Coronaviruses: Methods and Protocols

273 Pages·2020·6.868 MB·English

by  Helena J. Maier

Methods in
Molecular Biology 2203
Helena J. Maier
Erica Bickerton Editors
Coronaviruses
Methods and Protocols
Second Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
Forfurther volumes:
http://www.springer.com/series/7651
For over 35 years, biological scientists have come to rely on the research protocols and
methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas
thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall
biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by-
step fashion, opening with an introductory overview, a list of the materials and reagents
neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported
with a helpful notes section offering tips and tricks of the trade as well as troubleshooting
advice. These hallmark features were introduced by series editor Dr. John Walker and
constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology
series. Tested and trusted, comprehensive and reliable, all protocols from the series are
indexedinPubMed.
Coronaviruses
Methods and Protocols
Second Edition
Edited by
Helena J. Maier and Erica Bickerton
The Pirbright Institute, Surrey, UK
Editors
HelenaJ.Maier EricaBickerton
ThePirbrightInstitute ThePirbrightInstitute
Surrey,UK Surrey,UK
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-0899-9 ISBN978-1-0716-0900-2 (eBook)
https://doi.org/10.1007/978-1-0716-0900-2
©SpringerScience+BusinessMedia,LLC,partofSpringerNature2020
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction
onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation,
computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations
andthereforefreeforgeneraluse.
Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,
expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen
made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations.
Coverillustration:Infectiousbronchitisvirus-infectedchickenDF1celllabelledtoshowviralRNAspeciesinredand
green.
ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer
Nature.
Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A.
Preface
In December 2019, a novel Coronavirus, SARS-CoV-2, emerged into the human popula-
tion following a cross-species transmission event from an animal source. Since then it has
spreadgloballyresultinginthelargestpandemicinacentury,causingsignificantnumbersof
fatalities. Following widespread use of social distancing measures, the SARS-CoV-2 pan-
demichashadunprecedentedimpactsonday-to-daylifeworldwide.Thewiderimpactson
the global economy and how emergence of this virus will alter society in the long term
remain to be seen after the current pandemic ends. Coronaviruses have long been recog-
nized to have the potential to cause such devastating outbreaks, and the current situation
highlightstheimportanceofstudyingthisfamilyofvirusestounderstandhowtheyemerge,
evolve,replicate,andcausedisease.Onlywiththisknowledgewillitbepossibletoidentify
and control viruses with increased potential to cross the species barrier and to develop the
diagnostics,vaccines,andantiviraltherapeuticsthatarerequiredtomanagefutureoutbreaks
inbothhumansandanimals.
Althoughithasnotbeenpossibletoincludechaptersdescribingprotocolsfor working
with SARS-CoV-2 specifically in this current book, the protocols described here are appli-
cable to all members of the Coronavirinae subfamily. Indeed, we aim with this book to
provideacomprehensivecollectionofprotocolsbeingusedinthecoronavirusresearchfield
currently and that are also transferrable to other fields of virology. We hope it will be
informative for both long-standing coronavirus researchers and those joining the field in
thewakeoftheSARS-CoV-2pandemic.
Wewouldliketothanktheauthorswhohavecontributedtothisbookforthetimethey
havetakentopreparedetailedmethodsaswellasforprovidingpracticalhintsandtipsthat
areoftenessentialtogetanewprotocolworking.Wewouldalsoliketogiveaspecialthanks
to Nicole Doyle who has been a tremendous help with final edits during a very
challengingtime.
Surrey,UK HelenaJ.Maier
EricaBickerton
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 Coronaviruses:AnUpdatedOverviewofTheirReplication
andPathogenesis ....................................................... 1
