi Shimomoto, Jin‑Won Song, Ayato Takada, Shigeharu Takeuchi, Yasuhiro Tomitaka, Keizō Tomonaga, Shinya Tsuda, Changchun Tu, Tomio Usugi, Nikos Vasilakis, Jiro Wada, Lin‑Fa Wang, Guoping Wang, Yanxiang Wang, Yaqin Wang, Tàiyún Wèi, Shaohua Wen, Jiangxiang Wu, Lei Xu, Hironobu Yanagisawa, Caixia Yang, Zuokun Yang, Lifeng Zhai, Yong‑Zhen Zhang, Song Zhang, Jinguo Zhang, Zhe Zhang, Xueping Zhou. In addition, the publication call-out in the supplementary material was updated from issue 11 to issue 12. The original article has been corrected.

Published
2021

11. Expanding the Arterivirus Host Spectrum: Olivier's Shrew Virus 1, A Novel Arterivirus Discovered in African Giant Shrews

Author

Fara Raymond Koundouno, Bert Vanmechelen, Jiro Wada, Valentijn Vergote, Joseph Akoi Bore, Miles W. Carroll, Lies Laenen, Piet Maes, and Jens H. Kuhn

Subjects
0301 basic medicine, Arterivirus, lcsh:Medicine, PROTEIN, Genome, Viral, Genome, Article, Arteriviridae, Virus, Open Reading Frames, 03 medical and health sciences, biology.animal, Animals, TOOL, lcsh:Science, Phylogeny, Genomic organization, Multidisciplinary, Science & Technology, Host Microbial Interactions, Whole Genome Sequencing, biology, Phylogenetic tree, IDENTIFICATION, Sequence Analysis, RNA, Host (biology), Shrews, lcsh:R, Shrew, Frameshifting, Ribosomal, Bayes Theorem, biology.organism_classification, Multidisciplinary Sciences, 030104 developmental biology, Evolutionary biology, Science & Technology - Other Topics, Guinea, lcsh:Q, NIDOVIRUS, SIMIAN HEMORRHAGIC-FEVER, Crocidura olivieri
Abstract

The family Arteriviridae harbors a rapidly expanding group of viruses known to infect a divergent group of mammals, including horses, pigs, possums, primates, and rodents. Hosts infected with arteriviruses present with a wide variety of (sub) clinical symptoms, depending on the virus causing the infection and the host being infected. In this study, we determined the complete genome sequences of three variants of a previously unknown virus found in Olivier’s shrews (Crocidura olivieri guineensis) sampled in Guinea. On the nucleotide level, the three genomes of this new virus, named Olivier’s shrew virus 1 (OSV-1), are 88–89% similar. The genome organization of OSV-1 is characteristic of all known arteriviruses, yet phylogenetic analysis groups OSV-1 separately from all currently established arterivirus lineages. Therefore, we postulate that OSV-1 represents a member of a novel arterivirus genus. The virus described here represents the first discovery of an arterivirus in members of the order Eulipotyphla, thereby greatly expanding the known host spectrum of arteriviruses.

Published
2018

12. MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells

Author

Huanying Zhou, Jiro Wada, Laura Bollinger, Robin Gross, Julie Dyall, Peter B. Jahrling, Michael R. Holbrook, Brit J. Hart, Matthew B. Frieman, Lisa E. Hensley, and Yu Cong

