Reeti Khare, PhD, D(ABMM), is the Director of Microbiology at Northwell Health Laboratories in New York. She received her PhD in Virology and Gene Therapy at Mayo Clinic and did a postdoctoral fellowship at the University of Washington. Her research involved reengineering viral vectors, developing adenoviruses for liver gene therapy, and creating viral vector vaccines against MRSA. She returned to Mayo Clinic for her clinical microbiology fellowship and is a diplomate of the American Board of Medical Microbiology. Reeti enjoys teaching and learning about microbiology and has authored numerous publications, chapters, and reviews. At Northwell Health Labs she continues to pursue clinical research and provide student education, and is responsible for laboratory oversight, improving efficiency, designing workflows, and diagnostic microbiology testing.

Preface xi Acknowledgments xii Abbreviations xiii About the Author xvi SECTION I: Foundations of Clinical Virology 3 1 Introduction to Viruses 5Virus structure, life cycle, Baltimore classification, transmission, nomenclature 2 Laboratory Diagnosis of Viral Infections 17Differential diagnosis for viral syndromes, specimen collection, general comparison of diagnostic techniques SECTION II: Viral Pathogens and Clinical Presentation 23 3 Respiratory Viruses 25Influenza virus, respiratory syncytial virus, parainfluenza virus, human metapneumovirus, rhinovirus, coronaviruses, mumps virus 4 Viruses with Dermatologic Manifestations 43Herpes simplex virus 1 and 2, varicella-zoster virus, measles virus, rubella virus, human herpesviruses 6 and 7, molluscum contagiosum virus, smallpox virus, comparison of herpesviruses 1 to 8 5 Gastrointestinal and Fecal-Oral Hepatitis Viruses 61Rotavirus, norovirus, astrovirus, sapovirus, hepatitis A virus, hepatitis E virus 6 Viruses That Can Cause Multiple Syndromes 71Enteroviruses and parechoviruses, adenoviruses, parvovirus B19, human bocavirus 7 Opportunistic Viruses Associated with Immunosuppression 83Cytomegalovirus, BK virus, JC virus 8 Blood-Borne Hepatitis Viruses 91Hepatitis B, C, and D viruses, and comparison of hepatitis viruses A through E 9 Human Retroviruses 105Human immunodeficiency virus, human T-cell lymphotropic virus 10 Oncogenic Viruses 121Human papillomavirus, Epstein-Barr virus, human herpesvirus 8 11 Zoonotic Viruses 133Rabies virus, Ebola and Marburg viruses, Lassa virus, Crimean-Congo hemorrhagic fever virus, hantaviruses, lymphocytic choriomeningitis virus, monkeypox virus, herpes B virus, Hendra and Nipah viruses, comparison of zoonotic viruses 12 Arboviruses 147Mosquitoes, ticks, dengue virus, yellow fever virus, chikungunya virus, West Nile virus, Zika virus, eastern, western, and Venezuelan equine encephalitis viruses, Japanese encephalitis virus, Powassan virus, tick-borne encephalitis virus, Rift Valley fever virus, comparison of arboviruses SECTION III: Diagnostic Assays and Techniques 161 13 Culture and Tissue-Based Diagnostic Techniques 163Conventional viral culture and cell lines, cytopathic effect, viral growth rates, shell vial assays, hemadsorption, quantification by plaque-forming units and TCID50, histopathology and cytopathology of viruses, in situ hybridization 14 Diagnostic Techniques Based on Immunological Interactions 175Enzyme immunoassays including ELISAs, chemiluminescent immunoassays, and immunoblot assays, immunofluorescence assays, immunochromatographic (lateral flow) assays, hemagglutination inhibition and plaque reduction neutralization assays, serologic assays, kinetics and interpretation of antibody responses, comparison of immunoassays 15 Molecular Techniques: Nucleic Acid Amplification 189Importance of nucleic acid structure, sample processing, PCR, reverse transcription-PCR, real-time PCR, quantitative vs. qualitative PCR, melt curve analysis, droplet digital PCR, nested PCR, multiplex PCR, transcription-mediated amplification, PCR controls, minimizing contamination 16 Molecular Techniques: Sequencing 207Applications of sequencing, first generation (Sanger, dideoxy chain termination) and next generation (Illumina, Ion Torrent, PacBio, and Oxford Nanopore) sequencing, sample preprocessing, library generation, amplification techniques, quality and depth of coverage, data analysis, comparison of all platforms SECTION IV: Prevention and Management of Viral Infections 227 17 Biosafety 229Biosafety levels, select agents, reportable diseases, personal protective equipment, biosafety cabinets, isolation precautions 18 Vaccines 237Active and passive immunity, types of vaccines, route of administration, risk and other consequences of vaccination, antibody-dependent enhancement, table of available viral and other vaccines, diagram of routine vaccination schedule 19 Antivirals 249Antivirals against herpesviruses, human papillomaviruses, influenza virus, respiratory syncytial virus, hepatitis B virus, hepatitis C virus, antiretrovirals and antivirals with broad coverage, immunomodulators, comparison of antivirals, mechanisms of action SECTION V: The Regulatory Environment for Laboratory Testing 265 20 Regulatory Requirements 267Classification of diagnostic assays, test complexity, role of CMS, CDC, CLSI, CLIA, inspections, proficiency testing, billing and coding 21 Assay Performance and Interpretation 275Validation/verification, performance characteristics (precision, accuracy, reportable range, reference range, analytic sensitivity, analytic specificity), diagnostic and clinical sensitivity and specificity, prevalence, predictive value, ROC curves References 285 Answers 289 Index 293