Influenza Virus: Methods and Protocols

660 Pages·2018·17.024 MB·English

by  Yohei Yamauchi

Methods in
Molecular Biology 1836
Yohei Yamauchi Editor
Infl uenza
Virus
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Influenza Virus
Methods and Protocols
Edited by
Yohei Yamauchi
School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
Editor
YoheiYamauchi
SchoolofCellularandMolecularMedicine
UniversityofBristol
Bristol,UK
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8677-4 ISBN978-1-4939-8678-1 (eBook)
https://doi.org/10.1007/978-1-4939-8678-1
LibraryofCongressControlNumber:2018949617
©SpringerScience+BusinessMedia,LLC,partofSpringerNature2018
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,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,
expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade.
Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations.
Printedonacid-freepaper
This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC part of
SpringerNature.
Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A.
Preface
In1918theSpanishFlupandemickilledanestimated40millionpeoplearoundtheworld.
Onehundredyearslater,in2018,influenzavirusstillmaintainsasignificantpresenceinthe
medicalandveterinaryspheres.Sincethefirstisolationofahumaninfluenzavirusstrainin
1933,influenzahasbeenresearchedintensivelyandremarkableprogresshasbeenmade:the
recent discovery of bat influenza, decoding of the heterotrimeric influenza A polymerase
structure,andidentificationofthehostgeneresponsibleforavianviruspolymeraseadapta-
tioninmammals,areafewexamples.Thedevelopmentofinfluenzavirusreversegeneticsin
thelate1990sfurtheredourunderstandingofviralpathogenesisandviralproteinfunctions.
It also promoted the generation of novel vaccine strategies. In the early 2000s, genome-
wide siRNA screening, systems biology and bioinformatics were applied to influenza and
othermajorhumanviruses,revealingglobalvirus-hostinteractionnetworksandidentifying
newhostgenesandprocessesthatregulateinfection.Recenttechnologicalbreakthroughsin
super-resolutionimagingandcryoelectronmicroscopyhaveopenednewavenuesofdetect-
ing molecular interactions and viral structures at very high resolution. However, influenza
viruscontinuestoeludeourpersistenteffortstodevelopaflawlessvaccineorantiviral,and
thecurrentknowledgeofinfluenzavirusentry,replicationandpathogenesisisincomplete.
This book will equip researchers – from newcomers to experienced – with various
techniques applicable to influenza biology research in the age of big data. The protocols
containplentyofvisualaidstohelpthereaderreplicateanexperimentinhis/herlaboratory.
Thechaptersareweightedonmolecularbiology,viralcellbiologyandimagingapproaches
thatfacilitatemechanisticinvestigationofvirus-hostinteractions.Leadingscientists–whose
biosandphotosarepresentedattheendofthebook–havebeenbroughttogethertocover
abroadrangeoftopicssuchasinfluenzadiagnosis,viruspropagation,proteomics,haploid
and lentiviral screening, virus entry, single-molecule RNA imaging, correlative light and
electron microscopy (CLEM), EM, light-sheet microscopy, biochemistry, viral transcrip-
tion, physiological infection models (bacterial co-infections, aerosol infection), animal
models, in vivo imaging, antigenic evolution, immunology and mathematical modeling.
Thebookopenswithanintroductiontoinfluenzaandcloseswithfourperspectivechapters
that discuss the challenges ofclinical vaccine trials, debateson the gain-of-functionexperi-
ments with pathogens of pandemic potential, and how mathematical modeling provides
mechanistic insights into infection. This book will hopefully help researchers perform
experiments that fill in the gaps of our knowledge and improve the overall understanding
ofinfluenza.
Bristol,UK YoheiYamauchi
v
Acknowledgments
Iwouldliketothankmembersofmylaboratory,AlinaRozanova,CaitlinSimpson,andSho
Iketanifor theireditorialassistance.
