Methods in Molecular Biology 1604 Maria S. Salvato Editor Hemorrhagic Fever Viruses Methods and Protocols M M B ethods in olecular iology Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Hemorrhagic Fever Viruses Methods and Protocols Edited by Maria S. Salvato School of Medicine, University of Maryland, Baltimore, MD, USA Editor Maria S. Salvato School of Medicine University of Maryland Baltimore, MD, USA ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-6980-7 ISBN 978-1-4939-6981-4 (eBook) DOI 10.1007/978-1-4939-6981-4 Library of Congress Control Number: 2017935485 © Springer Science+Business Media LLC 2018 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Cover illustration: Detecting Ebola virus replication by the RNA-FISH method, Lindquist and Schmaljohn, Chapter 14 Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Preface Hemorrhagic fever viruses (HFV) include some of the most lethal agents of the microbial world. Disease onset can be rapid and fatal. HFV can be extraordinarily contagious and will spread in hospitals without sophisticated infection control. HVF disease is characterized by a rapid onset of fever, muscle ache, and “flu-like” symptoms, followed by liver necrosis, lymph node depletion, coagulation defects, and organ systems failure. Most people have subclinical HFV infections but the potential for severe disease distinguishes the HFV as a major public health threat. As high level threat agents, there will be unique rules for han- dling HFV in research settings [1, 2]. Most virology texts do not embrace the classification of “hemorrhagic fever viruses.” According to the rules for virus classification [3], viruses should not be classified according to the diseases they cause since a virus that makes one organism ill might not affect another. The most useful classifications should allude to the structure of the virion or the region where the virus was found. The appellation “hemorrhagic fever virus” is an operational name given to those viruses with unique potential to cause severe vascular leakage disease. Hemorrhagic fever viruses frequently belong to the taxonomic families Hantaviridae, Nairoviridae, Peribunyaviridae, Phenuiviridae, Arenaviridae1, Flaviviridae, Filoviridae and Rhabdoviridae. Arenaviridae include the largest number of viruses causing viral hem- orrhagic fever (VHF) [4]. The importance of Arenaviridae is reflected in this book as 19 of 30 chapters focus on arenaviruses as experimental examples of HVF. This compilation of work from many laboratories makes reference to high-containment facilities and precau- tions for working with high risk-group agents, even though most of the protocols herein have broad utility and are applicable to less virulent Risk Group 2 agents, as well as to highly virulent Risk Group 4 Select Agents. In May of 2015, during the height of the Ebolavirusdiseaseoutbreak in Western Africa, the world faced the ravages of Ebola virus disease and the toll it took on populations and health care workers who voluntarily entered the danger zones. While it is important to encourage appropriate responses to epidemic disease, this type of information blurs the lines between fearsome natural infections and the attenuated versions that are so necessary for effective biomedical research. For example, Reston virus, so named because it was dis- covered in a dying monkey colony in Reston Virginia, was later suspected to be an attenu- ated virus that had co-infected the monkeys with a simian hemorrhagic fever virus [5]. Because it was an ebolavirus, similar in form to the ebolaviruses that ravaged Zaire and Sudan, Reston virus was branded a Risk Group 4 Select Agent. A surveillance team traveled to the Philippines, the origin of the ill-fated monkey colony, to find the source of Reston virus. The virus was not found in bats or rodents, but was detected on farms where both pigs and farmers had been infected [6–8]. As a result, pigs were exterminated and the farm- ers were quarantined. Since the domestic pigs that became ill were also co-infected with porcine arteriviruses