Hemorrhagic Fever Viruses: Methods and Protocols

416 Pages·2018·11.58 MB·English

by  Maria S. Salvato (eds.)

Methods in
Molecular Biology 1604
Maria S. Salvato Editor
Hemorrhagic
Fever Viruses
Methods and Protocols
M M B
ethods in olecular iology
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John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
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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
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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
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2016
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4. Zapata JC, Pauza CD, Djavani MM, Rodas JD, Moshkoff D, Bryant J, Ateh E, Garcia C, Lukashevich
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(2):125–138
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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