Clinical Virology Manual

639 Pages·2016·12.11 MB·English

CLINICAL
VIROLOGY
MANUAL
FIFTH EDITION

CLINICAL
VIROLOGY
MANUAL
FIFTH EDITION
EditorinChief
MichaelJ.Loeffelholz
ProfessorintheDepartmentofPathology,DirectoroftheClinical
MicrobiologyLaboratoryattheUniversityofTexasMedicalBranch
(UTMB)atGalveston.
Editors
RichardL.Hodinka
ProfessorintheMicrobiologyDepartmentandChairofthe
DepartmentofBiomedicalSciencesattheUniversityofSouth
CarolinaSchoolofMedicine
StephenA.Young
DirectorofResearchandClinicalTrialsatTriCoreReference
Laboratories
BenjaminA.Pinsky
AssistantProfessorintheDepartmentsofPathologyandMedicine,
DivisionofInfectiousDiseasesandGeographicMedicine,atthe
StanfordUniversitySchoolofMedicine
Washington, DC
Copyrightª2016byASMPress.ASMPressisaregisteredtrademarkoftheAmericanSocietyforMicrobiology.Allrightsreserved.
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LibraryofCongressCataloging-in-PublicationData
Names:Loeffelholz,MichaelJ.,editor.|Hodinka,RichardL.,editor.|
Young,StephenA.,editor.|Pinsky,BenjaminA.,editor.
Title:ClinicalVirologyManualFifthEdition/editorinchief,MichaelJ.Loeffelholz;
editors,RichardL.Hodinka,StephenA.Young,BenjaminA.Pinsky.
Description:Fifthedition.|Washington,DC:ASMPress,[2016]
Identifiers:LCCN2016020815|ISBN9781555819149(hardcover)|ISBN9781555819156(e-ISBN)
Subjects:LCSH:Diagnosticvirology—Handbooks,manuals,etc.
Classification:LCCQR387.C482016|DDC616.9/101—dc23LCrecordavailableathttps://lccn.loc.gov/2016020815
ISBN978-1-55581-914-9
e-ISBN978-1-55581-915-6
doi:10.1128/9781555819156
PrintedinCanada
10 9 8 7 6 5 4 3 2 1
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DEDICATION
WededicatethiseditionoftheClinicalVirologyManualtoourfamiliesfortheirpatienceandsupport
duringthisandourotherprofessionalendeavors. Wearetrulyblessedtobepartoftheirlivesandto
receive their unconditional love.
We would also like to thank, and gratefully acknowledge the support andleadership of, ourclose
colleague,mentor,and friend, Dr.Steven Specter,who has worked tirelessly over theyears in
deliveringthefirstfoureditionsoftheManual,toadvancethefieldofviraldiagnostics,andtoprovide
aforumforclinicalvirologists,academicians,andclinicianstopresentanddiscussthelatestscientific
discoveries. We will beforever appreciative of his unwavering efforts.

