Antiviral Resistance Testing

Abstract The number of antiviral drugs approved for clinical use has dramatically increased in the past 25 years. However, the use of the drugs may result in the development of resistance mutations in viral genes targeted for therapy. As a result, antiviral resistance testing is commonplace in many molecular diagnostic laboratories and has become a useful tool for the clinical management of viral infections that can be treated with antivirals. Antiviral resistance testing involves identification of the mutations using sequencing methods (genotyping) and determination of their effect on viral drug susceptibility using in‐vitro cell‐based assays (phenotyping). For viruses with well characterised resistance mutations, such as human immunodeficiency virus, genotypic methods that are fast and easier to perform are sufficient. However, phenotypic methods or a combination of both methods provide a comprehensive strategy for other viruses. Key Concepts: The majority of antiviral drugs target virus‐specific proteins important for viral replication. Antiviral resistance develops via the emergence of mutations in viral genes targeted for therapy. There are two main methods for the measurement of antiviral resistance namely, genotypic antiviral resistance testing and phenotypic drug susceptibility testing. Genotypic antiviral resistance testing identifies mutations associated with drug resistance using sequencing techniques. Genotypic interpretation systems (GISs) are rule‐based computational tools that rely on a database of sequence, clinical and laboratory information to translate the mutational pattern in amplified sequence into drug susceptibility levels using arbitrary scores. Phenotypic drug susceptibility testing is a direct measure of the ability of a virus isolate to replicate in the presence of a specific drug using an in‐vitro cell culture system. The clinical significance and utility of detecting minority drug resistance mutations present at less than 20% of the population has yet to be fully determined.