Guide to Clinical and Diagnostic Virology
ASM Books Series

The explosion in clinical testing has been especially rapid in virology, where emerging viruses and growing numbers of viral infections are driving advances. The Guide to Clinical and Diagnostic Virology offers a digestible view of the breadth and depth of information related to clinical virology, providing a practical, working knowledge of the wide array of viruses that cause human disease.

Introductory chapters cover the basics of clinical virology and laboratory diagnosis of infections, including virus structure, life cycle, transmission, taxonomy, specimen types and handling, and a comparison of assays used for detection. Detailed sections on important topics include

• Viral pathogens and their clinical presentations
• Diagnostic assays and techniques, including culture-based, immunological, and molecular
• Prevention and management of viral infections, with guidance on biosafety, vaccines, and antiviral therapies
• The regulatory environment for laboratory testing, including regulatory requirements and assay performance and interpretation

Critical concepts are carefully curated and concisely summarized and presented with detailed illustrations that aid comprehension, along with important highlights and helpful hints. These features, plus question sections that reinforce significant ideas and key concepts, make this an invaluable text for anyone looking for an accessible route through clinical and diagnostic virology. Laboratory technologists, medical students, infectious disease and microbiology fellows, pathology residents, researchers, and everyone involved with viruses in the clinical setting will find the Guide to Clinical and Diagnostic Virology an excellent text as well as companion to clinical virology references.

Preface xi

Acknowledgments xii

Abbreviations xiii

About the Author xvi

SECTION I: Foundations of Clinical Virology 3

1 Introduction to Viruses 5
Virus structure, life cycle, Baltimore classification, transmission, nomenclature

2 Laboratory Diagnosis of Viral Infections 17
Differential diagnosis for viral syndromes, specimen collection, general comparison of diagnostic techniques

SECTION II: Viral Pathogens and Clinical Presentation 23

3 Respiratory Viruses 25
Influenza virus, respiratory syncytial virus, parainfluenza virus, human metapneumovirus, rhinovirus, coronaviruses, mumps virus

4 Viruses with Dermatologic Manifestations 43
Herpes 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 61
Rotavirus, norovirus, astrovirus, sapovirus, hepatitis A virus, hepatitis E virus

6 Viruses That Can Cause Multiple Syndromes 71
Enteroviruses and parechoviruses, adenoviruses, parvovirus B19, human bocavirus

7 Opportunistic Viruses Associated with Immunosuppression 83
Cytomegalovirus, BK virus, JC virus

8 Blood-Borne Hepatitis Viruses 91
Hepatitis B, C, and D viruses, and comparison of hepatitis viruses A through E

9 Human Retroviruses 105
Human immunodeficiency virus, human T-cell lymphotropic virus

10 Oncogenic Viruses 121
Human papillomavirus, Epstein-Barr virus, human herpesvirus 8

11 Zoonotic Viruses 133
Rabies 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 147
Mosquitoes, 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 163
Conventional 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 175
Enzyme 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 189
Importance 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 207
Applications 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 229
Biosafety levels, select agents, reportable diseases, personal protective equipment, biosafety cabinets, isolation precautions

18 Vaccines 237
Active 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 249
Antivirals 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 267
Classification of diagnostic assays, test complexity, role of CMS, CDC, CLSI, CLIA, inspections, proficiency testing, billing and coding

21 Assay Performance and Interpretation 275
Validation/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

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.