Contents
Contributors 7 Primary Isolation of Viruses / 79
EditorBiographies MARIEL.LANDRYANDDIANELELAND
PrefacetotheFifthEdition
8 Viral Antigen Detection / 95
SECTION I DIANES.LELANDANDRYANF.RELICH
9 Serologic (Antibody Detection)
GENERALTOPICS IN CLINICALVIROLOGY
Methods / 105
DONGXIANGXIA,DEBRAA.WADFORD,
1 The Taxonomy, Classification, CHRISTOPHERP.PREAS,ANDDAVIDP.SCHNURR
and Characterization of Medically
Important Viruses / 3 10 Nucleic Acid Extraction in Diagnostic
STEVENJ.DREWS Virology / 117
RAYMONDH.WIDENANDSUZANESILBERT
2 Quality Assurance and Quality Control
in Clinical and Molecular Virology / 27 11 Nucleic Acid Amplification by Polymerase
MATTHEWJ.BANKOWSKI
Chain Reaction / 129
ANAMARÍACÁRDENASANDKEVINALBY
3 Regulatory Compliance / 35
LINOJSAMUEL
12 Isothermal Nucleic Acid Amplification
Methods / 137
4 Laboratory Safety / 41
HARALDH.KESSLERANDEVELYNSTELZL
K.SUEKEHL
13 Quantitative Molecular Methods / 145
5 Laboratory Design / 51
NATALIEN.WHITFIELDANDDONNAM.WOLK
MATTHEWJ.BINNICKER
14 Signal Amplification Methods / 167
YUN(WAYNE)WANG
SECTION II
15 DNA Sequencing for Clinical and Public
LABORATORY PROCEDURES FOR HealthVirology:SomeAssemblyRequired / 173
DETECTING VIRUSES JOANNEBARTKUS
6 Specimen Requirements Selection, 16 Phenotypic and Genotypic Antiviral
Collection, Transport, and Processing / 59 Susceptibility Testing / 201
REETIKHAREANDTHOMASE.GRYS MARTHAT.VANDERBEEKANDERICC.J.CLAAS
vii
viii - CONTENTS
17 Point-of-Care Diagnostic Virology / 229 31 Human Polyomaviruses / 427
JAMESJ.DUNNANDLAKSHMICHANDRAMOHAN REBECCAJ.ROCKETT,MICHAELD.NISSEN,THEO
P.SLOOTS,ANDSEWERYNBIALASIEWICZ
18 Future Technology / 243
32 Parvoviruses / 443
ERINMCELVANIATEKIPPEANDCAREY-ANND.
BURNHAM RICHARDS.BULLER
33 Poxviruses / 457
SECTION III ASHLEYV.KONDASANDVICTORIAA.OLSON
34 Rabies Virus / 473
VIRAL PATHOGENS
ROBERTJ.RUDDANDAPRILD.DAVIS
19 Respiratory Viruses / 257 35 Arboviruses / 493
CHRISTINEROBINSON,MICHAELJ.LOEFFELHOLZ, LAURAD.KRAMER,ELIZABETHB.KAUFFMAN,
ANDBENJAMINA.PINSKY NORMAP.TAVAKOLI
20 Enteroviruses and Parechoviruses / 277 36 Animal-Borne Viruses / 515
M.STEVENOBERSTEANDMARKA.PALLANSCH GREGORYJ.BERRY,MICHAELJ.LOEFFELHOLZ,
ANDGUSTAVOPALACIOS
21 Measles, Mumps, and Rubella
37 Human Immunodeficiency Viruses and
Viruses / 293
Human T-lymphotropic Viruses / 527
WILLIAMJ.BELLINI,JOSEPHP.ICENOGLE,AND
JÖRGSCHÜPBACH
CAROLEJ.HICKMAN
38 Chlamydiae / 545
22 Gastrointestinal Viruses / 311
BARBARAVANDERPOLANDCHARLOTTEA.
MICHAELD.BOWEN GAYDOS
23 Hepatitis A and E Viruses / 329 39 The Human Virome / 561
GILBERTOVAUGHANANDMICHAELA.PURDY MATTHEWC.ROSS,NADIMJ.AJAMI,
ANDJOSEPHF.PETROSINO
24 Hepatitis B and D Viruses / 341
40 Human Susceptibility and Response
REBECCAT.HORVAT
to Viral Diseases / 567
VILLEPELTOLAANDJORMAILONEN
25 Hepatitis C Virus / 351
MELANIEMALLORYANDDAVIDHILLYARD
APPENDIXES: REFERENCE VIROLOGY
LABORATORIES
26 Herpes Simplex Viruses and Varicella
Zoster Virus / 363
SCOTTH.JAMESANDMARKN.PRICHARD APPENDIX 1 Reference Virology Laboratory
Testing Performed at the Centers for Disease
Control / 581
27 Cytomegalovirus / 373
ROBERTAB.CAREY
PREETIPANCHOLIANDSTANLEYI.MARTIN
APPENDIX 2 Public Health Laboratory
28 Epstein-Barr Virus / 387
Virology Services / 585
DERRICKCHENANDBELINDAYEN-LIEBERMAN
JANEGETCHELL
29 Human Herpesviruses 6, 7, and 8 / 399 APPENDIX 3 International Reference
SHEILAC.DOLLARDANDTIMOTHYM. Laboratories Offering Virology Services / 595
KARNAUCHOW
ARIELI.SUAREZANDCRISTINAVIDELA
30 Human Papillomaviruses / 413
SUSANNOVAK-WEEKLEYANDROBERTPRETORIUS INDEX / 607
Contributors
NADIM AJAMI RICHARD BULLER
BaylorCollegeofMedicine,DepartmentofMolecularVirology WashingtonUniversitySchoolofMedicine,Departmentof
andMicrobiology,AlkekCenterforMetagenomicsand PediatricsSaintLouis,MO63110
MicrobiomeResearchHouston,TX77030
CAREY-ANN BURNHAM
KEVINALBY WashingtonUniversitySchoolofMedicine,Departmentof
UniversityofPennsylvania,DepartmentofPathologyand Pathology&ImmunologySaintLouis,MO63110
LaboratoryMedicine,Philadelphia,PA19104
ANA MARIA CARDENAS
MATTHEW J. BANKOWSKI UniversityofPennsylvania,DepartmentofPathologyand
DiagnosticLaboratoryServices(TheQueen’sMedicalCenter) LaboratoryMedicinePhiladelphia,PA19103
Aiea,HI96701
ROBERTA CAREY
JOHN A. BURNS
CentersforDiseaseControlandPrevention,LaboratoryQuality
SchoolofMedicine,DepartmentofPathology,Universityof ManagementAtlanta,GA30333
HawaiiatManoaHonolulu,HI96813
LAKSHMI CHANDRAMOHAN
JOANNE BARTKUS
TexasChildren’sHospital,DepartmentofPathologyHouston,
MinnesotaDepartmentofHealth,PublicHealthLaboratory
TX77030
StPaul,MN55164
DERRICK CHEN
WILLIAM BELLINI
MayoClinic,LaboratoryMedicineandPathologyRochester,
CentersforDiseaseControlandPrevention,MMRHLB/DVD/
MN55905
NCIRDAtlanta,GA30329
GREGORYBERRY ERIC C.J. CLAAS
LeidenUniversityMedicalCentre,MedicalMicrobiology
UniversityofTexasMedicalBranch,ClinicalMicrobiology
Leiden2333ZA
LaboratoryGalveston,TX77555
SEWERYNBIALASIEWICZ APRIL DAVIS
CentreforChildren’sHealthResearch,Children’sHealth NewYorkStateHealthDepartment,WadsworthCenter
Queensland,andtheChildHealthResearchCentre,The Slingerlands,NY12159
UniversityofQueenslandSouthBrisbane,QLD4101Australia
SHEILA C. DOLLARD
MATTHEW J. BINNICKER CentersforDiseaseControlandPrevention,DivisionofViral
MayoClinic,DivisionofClinicalMicrobiology,Departmentof DiseasesAtlanta,GA30329
LaboratoryMedicineandPathologyRochester,MN55905
STEVEN J. DREWS
MICHAEL D. BOWEN ProvLabAlberta,DiagnosticVirologyUniversityofAlberta,
CentersforDiseaseControlandPrevention,NationalCenter DepartmentofLaboratoryMedicineandPathologyEdmonton,
forImmunizationandRespiratoryDiseasesAtlanta,GA30333 ABCanada
ix