YuhangWang,MatthewGrunewald,andStanleyPerlman
PART I CORONAVIRUS DETECTION, DISCOVERY, AND EVOLUTION
2 DiscoveryofNovelCoronavirusesinRodents.............................. 33
TheocharisTsoleridisandJonathanK.Ball
3 DetectionandDiscoveryofCoronavirusesinWildBirdPopulations .......... 41
ChantalJ.SnoeckandSiamakZohari
4 CompetitiveELISAfor theDetectionofSerumAntibodiesSpecific
forMiddleEastRespiratorySyndromeCoronavirus(MERS-CoV)............ 55
ShuetsuFukushi
5 Whole-GenomeSequencingProtocolsforIBVandOther
CoronavirusesUsingHigh-ThroughputSequencing ........................ 67
GrahamL.FreimanisandMichaelS.Oade
PART II PROPAGATION AND TITRATION OF CORONAVIRUSES
6 IsolationandTissueCultureAdaptationofPorcineDeltacoronavirus:
ACaseStudy........................................................... 77
HuiHu,KwonilJung,ScottP.Kenney,andLindaJ.Saif
7 ThePreparationofChickenKidneyCellCulturesforVirus
Propagation............................................................ 89
ElenaLokhman,SrijanaRai,andWilliamMatthews
8 ThePreparationofChickenTrachealOrganCulturesandTheir
ApplicationforCiliostasisTest,GrowthKineticsStudies,andVirus
Propagation............................................................ 97
GiuliaDowgierandEricaBickerton
9 IsolationandPropagationofCoronavirusesinEmbryonatedEggs............ 107
JamesS.Guy
10 Well-DifferentiatedPrimaryMammalianAirwayEpithelialCell
Cultures ............................................................... 119
MitraGultom,LauraLaloli,andRonaldDijkman
11 QuantificationofCoronavirusesbyTitrationInVitroandExVivo ........... 135
GiuliaDowgierandHelenaJ.Maier
vii
viii Contents
PART III MANIPULATING THE GENOMES OF CORONAVIRUSES
12 TransientDominantSelectionfor theModification
andGenerationofRecombinantInfectiousBronchitis
Coronaviruses.......................................................... 147
SarahKeep,PaulBritton,andEricaBickerton
13 In-YeastAssemblyofCoronavirusInfectiouscDNAClones
UsingaSyntheticGenomicsPipeline...................................... 167
TranThiNhuThao,FabienLabroussaa,NadineEbert,
JoergJores,andVolkerThiel
PART IV STUDYING VIRUS-HOST INTERACTIONS
14 ProximityLabelingfor theIdentificationofCoronavirus–Host
ProteinInteractions..................................................... 187
PhilipV’kovski,SilvioSteiner,andVolkerThiel
15 UsingYeasttoIdentifyCoronavirus–HostProteinInteractions............... 205
StuartWestonandMatthewFrieman
16 DeterminingHowCoronavirusesOvercometheInterferon
andInnateImmuneResponse............................................ 223
ChristopherM.Coleman
17 RibopuromycylationinCoronavirus-InfectedCells ......................... 231
MatthewJ.Brownsword,HelenaJ.Maier,andNicolasLocker
PART V IMAGING CORONAVIRUS INFECTIONS
18 VisualizingCoronavirusEntryintoCells .................................. 241
AleksandraMilewska,KatarzynaOwczarek,
ArturSzczepanski,andKrzysztofPyrc
19 PreparationofCulturedCellsUsingHigh-PressureFreezing
andFreezeSubstitutionforSubsequent2Dor3DVisualization
intheTransmissionElectronMicroscope.................................. 263
NicoleDoyleandPhilippaC.Hawes
Index ...................................................................... 277
Contributors
JONATHANK.BALL • CentreforGlobalVirusInfections,UniversityofNottingham,
Nottingham,UK;SchoolofLifeSciences,UniversityofNottingham,Nottingham,UK
ERICA BICKERTON • ThePirbrightInstitute,Surrey,UK
PAULBRITTON • ThePirbrightInstitute,Surrey,UK
MATTHEWJ.BROWNSWORD • ThePirbrightInstitute,Surrey,UK;FacultyofHealthand
MedicalSciences,SchoolofBiosciencesandMedicine,UniversityofSurrey,Surrey,UK
CHRISTOPHERM.COLEMAN • SchoolofLifeSciences,QueensMedicalCentre,Universityof
Nottingham,Nottingham,UK
RONALD DIJKMAN • InstituteofVirologyandImmunology,Bern&Mittelha€usern,
Switzerland;DepartmentofInfectiousDiseasesandPathobiology,VetsuisseFaculty,
UniversityofBern,Bern,Switzerland;InstituteforInfectiousDiseases,UniversityofBern,
Bern,Switzerland
GIULIADOWGIER • ThePirbrightInstitute,Surrey,UK
NICOLEDOYLE • ThePirbrightInstitute,Surrey,UK
NADINEEBERT • InstituteofVirologyandImmunologyIVI,Bern,Switzerland;Department
ofInfectiousDiseasesandPathobiology,VetsuisseFaculty,UniversityofBern,Bern,
Switzerland
GRAHAM L.FREIMANIS • ThePirbrightInstitute,Surrey,UK