and/or circoviruses, it was not clear that clinical disease was due solely 1 As of June 2017, the former Bunyaviridae family is now the order Bunyavirales containing the virus families Hantaviridae, Nairoviridae, Peribunyaviridae, Phenuiviridae and Arenaviridae. v vi Preface or even mainly to Reston virus infection. Fear instilled by the name “Ebola” may have caused scientists to overlook the potential benefits of having an attenuated virus for vaccine development and even overlooked the contribution of other infectious agents to the disease in Philippine pig farms. These challenges must be met by rigorous studies using commonly accepted practices and standards. This book is intended to help develop a common under- standing of how best to approach the study of hemorrhagic fever viruses of many types and in many places. This book has five parts. The first part on Surveillance, diagnosis, and classification of hemorrhagic fever viruses begins by discussing methods used to predict viral pandemics. Following this introductory chapter are two chapters on the methods and strategies for classifying viruses: one describes the open-source software available for classifying sequences obtained during surveillance, and the other describes Pairwise Sequence Comparison (PASC) to help determine genetic distances between taxa. Next, there is a chapter on viral diagnostics with specific methods for antibody capture using Lassa virus antigens. Three chapters address approaches for epidemiological surveillance: one on surveillance of clinical samples, one on field surveillance of arthropod-borne viruses, and the other on surveillance of rodent-borne viruses. The second part of the book covers Structural studies and reverse genetics of hemor- rhagic fever viruses. Three chapters describe studies on viral entry and on envelope mem- brane fusion. One chapter describes assays for glycoprotein function, another, assays for Z matrix protein functions, and two chapters cover the structure and functions of the arena- virus nucleocapsid protein (NP). A chapter on RNA fluorescence in situ hybridization (FISH) describes the subcellular localization of viral gene expression. The techniques suc- cessfully used to reveal universal budding mechanisms for filoviruses, arenaviruses, and rhabdoviruses are described in a chapter on using virus-like particles to study virus egress. One chapter describes polymerase function of the Crimean-Congo hemorrhagic fever virus, typical of the large multi-functional polymerases of the hemorrhagic fever viruses. Finally, there are two chapters devoted to reverse genetic systems: one for filoviruses and the other giving us two reverse genetic approaches for Pichindé virus. The third part contains chapters on In vivo models of hemorrhagic fever virus infection. The chapter on murine models for VHF describes a quantitative measure for vascular leak- age using Evan’s blue dye that could be applied to other animal models of VHF. The authors who gave us a chapter on the guinea pig model for VHF also used this model to test their antibody therapy for Ebola virus infection. A primate model for VHF summarizes the methods used to sample infected rhesus monkeys. Finally, we present a method to obtain a subset of primary human liver cells that can be cultured long term and used for HFV infections. The fourth part contains Immune assays and vaccine production for hemorrhagic fever viruses. The first chapter in this part is a remarkable description of the facilities and proce- dures used to produce the live attenuated-Junín vaccine against Argentinian hemorrhagic fever. Next is a chapter on detecting virus-antibody immune complexes in secondary den- gue infection. The last chapter in this part is on DNA vaccines from a laboratory renowned for promoting such vaccines for a number of hemorrhagic fever viruses. The fifth and final part describes Host responses to viral hemorrhagic fever. First is a method for identifying host restriction factors controlling Junín or dengue virus infection. Then we present two chapters analyzing