Vaccinia Virus: Methods and Protocols

318 Pages·2019·7.685 MB·English

by  Jason Mercer

Methods in
Molecular Biology 2023
Jason Mercer Editor
Vaccinia
Virus
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, UK
For further volumes:
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For over 35 years, biological scientists have come to rely on the research protocols and
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Vaccinia Virus
Methods and Protocols
Edited by
Jason Mercer
MRC-Laboratory for Molecular Cell Biology, University College London,
London, UK
Editor
Jason Mercer
MRC-Laboratory for Molecular Cell Biology
University College London
London, UK
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-9592-9 ISBN 978-1-4939-9593-6 (eBook)
https://doi.org/10.1007/978-1-4939-9593-6
© Springer Science+Business Media, LLC, part of Springer Nature 2019
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Cover illustration: Pictured is an electron micrograph of a cell infected with vaccinia virus. The red objects are called
viral crescents, which grow to form the violet circles called immature virions, when the viral genome is encapsidated into
these they become known as immature virions with nucleoid (the genome is the very dense structure within), the green
objects are fully assembled infectious vaccinia viruses, which are called mature virions. Image credit: Ian J. White; MRC-
LMCB UCL
This Humana imprint is published by the registered company Springer Science+Business Media, LLC part of Springer
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Foreword
Poxvirology has a long and storied history. Part of that history includes a significant list of
“firsts.” The first vaccine was the smallpox vaccine. Smallpox was the first and only human
disease that has been eradicated from afflicting humankind. A new first has been added to
this illustrious list. A new poxvirus therapeutic has been FDA approved. It is the first drug
to gain approval through the FDA’s “Animal Rule” because efficacy studies in humans were
not ethical or feasible. The drug that was known as ST-246 is now named tecovirimat
(commercial name TPOXX), the first drug that specifically treats smallpox.
The scientific understanding and advances in poxvirology are based on the work of
generations of scientists. Since the publication of the last vaccinia virus methods book in
this series, we have lost a number of contributors to the field of poxvirology. We note the
passage of Donald (D.A.) Henderson (1928–2016), R. Mark Buller (1949–2017), Enzo
Paoletti (1943–2018), and Keith R. Dumbell (1922–2018).
This scientific understanding of vaccinia virus and poxviruses continues to grow. This
new volume of Methods in Molecular Biology provides a resource for scientists to bring
new methods and procedures into their lab to make exciting discoveries that will continue
to deepen our understanding of this fascinating virus family.
Stuart N. Isaacs
Perelman School of Medicine
at the University of Pennsylvania
Philadelphia, PA, USA
v
Preface
Vaccinia Virus: Methods and Protocols provides a resource of practical information for the
laboratory that can be applied to study vaccinia and other poxviruses. This methods edition
looks to emphasize long-standing field standards and complement the previous two edi-
tions (Volumes 269 and 890 in the Methods in Molecular Biology series). This includes a
range of chapters focused on emerging new technologies applied in the field of poxvirology.
The methods and protocols have been designed with the bench scientist in mind, being
presented in a fashion that makes them useful for both starting and veteran poxvirus
researchers.
London, UK Jason Mercer
vii
Acknowledgments
I would like to acknowledge the poxvirus community for all the great meetings and discus-
sions over the years (science and non-science). I want to specifically thank Paula Traktman,
who convinced me that poxviruses are amazing, and the fab five, Rich Condit, Nissan
Moussatche, Grant Mcfadden, Ed Niles, and Stewart Shuman, who dared to let a first-year
graduate student compete in the famed Poxvirus Open (PVO), if only to FROOB. I want
to thank all of the authors for their outstanding contributions to this book and all the mem-
bers of my lab for remembering to keep poxvirology fun.
ix
Contents
Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
1 Working Safely with Vaccinia Virus: Laboratory Technique
and Review of Published Cases of Accidental Laboratory
Infections with Poxviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Stuart N. Isaacs
2 Bioinformatics for Analysis of Poxvirus Genomes . . . . . . . . . . . . . . . . . . . . . . . . . 29
Shin-Lin Tu and Chris Upton
3 Simple, Rapid Preparation of Poxvirus DNA for PCR Cloning
and Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Rachel L. Roper
4 Construction and Isolation of Recombinant Vaccinia Virus
Expressing Fluorescent Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
N. Bishara Marzook and Timothy P. Newsome
5 Generation of Vaccinia Virus Gene Deletion Mutants Using
Complementing Cell Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Amber B. Rico, Annabel T. Olson, and Matthew S. Wiebe
6 Vaccinia Virus Genome Editing Using CRISPR . . . . . . . . . . . . . . . . . . . . . . . . . 109
Carmela Di Gioia, Ming Yuan, and Yaohe Wang
7 RNAi-Mediated Depletion of Poxvirus Proteins . . . . . . . . . . . . . . . . . . . . . . . . . 119
Caroline Martin and Samuel Kilcher
8 Assessing the Structure and Function of Vaccinia Virus Gene
Products by Transient Complementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Nouhou Ibrahim and Paula Traktman
9 Preliminary Screening and In Vitro Confirmation of Orthopoxvirus
Antivirals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Douglas W. Grosenbach and Dennis E. Hruby
10 Vaccinia Virus Transcriptome Analysis by RNA Sequencing . . . . . . . . . . . . . . . . 157
Shuai Cao, Yongquan Lin, and Zhilong Yang
11 Ribosome Profiling of Vaccinia Virus-Infected Cells . . . . . . . . . . . . . . . . . . . . . . 171
Yongquan Lin, Wentao Qiao, and Zhilong Yang
12 Quantitative PCR-Based Assessment of Vaccinia Virus RNA
and DNA in Infected Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Moona Huttunen and Jason Mercer
xi
xii Contents
13 Click Chemistry-Based Labeling of Poxvirus Genomes . . . . . . . . . . . . . . . . . . . . 209
Harriet Mok and Artur Yakimovich
14 Visualizing Poxvirus Replication and Recombination
Using Live-Cell Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Quinten Kieser, Patrick Paszkowski, James Lin, David Evans,
and Ryan Noyce
15 High-Content Analyses of Vaccinia Plaque Formation . . . . . . . . . . . . . . . . . . . . 237
Artur Yakimovich and Jason Mercer
16 Super-resolution Microscopy of Vaccinia Virus Particles . . . . . . . . . . . . . . . . . . . 255
Robert Gray and David Albrecht
17 Bioluminescence Imaging as a Tool for Poxvirus Biology . . . . . . . . . . . . . . . . . . 269
Beatriz Perdiguero, Carmen Elena Gómez, and Mariano Esteban
18 Growth and Purification of Vaccinia Virus Stocks for MPM Imaging . . . . . . . . . 287
Glennys V. Reynoso, John P. Shannon, Jeffrey L. Americo, James Gibbs,
and Heather D. Hickman
19 Intravital Imaging of Vaccinia Virus-Infected Mice . . . . . . . . . . . . . . . . . . . . . . . 301
John P. Shannon, Olena Kamenyeva, Glennys V. Reynoso,
and Heather D. Hickman
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313