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Viruses remain a continuing threat to humankind, regardless of age, gender, race, ethnicity, or socioeconomic status. They are a leading cause of morbidity and mortality worldwide, and severe illness commonly occurs in infants, the elderly, the chronically ill, the malnourished, and the immunocompromised.

The clinical diagnosis of viral diseases can be difficult, and laboratory confirmation is required in patients with serious illnesses since signs and symptoms are often overlapping and not always specific for any one viral agent. This is particularly true in children. Early detection of viral diseases can have a prompt and significant impact on patient care by increasing clinical awareness and providing for more informed decision making for better patient management.1–8 A rapid and specific diagnosis can help in decreasing the use of unwarranted laboratory tests, hospital procedures, and antimicrobial drugs, resulting in reduced costs related to supportive care and a reduction in hospital stay.1,3,4,8–13 In some cases where antiviral therapy is available, rapid and accurate viral detection can provide the opportunity for prophylaxis against certain viral infections or early treatment that may limit the extent of disease and reduce associated sequelae.1,14 Finally, timely laboratory surveillance for viruses can provide for rapid outbreak identification and assist in the prevention of community and hospital spread.15–18

Many methods are available for the diagnosis and management of viral diseases (Table 2-1).19,20 These include (1) cell culture systems for the isolation of viruses in human or animal cells; (2) rapid immunologic and molecular assays for the direct detection and/or quantification of viral proteins or nucleic acids; (3) serologic tests to detect virus-specific IgG and/or IgM antibody responses; (4) electron microscopy to identify viruses on the basis of size and shape of viral particles; (5) histologic and cytologic techniques for detection of virus-induced morphological changes within tissues and exfoliated cells; (6) genotypic and phenotypic assays to detect antiviral drug resistance and to identify genetic variants that may not respond to therapy; and, most recently, (7) genomic sequencing for direct detection of anticipated or unexpected viruses from clinical specimens, the study of viral diversity, and the interactions between viral and host transcriptomes during disease, the discovery of new viral pathogens, and surveillance to detect and monitor outbreaks and public health emergencies. There are notable differences in the use and clinical performance of these methods, and the relative importance of certain tests has changed over the years. The most significant transformation in the clinical virology laboratory has involved the continuous development and introduction of rapid and highly accurate molecular assays for viral diagnosis. Where applicable, these tests have largely replaced the more traditional methods of virus culture and antigen detection for the direct identification of viruses from clinical specimens. For many viral illnesses, serology continues to play a meaningful role in the diagnosis of recent or chronic viral infections, for the determination ...

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