antivirals: one that determines the life cycle stage blocked by an antiviral, and another that uses high-throughput screening to find antivirals against a retroviral surrogate for a hemorrhagic fever virus. The last chapter is a cell culture method to assess coagulation after HFV infection. Preface vii Despite a tremendous amount of interest, there remains a gap between identifying viruses during surveillance and linking these agents to specific disease risks. Viruses that cause hepatitis, like the HFV, carry more risk for the malnourished, the immunosuppressed, or the aged [9] than for the young techies of Silicon Valley. Our goal here is to promote research on the disease mechanisms of HFV by offering detailed instructions on exploring structure/function of viral molecules and assessing virus effects in cell culture and in animal models. Armed with this type of information, we will eventually be able to do more than classify a virus’ taxon but also find its actual risk group. Such research will move HFV from the category of bio-terrors to the category of manageable bio-threats. Baltimore, MD, USA Maria S. Salvato References 1. BMBL rules. http://www.cdc.gov/biosafety/publications/bmbl5/index.htm. Accessed 10 Aug 2016 2. NIH Guidelines. http://osp.od.nih.gov/sites/default/files/NIH_Guidelines.html. Accessed April 2016 3. ICTV Code. http://www.ictvonline.org/codeOfVirusClassification.asp. Accessed Oct 2016 4. Zapata JC, Pauza CD, Djavani MM, Rodas JD, Moshkoff D, Bryant J, Ateh E, Garcia C, Lukashevich IS, Salvato MS (2011) LCMV infection of macaques: a model for Lassa fever. Antiviral Research 92 (2):125–138 5. McCormick JB, Fisher-Hoch S (1996) Level 4 virus hunters of the CDC. Turner Publishing, Inc, Atlanta p 308, ISBN 1-57036-277-7 6. WHO Reston report April 2009. http://www.who.int/csr/resources/publications/WHO_HSE_ EPR_2009_2/en/. Accessed Aug2016 7. Barrette RW, Metwally SA, Rowland JM, Xu L, Zaki SR, Nichol ST, Rollin PE, Towner JS, Shieh WJ, Batten B, Sealy TK, Carrillo C, Moran KE, Bracht AJ, Mayr GA, Sirios-Cruz M, Catbagan DP, Lautner EA, Ksiazek TG, White WR, McIntosh MT (2009) Discovery of swine as a host for the Reston ebolavi- rus. Science 325: 204–206 8. Burk R, Bollinger L, Johnson JC, Wada J, Radoshitzky SR, Palacios G, Bavari S, Jahrling PB, Kuhn JH (2016) Neglected filoviruses. FEMS Microbiol Rev 40(4): 494–519 9. Scrimshaw NS, SanGiovanni JP (1997) Synergism of nutrition, infection, and immunity: an overview. Am J Clin Nutr 66(2):464S–77S Contents Preface.......................................................... v Contributors...................................................... xiii Part I SurveIllance, DIagnoSIS anD claSSIfIcatIon of HemorrHagIc fever vIruSeS 1 Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics . . . . . . . . 3 Jean-Paul Gonzalez, Marc Souris, and Willy Valdivia-Granda 2 An Approach to the Identification and Phylogenetic Analysis of Emerging and Hemorrhagic Fever Viruses ......................... 33 Francisco J. Díaz, Luis E. Paternina, and Juan David Rodas 3 Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis..... 43 Yīmíng Bào and Jens H. Kuhn 4 Epidemiological Surveillance of Viral Hemorrhagic Fevers With Emphasis on Clinical Virology ................................ 55 Carolina Montoya-Ruiz and Juan David Rodas 5 Diagnostics for Lassa Fever: Detecting Host Antibody Responses .......... 79 Maria S. Salvato, Igor S. Lukashevich, Sandra Medina-Moreno, and Juan Carlos Zapata 6 Sampling Design and Mosquito Trapping for Surveillance of Arboviral Activity ............................................ 89 Luís E. Paternina and Juan David Rodas 7 Epidemiological Surveillance of Rodent-Borne Viruses (Roboviruses)....... 101 Juan David Rodas, Andrés F. Londoño, and Sergio Solari Part II Structural StuDIeS anD reverSe genetIcS of HemorrHagIc fever vIruSeS 8 Entry Studies of New World Arenaviruses............................ 113 María Guadalupe Martínez, María Belén Forlenza, Nélida A. Candurra, and Sandra M. Cordo 9 Studies of Lassa Virus Cell Entry................................... 