The clinical and laboratory diagnosis of the viral aetiology of an individual's illness involves understanding their clinical symptoms and signs, how the host's immune system responds to a viral infection as well as which diagnostic tests are the most sensitive and specific to detect that virus or the host's immune response. Once the choice of test is made, the correct specimen must be collected and the results of these tests interpreted in the context of the clinical picture. Detection of viral RNA and DNA has revolutionised clinical virology and has resulted in being able to detect emerging virus infections and measure the amount of the virus, known as viral load, in different samples. These tests are critical in monitoring viral infections as well as the response to antiviral therapy. In addition, automated nucleotide sequence analysis has helped in the investigation of outbreaks of infection.
- Viral infections cause a broad range of illness which depends on viral virulence, susceptibility of the host and in particular whether the host is immunocompetent or immunocompromised. The host immune response may also be critical in the pathogenesis of the infection.
- The relative importance of virus‐induced or immune‐mediated pathogenesis differs for each virus, and the symptoms that occur during a viral infection may be due to either mechanism or both.
- The symptoms with which the patient presents to the doctor and the signs that the doctor notes during a physical examination are important guides to make a differential diagnosis.
- Specific symptoms or symptom complexes may suggest a specific viral infection.
- An understanding of the central and/or peripheral target sites where viral replication occurs, as well as the assays available for detection of virus, viral antigen or viral nucleic acid, helps decide which type of specimen to collect.
- Staff safety, care in specimen separation to avoid errors and maintaining virus viability are important issues for proper handling of specimens for viral diagnosis.
- Laboratory diagnostic methods are divided into viral antigen or nucleic acid detection and serological techniques.
- Automated nucleic acid extraction, sample handling and real‐time PCR platforms have revolutionised nucleic acid detection and quantification, making these methods part of routine laboratory service provision.
- Automated nucleotide sequence analysis can be used to determine antiviral resistance mutations and subtype or genotype of the virus and investigate outbreaks of infection.
Keywords: nucleic acid; antigen; antibody; isolation; viral load; sequencing