Subjects
0301 basic medicine, RNA viruses, Chemokine, Pulmonology, Coronaviruses, Physiology, Cytotoxicity, Drug Evaluation, Preclinical, Pathology and Laboratory Medicine, Toxicology, Monocytes, White Blood Cells, Chloroquine, Animal Cells, Immune Physiology, Chlorocebus aethiops, Medicine and Health Sciences, Medicine, Drug Approval, Cells, Cultured, Innate Immune System, Multidisciplinary, biology, Chemotaxis, General Medicine, Cell Motility, Treatment Outcome, Medical Microbiology, Viral Pathogens, Viruses, Middle East Respiratory Syndrome Coronavirus, Cytokines, Pathogens, Cellular Types, Chemokines, General Agricultural and Biological Sciences, Coronavirus Infections, medicine.drug, Research Article, Science, Immune Cells, 030106 microbiology, Immunology, Antigen-Presenting Cells, Microbiology, Antiviral Agents, General Biochemistry, Genetics and Molecular Biology, Proinflammatory cytokine, 03 medical and health sciences, Immune system, Animals, Humans, Antigen-presenting cell, Microbial Pathogens, Vero Cells, Blood Cells, Biology and life sciences, business.industry, Macrophages, Organisms, Cell Biology, Dendritic Cells, Molecular Development, 030104 developmental biology, Cell culture, Immune System, Respiratory Infections, Vero cell, biology.protein, business, Developmental Biology
Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) presents an emerging threat to public health worldwide by causing severe respiratory disease in humans with high virulence and case fatality rate (about 35%) since 2012. Little is known about the pathogenesis and innate antiviral response in primary human monocyte-derived macrophages (MDMs) and dendritic cells (MDDCs) upon MERS-CoV infection. In this study, we assessed MERS-CoV replication as well as induction of inflammatory cytokines and chemokines in MDMs and immature and mature MDDCs. Immature MDDCs and MDMs were permissive for MERS-CoV infection, while mature MDDCs were not, with stimulation of proinflammatory cytokine and chemokine upregulation in MDMs, but not in MDDCs. To further evaluate the antiviral activity of well-defined drugs in primary antigen presenting cells (APCs), three compounds (chloroquine, chlorpromazine and toremifine), each with broad-spectrum antiviral activity in immortalized cell lines, were evaluated in MDMs and MDDCs to determine their antiviral effect on MERS-CoV infection. While chloroquine was not active in these primary cells, chlorpromazine showed strong anti-MERS-CoV activity, but it was associated with high cytotoxicity narrowing the potential window for drug utilization. Unlike in established cells, toremifene had marginal activity when tested in antigen presenting cells, with high apparent cytotoxicity, also limiting its potential as a therapeutic option. These results demonstrate the value of testing drugs in primary cells, in addition to established cell lines, before initiating preclinical or clinical studies for MERS treatment and the importance of carefully assessing cytotoxicity in drug screen assays. Furthermore, these studies also highlight the role of APCs in stimulating a robust protective immune response to MERS-CoV infection.

Published
2018

13. Neglected filoviruses

Author

Robin Burk, Laura Bollinger, Joshua C. Johnson, Jiro Wada, Sheli R. Radoshitzky, Gustavo Palacios, Sina Bavari, Peter B. Jahrling, and Jens H. Kuhn

Subjects
0301 basic medicine, viruses, 030106 microbiology, Neglected Diseases, Review Article, Filoviridae, Microbiology, Communicable Diseases, Emerging, Disease Outbreaks, 03 medical and health sciences, 030104 developmental biology, Infectious Diseases, Africa, Filoviridae Infections, Humans
Abstract

Eight viruses are currently assigned to the family Filoviridae. Marburg virus, Sudan virus and, in particular, Ebola virus have received the most attention both by researchers and the public from 1967 to 2013. During this period, natural human filovirus disease outbreaks occurred sporadically in Equatorial Africa and, despite high case-fatality rates, never included more than several dozen to a few hundred infections per outbreak. Research emphasis shifted almost exclusively to Ebola virus in 2014, when this virus was identified as the cause of an outbreak that has thus far involved more than 28 646 people and caused more than 11 323 deaths in Western Africa. Consequently, major efforts are currently underway to develop licensed medical countermeasures against Ebola virus infection. However, the ecology of and mechanisms behind Ebola virus emergence are as little understood as they are for all other filoviruses. Consequently, the possibility of the future occurrence of a large disease outbreak caused by other less characterized filoviruses (i.e. Bundibugyo virus, Lloviu virus, Ravn virus, Reston virus and Taï Forest virus) is impossible to rule out. Yet, for many of these viruses, not even rudimentary research tools are available, let alone medical countermeasures. This review summarizes the current knowledge on these less well-characterized filoviruses.

