SARS- and Other Coronaviruses: Laboratory Protocols

334 Pages·2008·7.36 MB·English

by  Leen Vijgen PhD

SARS- and Other Coronaviruses
M E T H O D S I N M O L E C U L A R B I O L O G YTM
John M. Walker,SERIESEDITOR
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M E T H O D S I N M O L E C U L A R B I O L O G YTM
SARS- and Other
Coronaviruses
Laboratory Protocols
Edited by
Dave Cavanagh
InstituteforAnimalHealth,Berkshire,UK
Editor
DaveCavanagh
InstituteforAnimalHealth
Berkshire
UK
[email protected]
SeriesEditor
JohnM.Walker
UniversityofHertfordshire
Hatfield,Hertfordshire
UK
ISBN:978-1-58829-867-6 e-ISBN:978-1-59745-181-9
DOI:10.1007/978-1-59745-181-9
LibraryofCongressControlNumber:2008933583
(cid:2)C 2008HumanaPress,apartofSpringerScience+BusinessMedia,LLC
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Preface
The year 2003 was the year when the name “coronavirus” went around the
world,somewhatfurtherthanthevirusthatsparkedpanic:severeacuterespira-
torysyndromecoronavirus(SARS-CoV).Itwasspreadrapidlybyinternational,
indeedtranscontinental,travelersfromitsepicenterinChina.Thehighmortality
rate, around 10% among clinical cases, and the particularly high price paid by
healthcareworkers,spreadfearglobally.Publichealthfacilitieswerestretched
to the limit, and the effect on local economies was immense. Never before had
acoronavirusmadesuchanimpactonthelivesofthehumanpopulation.
SARS enhanced interest in coronaviruses generally, including the hunt not
only for SARS-CoV-like viruses in wild animals, but also for unrelated coro-
naviruses in wild and semi-domesticated animals. Prior to SARS we knew of
only a dozen or so coronavirus species but it was always likely that there were
many more. Coronavirologists knew, from decades of experience, that coron-
aviruses could be devastating, causing mortality, especially among young, and
higheconomiclossamongdomesticanimals.Moreover,theyknewthatagiven
coronavirusspecieswasnotlimitedtoreplicationinonehostspecies.Thusthe
potential existed for the spread of novel coronaviruses from wild animals to
domestic animals and to man. It is with this potent threat in mind that I have
includednofewerthansevenchaptersdealingwiththedetectionanddiscovery
of coronaviruses by nucleic acid approaches, with antibody-based approaches
beingdescribedinthreeotherchapters.
Although one can detect a virus these days without having to grow it in the
laboratory, there is always a need to do this at some point, whether it be for
the development of diagnostics and vaccines or for the study of pathogene-
sis, pathogenicity, variation, and other virological properties. Therefore, I have
includedseveralchaptersonvirusisolationandpropagation.
For some purposes, e.g., structural studies (Section 3) and vaccine devel-
opment, it is necessary to rigorously purify a virus after propagating it, an art
that fewer virologists practice these days. Hence, two chapters contain detailed
procedures for this. For other structural, and functional, studies and for raising
antibodies for subsequent analytical use, it is sufficient, and, in the case of
nonstructural proteins, essential, to express viral proteins individually. Several
chapters address this task, including one that deals with crystallization of non-
structuralproteins.
v
vi Preface
Having antibodies specific to each viral protein is immensely useful for
structure-function studies, but getting good antibodies is often problematic.
Hence, I have included several chapters with protocols for raising antibodies
against the viral proteins, including peptides as well as proteins expressed in
vitro,andaspartofwholevirions.
Thepenultimatesectionofthisbookcomprisesfiveapproachestothemanip-
ulation of coronavirus genomes. These technical achievements have revolu-
tionized the study of coronavirus replication and the development of vaccines
against coronaviruses. SARS demonstrated that these approaches, developed
with long-known coronaviruses, could be readily adapted to the molecular
cloning,andsubsequentmanipulation,ofanewcoronavirus.Theseprotocolsare
here to assist those who will rise to the challenge of new coronaviruses, and to
providehard-wonpracticaladviceforthoseworkingwithcurrentcoronaviruses.
Finally,therearetwochaptersthatdescribehowtoinvestigateaspectsofthe
cellsurfacereceptorsforcoronaviruses.Oneofthesedealswiththesugarmoi-
etiesthatfrequentlyplayaroleinvirusattachmentandcanaffectpathogenicity
and tropism, but which tend to be overlooked once a protein has been identi-
fiedasbeingareceptor.Theotherchapterdescribeshowrecombinantvesicular
stomatitis virus can be used to study coronavirus receptors and tropism, safely,
andoffersanapproachtovaccinedevelopment.
I would like to thank all the authors in this book for their devotion to the
task. I am full of admiration for what they have achieved in their research and
their willingness to describe their protocols in minute detail, including the sort
ofpracticaladvicethatisneverincludedinprimarypublications.
Although the protocols focus on coronaviruses, it seems to me that all the
chaptershavesomethingtooffereveryvirologist.Indeed,Ibelievethat,among
us, we have produced a protocol book for virologists in general, as well as
