Molecular diagnosis of CNS infections

K K Jain MD (Dr. Jain is a consultant in neurology and has no relevant financial relationships to disclose.)
Originally released June 9, 1997; last updated October 12, 2020; expires October 12, 2023


Molecular diagnostics includes nucleic acid diagnostics, immunodiagnostics, and proteodiagnostics. Polymerase chain reaction (PCR) is the basis of most of the kits that are available commercially for the diagnosis of various infectious diseases. The most important uses are in the diagnosis of viral infections of the central nervous system. This article describes the advantages as well as limitations of molecular diagnostics for CNS infections. Standard laboratory techniques such as viral culture and serology provide only circumstantial or retrospective evidence of viral infections of the CNS. PCR is now considered to be the first-line diagnostic test for viral CNS infections such as herpes encephalitis, enterovirus meningitis, and other viral infections occurring in HIV-infected persons.

Key points


• Molecular diagnostics is important for the rapid diagnosis of infections as the time required for traditional laboratory methods is too long for effective management.


• Molecular diagnosis is possible from limited, small amounts of body fluids or tissues.


• Molecular diagnosis provides more accurate diagnosis to guide treatment.


• Use of next generation sequencing has refined and expanded the applications of molecular diagnostics for CNS infections.


• Technical refinements such as use of nanobiotechnology enable direct detection of single microorganisms without need for amplification.

Historical note and terminology

Clinical application of rapidly emerging molecular technologies to elucidate, diagnose, and monitor human diseases is frequently referred to as molecular diagnosis. A broad definition of molecular diagnostics includes nucleic acid diagnostics, immunodiagnostics, and proteodiagnostics using proteomic technologies. Nucleic acid technologies use both DNA and RNA. The most important landmark in molecular diagnostics was the discovery of polymerase chain reaction (PCR) in 1983. Although several other technologies for amplification and detection of nucleic acids without amplification have been developed since then, PCR, with its modifications, remains the mainstay of current molecular diagnosis of infectious diseases (Jain 2020).

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