Published
2016

14. Informing the Historical Record of Experimental Nonhuman Primate Infections with Ebola Virus: Genomic Characterization of USAMRIID Ebola Virus/H.sapiens-tc/COD/1995/Kikwit-9510621 Challenge Stock 'R4368' and Its Replacement 'R4415'

Author

Karla Garcia, Jiro Wada, Cynthia A. Rossi, Jeffrey R. Kugelman, Elyse R. Nagle, Karla Prieto, Gustavo Palacios, Michael R. Wiley, Bradley P. Pfeffer, Jens H. Kuhn, and Jason T. Ladner

Subjects
0301 basic medicine, RNA viruses, Glycobiology, lcsh:Medicine, medicine.disease_cause, Pathology and Laboratory Medicine, Genome, Biochemistry, Population genomics, Genome editing, Contaminants, Medicine and Health Sciences, lcsh:Science, Mammals, Viral Genomics, Multidisciplinary, Mammalian Genomics, Academies and Institutes, Genomics, Medical research, Ebolavirus, Medical Microbiology, Filoviruses, Viral Pathogens, Viruses, Vertebrates, Physical Sciences, Pathogens, Ebola Virus, Research Article, Primates, Materials Science, Microbial Genomics, Biology, Microbiology, 03 medical and health sciences, Genomic Medicine, Virology, medicine, Genetics, Animals, Microbial Pathogens, Historical record, Materials by Attribute, Glycoproteins, Ebola virus, Hemorrhagic Fever Viruses, lcsh:R, Organisms, Biology and Life Sciences, Hemorrhagic Fever, Ebola, United States, 030104 developmental biology, Animal Genomics, Amniotes, lcsh:Q
Abstract

The creation of licensed medical countermeasures against Select Agents such as Ebola virus (EBOV) is critically dependent on the use of standardized reagents, assays, and animal models. We performed full genome reconstruction, population genomics, contaminant analysis, and characterization of the glycoprotein gene editing site of historical United States Army Medical Research Institute of Infectious Diseases (USAMRIID) nonhuman-primate challenge stock Ebola virus Kikwit "R4368" and its 2014 replacement "R4415." We also provide characterization of the master stock used to create "R4415." The obtained data are essential to understanding the quality of the seed stock reagents used in pivotal animal studies that have been used to inform medical countermeasure development. Furthermore, these data might add to the understanding of the influence of EBOV variant populations on pathogenesis and disease outcome and inform attempts to avoid the evolution of EBOV escape mutants in response to current therapeutics. Finally, as the primary challenge stocks have changed over time, these data will provide a baseline for understanding and correlating past and future animal study results.

Published
2016

15. Grasp synthesis based on tactile sensation in robot manipulation of arbitrary located object

Author

Jiro Wada, Masahiro Ohka, and Hanafiah Yussof

Subjects
Engineering, Normal force, business.industry, Shear force, GRASP, Stiffness, Control arm, medicine, Robot, Computer vision, Artificial intelligence, medicine.symptom, business, Robotic arm, Tactile sensor
Abstract

This paper analyzes grasp synthesis in multi-fingered robot arm equipped with a tactile sensor to handle objects located at arbitrary positions. We developed an 11-dof multi-fingered arm and a novel optical three-axis tactile sensor system based on an optical waveguide transduction method. The tactile sensor can simultaneously acquire normal and shearing forces. We analyzed normal and shear force distribution to grasp real object. The slippage direction acquired from the shear force data was used to control arm movements in the incipient grasp and release motion. Normal force is used to distinguish object stiffness and to generate optimum grasp pressure. The analysis results are compiled in a control algorithm inside the robot control system. The algorithm was evaluated in experiments with real objects, and the results revealed good performance of the robot arm when handling arbitrary located objects.

Published
2009

16. Object handling tasks based on active tactile and slippage sensations in a multi-fingered humanoid robot arm

Author

Masahiro Ohka, Jiro Wada, and Hanafiah Yussof

Subjects
Robot kinematics, Engineering, business.industry, GRASP, Arm solution, Robot control, Robot, Computer vision, Artificial intelligence, business, Robotic arm, Tactile sensor, Simulation, Humanoid robot
Abstract

This paper presents a new algorithm for object handling tasks based on active tactile and slippage sensations using a humanoid robot multi-fingered arm for an object that exists at an arbitrary position. The idea is to enhance real-time object handling tasks based on tactile sensing in humanoid robotics, where grasp, move and release motions are involved. We developed a novel hemisphere-shaped optical three-axis tactile sensor to mount on fingertips of the robot arm. The tactile sensor is capable of defining normal and shearing forces simultaneously. For grasp and release motions, we designed the algorithm based on slippage direction analysis consisting of coordinate transformation of the sensing element for the arm global coordinate. The robot control system uses the analysis results to determine whether an object is in contact with the ground without needing to measure the height of the ground. The algorithm was evaluated in experiments with soft and hard objects, whereby results revealed good performance for the robot fingers in handling an object at an arbitrary position.