vii
Contents
Preface ..................................................................... v
Acknowledgments............................................................. vii
Contributors................................................................. xiii
1 UnderstandingInfluenza ................................................ 1
EdwardC.HutchinsonandYoheiYamauchi
2 ClinicalDiagnosisofInfluenza ........................................... 23
YoshinoriIto
3 InfluenzaAVirusGeneticTools:FromClinicalSample
toMolecularClone ..................................................... 33
Ste´phanieAnchisi,AnaRitaGonc¸alves,Be´rylMazel-Sanchez,
SamuelCordey,andMircoSchmolke
4 PropagationandTitrationofInfluenzaViruses............................. 59
UmutKarakus,MichelCrameri,CarolineLanz,andEmilioYa´ngu¨ez
5 PurificationandProteomicsofInfluenzaVirions............................ 89
EdwardC.HutchinsonandMonikaStegmann
6 HaploidScreeningfor theIdentificationofHostFactors
inVirusInfection....................................................... 121
EvelynFesslerandLucasT.Jae
7 PhenotypicLentivirusScreenstoIdentifyAntiviralSingle
DomainAntibodies ..................................................... 139
FlorianIngoSchmidt
8 DecipheringVirusEntrywithFluorescentlyLabeledViralParticles ........... 159
AnjaB.Hoffmann,MagalieMazelier,PsylviaLe´ger,
andPierre-YvesLozach
9 QuantitativeRT-PCRAnalysisofInfluenzaVirusEndocyticEscape........... 185
Wen-ChiSuandMichaelM.C.Lai
10 Single-MoleculeSensitivityRNAFISHAnalysisofInfluenza
VirusGenomeTrafficking................................................ 195
Yi-yingChouandTimothe´eLionnet
11 3DElectronMicroscopy(EM)andCorrelativeLightElectron
Microscopy(CLEM)MethodstoStudyVirus-HostInteractions ............. 213
Ine´sRomero-Brey
12 CorrelativeLightandElectronMicroscopyofInfluenza
VirusEntryandBudding................................................ 237
LornaHodgson,PaulVerkade,andYoheiYamauchi
13 InfluenzaVirus-LiposomeFusionStudiesUsingFluorescence
DequenchingandCryo-electronTomography.............................. 261
LongGuiandKellyK.Lee
ix
x Contents
14 Metal-TaggingTransmissionElectronMicroscopyandImmunogold
LabelingonTokuyasuCryosectionstoImageInfluenzaAVirus
RibonucleoproteinTransportandPackaging............................... 281
MartinSachse,IsabelFerna´ndezdeCastro,GuillaumeFournier,
NadiaNaffakh,andCristinaRisco
15 LiveImagingofInfluenzaViralRibonucleoproteinsUsing
Light-SheetMicroscopy ................................................. 303
AmarR.Bhagwat,ValerieLeSage,andSeemaS.Lakdawala
16 PurificationofUnanchoredPolyubiquitinChainsfromInfluenzaVirions...... 329
YasuyukiMiyake,PatrickMatthias,andYoheiYamauchi
17 AssaystoMeasuretheActivityofInfluenzaVirusPolymerase ................ 343
AartjanJ.W.teVelthuis,JasonS.Long,andWendyS.Barclay
18 InVitroModelstoStudyInfluenzaVirusandStaphylococcusaureus
Super-InfectiononaMolecularLevel ..................................... 375
ChristinBruchhagen,AndrevanKru¨chten,CarolinKlemm,
StephanLudwig,andChristinaEhrhardt
19 InfectionofCulturedMammalianCellswithAerosolizedInfluenzaVirus ..... 387
HannahM.Creager,TerrenceM.Tumpey,TaronnaR.Maines,
andJessicaA.Belser
20 AnimalModelsinInfluenzaResearch ..................................... 401
JohannekeD.Hemmink,CatherineJ.Whittaker,andHollyA.Shelton
21 MeasuringInfluenzaVirusInfectionUsingBioluminescent
ReporterVirusesforInVivoImagingandInVitroReplicationAssays ........ 431
ErikA.Karlsson,VictoriaA.Meliopoulos,VyTran,ChandraSavage,
BrandiLivingston,StaceySchultz-Cherry,andAndrewMehle
22 SelectionofAntigenicallyAdvancedVariantsofInfluenzaViruses............. 461
GabrieleNeumann,ShufangFan,andYoshihiroKawaoka
23 AssessmentofInfluenzaVirusHemagglutininStalk-Specific
AntibodyResponses..................................................... 487
Wen-ChunLiu,RaffaelNachbagauer,FlorianKrammer,
andRandyA.Albrecht
24 AnalysesofCellularImmuneResponsesinFerretsFollowing
