Diagnostic virology is of great importance particularly in disease management and for epidemiological purposes, but is slow and results are obtained when the patient has recovered or succumbed to the infection. In addition, consideration of antiviral chemotherapy is in short supply even where preliminary investigation results are available. Some viruses are highly unculturable, fastidious or hazardous to the laboratory personnel and diagnosis depends on serological methods or culture in an expensive bio-safety level. Molecular diagnostic techniques do not depend on pathogen isolation or growth or on the detection of an immune response to the pathogen, rather uses genotypic characteristics to identify specific pathogen. Nucleic acid of a given pathogen is unique, and therefore nucleic acid analysis can be used for unequivocal identification via amplification to increase the amount of material available for analysis. Nucleic acid-based diagnostic methods are extremely sensitive, reliable and to some extent affordable, and are widely used for clinical microbiology to detect pathogen.

Diagnosis is concerned with identifying the cause of a disease or precise and consistent outcomes that are results of direct or indirect actions, reactions and interactions between the cause of a disease and the host. That outcome, if accurate, would help the clinician in disease management, or the epidemiologist in identifying trends of diseases or the administrator in policy and decision making. Traditionally, infectious disease diagnosis involves identifying the causative agents of infectious diseases through the direct examination, culture and often immunological tests on clinical specimens. The traditional diagnostic techniques have varied sensitivities and specificities which influence their choice and applicability in a particular setting for the diagnosis of infectious diseases. However, the limitations of many traditional techniques particularly low specificity and long turnaround time often necessitate initiation of treatment before results are made available. Molecular diagnostic techniques involve a variety of techniques that explore the use of nucleic acid molecules for the identification of a particular pathogenic organism. These techniques include nucleic acid-based typing system, nucleic acid analysis without amplification, polymerase chain reaction (PCR) and other nucleic acid amplification techniques. Applications of molecular detection methods for infectious diseases have resolved many of the problems of the traditional diagnostic techniques, due to their exquisite sensitivity and specificity that allow the accurate and timely detection of very small numbers of organisms. This paper examines the principles and applications of molecular biology techniques in the identification of the causative agents of infectious diseases either in a routine setting or as research tools.