Procedures
This section the key concepts within Analytic Procedures for Virology, covering specimen sources, major pathogens and disease states, direct detection methods, and mechanisms of action and resistance for antiviral agents
Specimen Sources
- Key Concept: Proper specimen collection is critical for accurate virological testing. The correct specimen type, collection technique, timing, transport, and storage are essential
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Specimen Types and Associated Viruses
- Respiratory Specimens: Nasopharyngeal swabs/aspirates, nasal swabs, throat swabs, BAL, sputum (Influenza, RSV, SARS-CoV-2, Adenovirus)
- Blood Specimens: Whole blood, plasma/serum (HIV, Hepatitis viruses, West Nile Virus, Dengue Virus, Zika Virus, EBV, Parvovirus B19)
- Cerebrospinal Fluid (CSF): (Enteroviruses, HSV, VZV, West Nile Virus)
- Stool Specimens: (Norovirus, Rotavirus, Adenoviruses, Astrovirus)
- Urine Specimens: (Cytomegalovirus (CMV), BK Virus, JC Virus)
- Swabs from Vesicles/Lesions: (Herpes Simplex Virus (HSV-1 and HSV-2), Varicella-Zoster Virus (VZV))
- Tissue Biopsies: (Hepatitis viruses (HBV, HCV), Herpes simplex encephalitis (HSV), CMV, Adenovirus, etc)
- Cervical Specimens: (Human Papillomavirus (HPV))
- Key Considerations: Laboratory guidelines, proper labeling, relevant clinical information
Major Pathogens and Disease States
- Key Concept: Understanding the etiology, epidemiology, and transmission of major viral pathogens is crucial for laboratory diagnosis and public health management
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Categories of Viruses and Associated Diseases
- Respiratory Viruses: Influenza virus, RSV, parainfluenza virus, SARS-CoV-2 (Influenza, bronchiolitis, croup, COVID-19)
- Vesicles and Lesions: HSV, VZV (Oral herpes, genital herpes, chickenpox, shingles)
- Cervical Cancer Screening: HPV (Genital warts, cervical dysplasia, cervical cancer)
- Meningitis: Enteroviruses, HSV (Viral meningitis, encephalitis)
- Gastroenteritis: Norovirus, rotavirus, adenovirus (Viral gastroenteritis)
- Immunocompromised Host: CMV, HSV, EBV, BKV, JCV (Pneumonitis, retinitis, PTLD, BKVAN, PML)
- Hepatitis: HAV, HBV, HCV (Acute hepatitis, chronic hepatitis, cirrhosis, liver cancer)
- HIV: HIV (Acute HIV infection, clinical latency, AIDS)
- Other Viruses: HTLV, West Nile, Zika, MERS, dengue, Ebola (ATL/HAM-TSP, West Nile fever/neuroinvasive disease, Zika fever/congenital Zika syndrome, MERS, dengue fever/severe dengue, Ebola)
Direct Detection of Pathogens
- Key Concept: Direct detection methods identify the virus by detecting viral components (particles, antigens, or nucleic acids)
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Methods
- Microscopy: Electron microscopy, light microscopy (Visualization of viral particles or inclusions)
- Antigen Detection Assays: EIA/ELISA, IFA, rapid antigen tests (Detection of viral antigens)
- Nucleic Acid Amplification Tests (NAATs): PCR, RT-PCR, real-time PCR, TMA, LAMP (Amplification and detection of viral DNA or RNA)
- Viral Culture: Growing viruses in cell culture (Isolation and identification of viruses)
- Next-Generation Sequencing (NGS): High-throughput sequencing (Identification of novel viruses, characterization of viral genomes)