Published
2009

17. Generation and characterization of large-particle aerosols using a center flow tangential aerosol generator with a nonhuman-primate, head-only aerosol chamber

Author

Jiro Wada, J. Kyle Bohannon, Laura Bollinger, Matthew G. Lackemeyer, Jens H. Kuhn, Peter B. Jahrling, and Reed F. Johnson

Subjects
Aerosols, Primates, Large particle, Non human primate, Meteorology, Health, Toxicology and Mutagenesis, Mechanics, Toxicology, complex mixtures, Article, Disease course, Aerosol, Human disease, Aerosol generator, Administration, Inhalation, Toxicity Tests, Environmental science, Animals, Class III biological safety cabinet, Particle size, Particle Size
Abstract

Aerosol droplets or particles produced from infected respiratory secretions have the potential to infect another host through inhalation. These respiratory particles can be polydisperse and range from 0.05–500 μm in diameter. Animal models of infection are generally established to facilitate the potential licensure of candidate prophylactics and/or therapeutics. Consequently, aerosol-based animal infection models are needed to properly study and counter airborne infections. Ideally, experimental aerosol exposure should reliably result in animal disease that faithfully reproduces the modelled human disease. Few studies have been performed to explore the relationship between exposure particle size and induced disease course for infectious aerosol particles. The center flow tangential aerosol generator (CenTAG™) produces large-particle aerosols capable of safely delivering a variety of infectious aerosols to nonhuman primates within a Class III Biological Safety Cabinet (BSC) for establishment or refinement of nonhuman primate infectious disease models. Here we report the adaptation of this technology to the Animal Biosafety Level 4 (ABSL-4) environment for the future study of high-consequence viral pathogens and the characterization of CenTAG™-created sham (no animal, no virus) aerosols using a variety of viral growth media and media supplements.

Published
2015

18. Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014

Author

Gael Darren Maganga, Magassouba N’Faly, Martin Gabriel, Augustine Goba, Sunday Omilabu, Eric M. Leroy, J. Rodney Brister, Stephen K. Gire, Jens H. Kuhn, Nathan L. Yozwiak, Placide Mbala, Rachel Sealfon, Lina M. Moses, Jeffrey R. Kugelman, Kristian G. Andersen, Olga Blinkova, Christian T. Happi, Jimmy Kapetshi, Peter B. Jahrling, P. Formenty, Nicolas Berthet, Cynthia A. Rossi, Yīmíng Bào, Joseph N. Fair, John S. Schieffelin, Jonathan S. Towner, Gustavo Palacios, Robert Swanepoel, Robert F. Garry, Daniel Park, Janusz T. Paweska, Jiro Wada, Anna N. Clawson, Gary Kobinger, Sylvain Baize, Nadia Wauquier, Jean-Paul Gonzalez, Sina Bavari, Stuart T. Nichol, Randal J. Schoepp, Sheli R. Radoshitzky, Stephan Günther, Jean-Jacques Muyembe-Tamfum, Pardis C. Sabeti, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), FAS Center for Systems Biology, Harvard University, Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP), National Center for Biotechnology Information (NCBI), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Centre International de Recherches Médicales de Franceville (CIRMF), Fondation Mérieux, Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), German Center for Infection Research, Partnersite Munich (DZIF), Tulane University, Harvard FAS Center for Systems Biologyy, Kenema Government Hospital, Metabiota Inc. [San Francisco], Redeemer's University [Lagos, Nigeria], Institut National de Recherche Biomédicale [Kinshasa] (INRB), Special Pathogens Programme, National Microbiology Laboratory, Public Health Agency of Canada, Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Donka National Hospital, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos, Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), National Institute for Communicable Diseases [Johannesburg] (NICD), Computer Science and Artificial Intelligence Laboratory [Cambridge] (CSAIL), Massachusetts Institute of Technology (MIT), University of Pretoria [South Africa], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Harvard University [Cambridge], Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], U.S. Army Medical Research Institute of Infectious Diseases, and Massachusetts Institute of Technology (MIT)-Harvard University [Cambridge]