135 Antonella Pasquato, Antonio Herrador Fernandez, and Stefan Kunz 10 A Cell-Cell Fusion Assay to Assess Arenavirus Envelope Glycoprotein Membrane-Fusion Activity ....................................... 157 Joanne York and Jack H. Nunberg 11 Assays to Assess Arenaviral Glycoprotein Function...................... 169 Junjie Shao, Xiaoying Liu, Yuying Liang, and Hinh Ly ix x Contents 12 Expression and X-Ray Structural Determination of the Nucleoprotein of Lassa Fever Virus ............................................ 179 Xiaoxuan Qi, Wenjian Wang, Haohao Dong, Yuying Liang, Changjiang Dong, and Hinh Ly 13 Assays to Demonstrate the Roles of Arenaviral Nucleoproteins (NPs) in Viral RNA Synthesis and in Suppressing Type I Interferon ........ 189 Qinfeng Huang, Junjie Shao, Yuying Liang, and Hinh Ly 14 Intracellular Detection of Viral Transcription and Replication Using RNA FISH ................................. 201 Michael E. Lindquist and Connie S. Schmaljohn 15 Hemorrhagic Fever Virus Budding Studies ........................... 209 Ronald N. Harty 16 Roles of Arenavirus Z Protein in Mediating Virion Budding, Viral Transcription-Inhibition and Interferon-Beta Suppression............ 217 Junjie Shao, Yuying Liang, and Hinh Ly 17 Structure–Function Assays for Crimean–Congo Hemorrhagic Fever Virus Polymerase.......................................... 229 Marko Zivcec 18 Minigenome Systems for Filoviruses ................................ 237 Thomas Hoenen 19 Establishment of Bisegmented and Trisegmented Reverse Genetics Systems to Generate Recombinant Pichindé Viruses ............. 247 Rekha Dhanwani, Qinfeng Huang, Shuiyun Lan, Yanqing Zhou, Junjie Shao, Yuying Liang, and Hinh Ly Part III In VIVo moDelS of HemorrHagIc fever vIruS InfectIon 20 Murine Models for Viral Hemorrhagic Fever.......................... 257 Rosana Gonzalez-Quintial and Roberto Baccala 21 Testing Experimental Therapies in a Guinea Pig Model for Hemorrhagic Fever .......................................... 269 Gary Wong, Yuhai Bi, Gary Kobinger, George F. Gao, and Xiangguo Qiu 22 A Primate Model for Viral Hemorrhagic Fever ........................ 279 Maria S. Salvato, Igor S. Lukashevich, Yida Yang, Sandra Medina- Moreno, Mahmoud Djavani, Joseph Bryant, Juan David Rodas, and Juan Carlos Zapata 23 A Primary Human Liver Cell Culture Model for Hemorrhagic Fever Viruses ................................................. 291 Mahmoud Djavani Part Iv Immune aSSayS anD vaccIne ProDuctIon for HemorrHagIc fever vIruSeS 24 Protocol for the Production of a Vaccine Against Argentinian Hemorrhagic Fever ................................... 305 Ana María Ambrosio, Mauricio Andrés Mariani, Andrea Soledad Maiza, Graciela Susana Gamboa, Sebastián Edgardo Fossa, and Alejando Javier Bottale Contents xi 25 Detection of Virus-Antibody Immune Complexes in Secondary Dengue Virus Infection.......................................... 331 Meng Ling Moi, Tomohiko Takasaki, and Ichiro Kurane 26 Future Approaches to DNA Vaccination Against Hemorrhagic Fever Viruses ................................................. 339 John J. Suschak and Connie S. Schmaljohn Part v HoSt reSPonSeS to vIral HemorrHagIc fever 27 Identifying Restriction Factors for Hemorrhagic Fever Viruses: Dengue and Junín.............................................. 351 Federico Giovannoni, Jose Rafael Peña Cárcamo, María Laura Morell, Sandra Myriam Cordo, and Cybele C. García 28 Determining the Virus Life-Cycle Stage Blocked by an Antiviral ........... 371 Claudia S. Sepúlveda, Cybele C. García, and Elsa B. Damonte 29 Retrovirus-Based Surrogate Systems for BSL-2 High- Throughput Screening of Antivirals Targeting BSL-3/4 Hemorrhagic Fever-Causing Viruses....... 393 Sheli R. Radoshitzky, Veronica Soloveva, Dima Gharaibeh, Jens H. Kuhn, and Sina Bavari 30 Protocols to Assess Coagulation Following In Vitro Infection with Hemorrhagic Fever Viruses................................... 405 Melissa L. Tursiella, Shannon L. Taylor, and Connie S. Schmaljohn Index........................................................... 419