for those, present and future, who, through choice or circumstance, work with
coronaviruses.
DaveCavanagh
Compton
Contents
Preface........................................................................................... v
Contributors.................................................................................... xi
ExtraNotesFromtheEditor ................................................................xv
PART I DETECTION AND DISCOVERY OF CORONAVIRUSES
1 A Pancoronavirus RT-PCR Assay for Detection
ofAllKnownCoronaviruses..................................................... 3
LeenVijgen,ElienMoës,ElsKeyaerts,SandraLi,andMarcVanRanst
2 Detection of Group 1 Coronaviruses in Bats Using Universal
CoronavirusReverseTranscriptionPolymeraseChainReactions...... 13
LeoL.M.PoonandJ.S.MalikPeiris
(cid:2)
3 Detection and Sequence Characterization of the 3-End of
CoronavirusGenomesHarboringtheHighlyConservedRNAMotif
s2m.................................................................................. 27
ChristineMonceyronJonassen
4 RT-PCR Detection of Avian Coronaviruses
of Galliform Birds (Chicken, Turkey, Pheasant)
andinaParrot .................................................................... 35
FrancescaAnneCulver,PaulBritton,andDaveCavanagh
5 Detection of Group 2a Coronaviruses with Emphasis
onBovineandWildRuminantStrains....................................... 43
MustafaHasoksuz,AnastasiaVlasova,andLindaJ.Saif
6 Detection of SARS Coronavirus in Humans and Animals by
Conventional andQuantitative(RealTime)ReverseTranscription
PolymeraseChainReactions................................................... 61
J.S.MalikPeirisandLeoL.M.Poon
7 DetectionofNewVirusesbyVIDISCA ......................................... 73
KrzysztofPyrc,MaartenF.Jebbink,BenBerkhout,
andLiavanderHoek
PART II ISOLATION, GROWTH, TITRATION, AND PURIFICATION
OF CORONAVIRUSES
8 Titration of Human Coronaviruses, HCoV-229E
and HCoV-OC43, by an Indirect
ImmunoperoxidaseAssay...................................................... 93
FrancineLambert,HélèneJacomy,GabrielMarceau,
andPierreJ.Talbot
vii
viii Contents
9 The Preparation of Chicken Tracheal Organ Cultures for Virus
Isolation,Propagation,andTitration........................................103
BrendaV.JonesandRuthM.Hennion
10 IsolationandPropagationofCoronavirusesinEmbryonatedEggs...... 109
JamesS.Guy
11 Large-ScalePreparationofUV-InactivatedSARSCoronavirusVirions
forVaccineAntigen.............................................................119
YasukoTsunetsugu-Yokota
PART III STRUCTURE OF CORONAVIRUSES ANALYZED
BY ELECTRON MICROSCOPY
12 Purification and Electron Cryomicroscopy
ofCoronavirusParticles........................................................129
BenjaminW.Neuman,BrianD.Adair,MarkYeager,
andMichaelJ.Buchmeier
PART IV EXPRESSION OF CORONAVIRUS PROTEINS
AND CRYSTALLIZATION
13 Production of Coronavirus Nonstructural Proteins
inSolubleFormforCrystallization..........................................139
YvonnePiotrowski,RajeshPonnusamy,StephanieGlaser,
AnnikenDaabach,RalfMoll,andRolfHilgenfeld
PART V RAISING ANTIBODIES TO CORONAVIRUS
PROTEINS
14 Generating Antibodies to the Gene 3 Proteins
ofInfectiousBronchitisVirus.................................................163
AmandaR.PendletonandCarolynE.Machamer
15 Establishment and Characterization of Monoclonal Antibodies
AgainstSARSCoronavirus.....................................................191
KazuoOhnishi
16 ProductionofMonospecificRabbitAntiseraRecognizingNidovirus
Proteins............................................................................205
JessikaC.Zevenhoven-Dobbe,AlfredL.M.Wassenaar,
YvonnevanderMeer,andEricJ.Snijder
PART VI MANIPULATING THE GENOMES OF CORONAVIRUSES
17 Manipulation of the Coronavirus Genome Using Targeted RNA
RecombinationwithInterspeciesChimericCoronaviruses............229
CornelisA.M.deHaan,BertJanHaijema,PaulS.Masters,
andPeterJ.M.Rottier
Contents ix
18 GenerationofRecombinant Coronaviruses UsingVaccinia Virusas
theCloning Vector and Stable Cell Lines Containing Coronaviral
RepliconRNAs...................................................................237
KlaraKristinEriksson,DivineMakia,andVolkerThiel
19 Transient Dominant Selection for the Modification
and Generation of Recombinant Infectious Bronchitis
Coronaviruses....................................................................255
MariaArmesto,RosaCasais,DaveCavanagh,andPaulBritton
20 Engineering Infectious cDNAs of Coronavirus as Bacterial Artificial
Chromosomes....................................................................275
FernandoAlmazán,CarmenGalán,andLuisEnjuanes
21 Systematic Assembly and Genetic Manipulation
oftheMouseHepatitisVirusA59Genome ...............................293
EricF.Donaldson,AmyC.Sims,andRalphS.Baric
PART VII IDENTIFYING CORONAVIRUS RECEPTORS
22 IdentificationofSugarResiduesInvolvedintheBindingofTGEVto
PorcineBrushBorderMembranes...........................................319
ChristelSchwegmann-WesselsandGeorgHerrler
23 Pseudotyped Vesicular Stomatitis Virus for Analysis of Virus Entry
MediatedbySARSCoronavirusSpikeProteins...........................331
ShuetsuFukushi,RieWatanabe,andFumihiroTaguchi
Index .......................................................................................... 339