Guide to Clinical and Diagnostic Virology

Reeti Khare is the Director of Microbiology at Northwell Health laboratories.

Section 1: Foundations of Clinical Virology 1. Introduction to Viruses Virus structure, life cycle, Baltimore classification, figures of DNA and RNA virus classification, transmission, nomenclature 2. Laboratory Diagnosis of Viral Infections Differential diagnosis for viral syndromes, specimen collection, comparison of diagnostic techniques Section 2: Viral Pathogens and Clinical Presentation 3. Respiratory Viruses Influenza virus, respiratory syncytial virus, human metapneumonvirus, rhinovirus, coronavirus, mumps virus, diagram of seasonality 4. Viruses with Dermatologic Manifestations Herpes simplex virus, varicella-zoster virus, measles virus, rubella virus, human herpesviruses 6 and 7, molluscum contagiosum, smallpox virus, figure of viral rashes, description and comparison of herpesviruses 1 to -8 5. Gastrointestinal and Fecal-Oral Hepatitis Viruses Rotavirus, norovirus, astrovirus, sapovirus, HAV, HEV, diagram of seasonality 6. Viruses That Can Cause Multiple Syndromes Enterovirus and parechovirus, adenovirus, parvovirus B19, human bocavirus 7. Opportunistic, Transplant-Associated Viruses Cytomegalovirus, BK virus, JC virus 8. Blood-Borne Hepatitis Viruses Hepatitis B, C, and D viruses, and comparison of hepatitis viruses A through E 9. Human Retroviruses HIV, HTLV-1/-2 10. Oncogenic Viruses HPV, EBV, HHV-8 11. Zoonotic Viruses Rabies virus, Ebola virus, Marburg virus, Lassa virus, Crimean Congo hemorrhagic virus, hantavirus, lymphochoriomeningitis virus, monkeypox virus, herpes B virus, Hendra virus, Nipah virus, comparison of zoonotic viruses 12. Arboviruses Mosquitoes, ticks, dengue virus, yellow fever virus, chikungunya virus, West Nile virus, eastern, western and Venezuelan equine encephalitis viruses, Japanese encephalitis virus, Powassan virus, comparison of arboviruses Section 3: Diagnostic Assays and Techniques 13. Culture- and Tissue-Based Diagnostic Techniques Conventional viral culture and cell lines, viral growth rates, hemagglutination, quantification of plaques, histology/cytology, histologic and cytologic images of virally infected cells 14. Diagnostic Techniques Based on Immunological Interactions Kinetics of immune responses, interpreting serologic results, antigen and antibody detection, ELISA and chemiluminescent immunoassay, immunohistochemistry, immunoblots, immunofluorescence, lateral-flow assay, comparison of immunologic assays 15. Molecular Techniques: Nucleic Acid Amplification Basics of nucleic acids, nucleic acid amplification, PCR, RT-PCR, real-time PCR, quantitative PCR, melt curve analysis, viral loads, droplet digital PCR, nested PCR, multiplex PCR, transcription-mediated amplification, controls, contamination 16. Molecular Techniques: Sequencing Sequencing terminology, applications, procedures, platforms (Sanger, NGS, Illumina, SMRT, Ion Torrent), data analysis, comparison of platforms Section 4: Prevention and Management of Viral Infections 17. Biosafety Biosafety levels, select agents, reportable diseases, PPE, techniques, biosafety cabinets, isolation precautions 18. Vaccines Active and passive immunity, intravenous immunoglobulin, types of vaccines, delivery, complications, antibody dependent enhancement, table of available viral and other vaccines, diagram of routine vaccination schedule 19. Antivirals Antivirals against herpesviruses, influenza virus, RSV, hepatitis C, other compounds, antiretrovirals and antivirals with broad coverage, mechanisms of action Section 5: The Regulatory Environment for Laboratory Testing 20. Regulatory Requirements Classification of assays by the FDA, test complexity, regulatory agencies, CLIA, inspections, proficiency testing, billing and coding 21. Assay Performance and Interpretation Validation/verification, performance characteristics (precision, accuracy, reportable range, reference range), diagnostic, clinical and analytic sensitivity and specificity, prevalence, predictive value, ROC curves