InfluenzaVirusInfection ................................................ 513
AnthonyT.DiPiazza,KatherineA.Richards,Wen-ChunLiu,
RandyA.Albrecht,andAndreaJ.Sant
25 ParameterEstimationinMathematicalModelsofViral
InfectionsUsingR...................................................... 531
VanKinhNguyenandEstebanA.Hernandez-Vargas
26 SoftwareforCharacterizingtheAntigenicandGeneticEvolution
ofHumanInfluenzaViruses ............................................. 551
SusanneReimeringandAliceC.McHardy
Contents xi
27 ClinicalTrialsofInfluenzaVaccines:SpecialChallenges ..................... 567
AdamFinn
28 TheSilverLininginGain-of-FunctionExperiments
withPathogensofPandemicPotential..................................... 575
MichaelJ.Imperiale,DonHoward,andArturoCasadevall
29 WhyDoExceptionallyDangerousGain-of-Function
ExperimentsinInfluenza?................................................ 589
MarcLipsitch
30 HowComputationalModelsEnableMechanistic
InsightsintoVirusInfection ............................................. 609
IvoF.SbalzariniandUrsF.Greber
AbouttheAuthors ........................................................... 633
Index ...................................................................... 659
Contributors
RANDYA.ALBRECHT (cid:2) DepartmentofMicrobiology,IcahnSchoolofMedicineatMountSinai,
NewYork,NY,USA;GlobalHealthandEmergingPathogensInstitute,IcahnSchoolof
MedicineatMountSinai,NewYork,NY,USA
STE´PHANIEANCHISI (cid:2) FacultyofMedicine,CMU,DepartmentofMicrobiologyandMolecular
Medicine,UniversityofGeneva,Geneva,Switzerland
WENDYS.BARCLAY (cid:2) FacultyofMedicine,DivisionofInfectiousDisease,ImperialCollege
London,London,UK
JESSICAA.BELSER (cid:2) InfluenzaDivision,NationalCenterforImmunizationandRespiratory
Diseases,CentersforDiseaseControlandPrevention,Atlanta,GA,USA
AMARR.BHAGWAT (cid:2) DepartmentofMicrobiologyandMolecularGenetics,Universityof
PittsburghSchoolofMedicine,Pittsburgh,PA,USA
CHRISTINBRUCHHAGEN (cid:2) InstituteofVirologyMuenster(IVM),WestfaelischeWilhelms-
UniversityMuenster,Muenster,Germany
ARTUROCASADEVALL (cid:2) DepartmentofMolecularMicrobiologyandImmunology,Johns
HopkinsBloombergSchoolofPublicHeath,Baltimore,MD,USA
YI-YINGCHOU (cid:2) PrograminCellularandMolecularMedicine,DepartmentofCellBiology,
HarvardMedicalSchool,BostonChildren’sHospital,Boston,MA,USA
SAMUELCORDEY (cid:2) LaboratoryofVirology,InfectiousDiseasesService,UniversityHospitalsof
Geneva,Geneva,Switzerland
MICHELCRAMERI (cid:2) InstituteofMedicalVirology,UniversityofZurich,Zu¨rich,Switzerland
HANNAHM.CREAGER (cid:2) InfluenzaDivision,NationalCenter forImmunizationand
RespiratoryDiseases,CentersforDiseaseControlandPrevention,Atlanta,GA,USA
ISABEL FERNA´NDEZ DE CASTRO (cid:2) CentroNacionaldeBiotecnologia,CNB-CSIC,Cell
StructureLab,Madrid,Spain
ANTHONYT.DIPIAZZA (cid:2) DepartmentofMicrobiologyandImmunology,DavidH.Smith
Center forVaccineBiologyandImmunology,UniversityofRochesterMedicalCenter,
Rochester,NY,USA
CHRISTINA EHRHARDT (cid:2) InstituteofVirologyMuenster(IVM),WestfaelischeWilhelms-
UniversityMuenster,Muenster,Germany
SHUFANGFAN (cid:2) DepartmentofPathobiologicalSciences,InfluenzaResearchInstitute,School
ofVeterinaryMedicine,UniversityofWisconsin-Madison,Madison,WI,USA
EVELYNFESSLER (cid:2) GeneCenterandDepartmentofBiochemistry,Ludwig-Maximilians-
Universita€tMu¨nchen,Munich,Germany
ADAMFINN (cid:2) BristolChildren’sVaccineCentre,SchoolsofCellular&MolecularMedicine
andofPopulationHealthSciences,UniversityofBristol,Bristol,UK
GUILLAUMEFOURNIER (cid:2) De´partementdeVirologie,InstitutPasteur,Unite´deGe´ne´tiqueMole´
culairedesVirus`aARN,Paris,France;CNRS,UMR3569,Paris,France;Universite´
ParisDiderot,SorbonneParisCite´,Paris,France
ANARITAGONC¸ALVES (cid:2) LaboratoryofVirology,InfectiousDiseasesService,University
HospitalsofGeneva,Geneva,Switzerland
URSF.GREBER (cid:2) DepartmentofMolecularLifeSciences,UniversityofZu¨rich,Zu¨rich,
Switzerland
xiii