Subjects
virus strain, MESH: Sequence Analysis, DNA, Letter, genome annotation, lcsh:QR1-502, Filoviridae, virus nomenclature, medicine.disease_cause, lcsh:Microbiology, Disease Outbreaks, West africa, virus variant, Ebola virus, Makona, Lokolia, MESH: Disease Outbreaks, Mononegavirales, virus classification, MESH: Phylogeny, Nomenclature, Phylogeny, MESH: Guinea, biology, 3. Good health, Lomela, Infectious Diseases, MESH: RNA, Viral, Ebola, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Democratic Republic of the Congo, RNA, Viral, filovirus, MESH: Terminology as Topic, filovirid, virus taxonomy, Terminology as Topic, Virology, medicine, Humans, virus isolate, MESH: Ebolavirus, Virus classification, ebolavirus, Ebolavirus, mononegavirus, MESH: Humans, mononegavirad, Outbreak, Sequence Analysis, DNA, MESH: Democratic Republic of the Congo, Hemorrhagic Fever, Ebola, biology.organism_classification, MESH: Hemorrhagic Fever, Ebola, Guinea
Abstract

International audience; In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: "Makona", Middle Africa: "Lomela") and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.

Published
2014
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20. Global Organization and Proposed Megataxonomy of the Virus World

Author

Yuri I. Wolf, Eugene V. Koonin, Mart Krupovic, Valerian V. Dolja, Natalya Yutin, F. Murilo Zerbini, Arvind Varsani, Jens H. Kuhn, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Department of Botany and Plant Pathology, Oregon State University (OSU), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), University of Cape Town, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), E.V.K., Y.I.W., and N.Y. are supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). M.K. was supported by l’Agence Nationale de la Recherche (project ENVIRA, no. ANR-17-CE15-0005-01). J.H.K. is supported through Battelle Memorial Institute’s prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272200700016I., We thank Jiro Wada (Integrated Research Facility at Fort Detrick) for help with figure preparation., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris], and Universidade Federal de Vicosa (UFV)

Subjects
DNA Replication, realm, Genes, Viral, viruses, megataxonomy, virus nomenclature, Genome, Viral, Review, Biology, phylogeny, virus taxonomy, Microbiology, Genome, Virus, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, ICTV, RNA polymerase, evolution, RNA Viruses, virus classification, Molecular Biology, Gene, Virus classification, 030304 developmental biology, virosphere, 0303 health sciences, 030306 microbiology, DNA Viruses, RNA, phylogenomics, Reverse transcriptase, Infectious Diseases, chemistry, Viral replication, Evolutionary biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Virus Physiological Phenomena
Abstract

International audience; SUMMARY : Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.

Published
2020
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21. Origins and Evolution of the Global RNA Virome

Author

Adriana Lucía-Sanz, Eugene V. Koonin, Jens H. Kuhn, Yuri I. Wolf, Valerian V. Dolja, Darius Kazlauskas, Mart Krupovic, Jaime Iranzo, National Center for Biotechnology Information (NCBI), Vilnius University [Vilnius], Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris], Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Biocomputing Unit [Madrid], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Oregon State University (OSU), Y.I.W. and E.V.K. are supported through the intramural program of the U.S. National Institutes of Health. D.K. was partly supported by a Short Term Fellowship from the Federation of European Biochemical Societies (FEBS). M.K. was supported by l’Agence Nationale de la Recherche (ANR) (France) project ENVIRA. This work was funded in part through Battelle Memorial Institute’s prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272200700016I (J.H.K.)., V.V.D. is grateful to Barbara and Simon Gvakharia for their support and inspiration. We thank Jiro Wada (Integrated Research Facility [IRF]—Frederick) for help with figure creation., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris] (IP), and Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)

Subjects
0301 basic medicine, RNA virus, viruses, [SDV]Life Sciences [q-bio], RNA-dependent RNA polymerase, Computational biology, Ecological and Evolutionary Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Virus, 03 medical and health sciences, chemistry.chemical_compound, Virology, RNA polymerase, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], evolution, Human virome, Gene, Capsid protein, Evolution, Virome, 030304 developmental biology, 0303 health sciences, virome, Phylogenetic tree, biology, 030306 microbiology, RNA, biology.organism_classification, QR1-502, capsid protein, RNA silencing, 030104 developmental biology, chemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Research Article
Abstract

The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses., Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.

Published
2018
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