MATTHEWFRIEMAN • DepartmentofMicrobiologyandImmunology,UniversityofMaryland
SchoolofMedicine,Baltimore,MD,USA
SHUETSUFUKUSHI • DepartmentofVirology,NationalInstituteofInfectiousDiseases,Tokyo,
Japan
MATTHEWGRUNEWALD • DepartmentofMicrobiologyandImmunology,UniversityofIowa,
IowaCity,IA,USA
MITRAGULTOM • InstituteofVirologyandImmunology,Bern&Mittelha€usern,
Switzerland;DepartmentofInfectiousDiseasesandPathobiology,VetsuisseFaculty,
UniversityofBern,Bern,Switzerland;GraduateSchoolforCellularandBiomedical
Sciences,UniversityofBern,Bern,Switzerland;InstituteforInfectiousDiseases,University
ofBern,Bern,Switzerland
JAMESS.GUY • DepartmentofPopulationHealthandPathobiology,CollegeofVeterinary
Medicine,NorthCarolinaStateUniversity,Raleigh,NC,USA
PHILIPPAC.HAWES • ThePirbrightInstitute,Surrey,UK
HUIHU • CollegeofAnimalScienceandVeterinaryMedicine,HenanAgricultural
University,Zhengzhou,China
JOERGJORES • DepartmentofInfectiousDiseasesandPathobiology,VetsuisseFaculty,
UniversityofBern,Bern,Switzerland;InstituteofVeterinaryBacteriology,Vetsuisse
Faculty,UniversityofBern,Bern,Switzerland
KWONILJUNG • FoodAnimalHealthResearchProgram,OhioAgriculturalResearchand
DevelopmentCenter,CollegeofFood,Agricultural,andEnvironmentalSciences,
DepartmentofVeterinaryPreventiveMedicine,TheOhioStateUniversity,Wooster,OH,
USA
SARAH KEEP • ThePirbrightInstitute,Surrey,UK
ix
x Contributors
SCOTTP.KENNEY • FoodAnimalHealthResearchProgram,OhioAgriculturalResearchand
DevelopmentCenter,CollegeofFood,Agricultural,andEnvironmentalSciences,
DepartmentofVeterinaryPreventiveMedicine,TheOhioStateUniversity,Wooster,OH,
USA
FABIENLABROUSSAA • DepartmentofInfectiousDiseasesandPathobiology,VetsuisseFaculty,
UniversityofBern,Bern,Switzerland;InstituteofVeterinaryBacteriology,Vetsuisse
Faculty,UniversityofBern,Bern,Switzerland
LAURALALOLI • InstituteofVirologyandImmunology,Bern&Mittelha€usern,Switzerland;
DepartmentofInfectiousDiseasesandPathobiology,VetsuisseFaculty,UniversityofBern,
Bern,Switzerland;GraduateSchoolforCellularandBiomedicalSciences,Universityof
Bern,Bern,Switzerland;InstituteforInfectiousDiseases,UniversityofBern,Bern,
Switzerland
NICOLAS LOCKER • FacultyofHealthandMedicalSciences,SchoolofBiosciencesand
Medicine,UniversityofSurrey,Surrey,UK
ELENALOKHMAN • ThePirbrightInstitute,Surrey,UK
HELENAJ.MAIER • ThePirbrightInstitute,Surrey,UK
WILLIAMMATTHEWS • ThePirbrightInstitute,Surrey,UK
ALEKSANDRAMILEWSKA • VirogeneticsLaboratoryofVirology,MalopolskaCentreof
Biotechnology,JagiellonianUniversity,Krakow,Poland
MICHAELS.OADE • ThePirbrightInstitute,Surrey,UK
KATARZYNAOWCZAREK • VirogeneticsLaboratoryofVirology,MalopolskaCentreof
Biotechnology,JagiellonianUniversity,Krakow,Poland
STANLEYPERLMAN • DepartmentofMicrobiologyandImmunology,UniversityofIowa,Iowa
City,IA,USA
KRZYSZTOF PYRC • VirogeneticsLaboratoryofVirology,MalopolskaCentreofBiotechnology,
JagiellonianUniversity,Krakow,Poland
SRIJANARAI • ThePirbrightInstitute,Surrey,UK
LINDAJ.SAIF • FoodAnimalHealthResearchProgram,OhioAgriculturalResearchand
DevelopmentCenter,CollegeofFood,Agricultural,andEnvironmentalSciences,
DepartmentofVeterinaryPreventiveMedicine,TheOhioStateUniversity,Wooster,OH,
USA
CHANTALJ.SNOECK • InfectiousDiseasesResearchUnit,DepartmentofInfectionand
Immunity,LuxembourgInstituteofHealth(LIH),Esch-sur-Alzette,Luxembourg
SILVIOSTEINER • InstituteofVirologyandImmunologyIVI,Bern,Switzerland;Department
ofInfectiousDiseasesandPathobiology,VetsuisseFaculty,UniversityofBern,Bern,
Switzerland;GraduateSchoolforBiomedicalScience,UniversityofBern,Bern,
Switzerland
ARTURSZCZEPANSKI • VirogeneticsLaboratoryofVirology,MalopolskaCentreof
Biotechnology,JagiellonianUniversity,Krakow,Poland
TRANTHINHUTHAO • InstituteofVirologyandImmunologyIVI,Bern,Switzerland;
DepartmentofInfectiousDiseasesandPathobiology,VetsuisseFaculty,UniversityofBern,
Bern,Switzerland;GraduateSchoolforBiomedicalScience,UniversityofBern,Bern,
Switzerland
VOLKERTHIEL • InstituteofVirologyandImmunologyIVI,Bern,Switzerland;Department
ofInfectiousDiseasesandPathobiology,VetsuisseFaculty,UniversityofBern,Bern,
Switzerland
THEOCHARISTSOLERIDIS • CentreforGlobalVirusInfections,UniversityofNottingham,
Nottingham,UK;SchoolofLifeSciences,UniversityofNottingham,Nottingham,UK