In his 1988 review, Tenover stated that the goal of DNA probe technology was to eliminate the need for routine viral, bacterial, and fungal cultures (Tenover, 1988). Although this goal could eventually be reached, the principal advantage of molecular diagnostic methods in current clinical virology laboratories is in the detection of nonculturable agents such as human papilloma virus, human parvovirus, astroviruses, caliciviruses, hepatitis B virus, and hepatitis C virus. Molecular methods are also valuable for detecting viruses that are difficult to culture, including enteric adenoviruses, some coxsackie A viruses, and hantavirus. Indeed, PCR methods played a significant role in confirming the presence of hantavirus in the fatal respiratory disease outbreak in the Four Corners region of the southwestern United States (Centers for Disease Control, 1993), and rapid sequencing methods helped establish that the suspect agent was a new hantavirus. Molecular diversity studies helped establish that this hantavirus had been in the southwestern United States for a long time and provided important epidemiological evidence that the United States was not facing an epidemic caused by a single virus that was spreading across the country.
Molecular diagnostic methods are especially useful when trying to detect viruses that are dangerous to culture, such as HIV. PCR is the method of choice for detecting HIV infections in neonates born to HIV-infected mothers. Molecular methods are also useful when trying to determine the HIV status of patients with unusual antibody reactivities (e.g., HIV antibody positive with only the p24 band present on the Western blot). We have also used molecular methods to test for HIV in needles that children found at the beach or in a parking lot.
DNA amplification methods can assist laboratories in detecting viruses that are present in low numbers, for example, HIV in antibody-negative patients or cytomegalovirus in transplanted organs. We have used molecular diagnostic methods to detect HSV in culture- and antibody-negative cerebrospinal fluids from patients with biopsy-proven HSV encephalitis. Molecular diagnostic methods are also important when a tiny volume of specimen is available (e.g., forensic samples or intra-ocular fluid specimens). For example, we routinely perform five PCR tests (HSV, cytomegalovirus, varicella-zoster virus, Epstein-Barr virus, and human herpesvirus 6) on a single 100-/a1 intra-ocular fluid specimen. This specimen volume is barely sufficient for a single culture procedure.
Molecular diagnostic methods allow the laboratory to predict antiviral drug susceptibilities (Chapter 5) and to detect infections when viable virus cannot be obtained (e.g., latent viral infections or viruses that are present in immune complexes or environmental samples). Molecular diagnostic methods may also be used to differentiate antigenically similar viruses such as adenoviruses types 40 and 41 and to detect viral genotypes that are associated with human cancers (e.g., human papilloma virus). Molecular epidemiological techniques have been used to identify point sources for hospital- and community-based virus outbreaks, and have been used to predict viral virulence (Liang et al., 1991; Omata et ai, 1991).
Overall, the potential applications for molecular diagnostic procedures appear to be limitless. The most critical near-term application of molecular diagnostic methods is the detection of fastidious viruses that grow poorly or not at all in cell cultures. In the not so distant future, molecular virology procedures will become more widespread as more and more antiviral drugs are released by the Food and Drug Administration. In the long run, Tenover's predictions may prove to be correct.
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