The detection of viral genome (that is, viral nucleic acid, either DNA or RNA) has gained enormous importance over the last decade in the diagnosis and management of viral infections and diseases (table 1). Nucleic acid testing (NAT) has proven its superiority over more conventional laboratory techniques in several areas, for example:

• for viruses that cannot be cultured in conventional cell culture systems or those that are hazardous to isolate;

• for clinical sample material of small volume or containing only small amounts of virus;

• where antibody seroconversion is delayed after an acute infection;

• in the immunocompromised patient who may have a suboptimal antibody response;

• for the diagnosis of congenital or perinatally acquired viral infections.

As well as qualitative analysis, the characterisation of viruses by analysis of the amplified region of the genome allows the detection and identification of viral types or subtypes and mutants. This is now used to monitor patients on highly active antiretroviral therapy (HAART), based on the multitude of resistance associated mutations that have been characterised in HIV infected patients receiving antiretroviral treatment.¹ This allows a more rational therapeutic approach. Sequence analysis has also proved to be a valuable epidemiological tool—for example, to investigate possible links between cases of infection, as in outbreaks of hepatitis B² and hepatitis C infection.³

In addition to qualitative analysis and genome sequencing, methods have been developed for the quantification of viral genomes. While initially largely applied in the research field, quantitative NAT has recently been introduced into routine diagnostic virology. In this review, we will briefly introduce the different methods available for viral genome quantification, define their place in clinical virology, and speculate on the possible future role of quantitative genomic testing for viral infections.