Coronaviruses: Methods and Protocols PDF
Preview Coronaviruses: Methods and Protocols
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
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