title: Antiviral resistance testing.
abstract: OBJECTIVE
  Current genotypic resistance tests fail to amplify drug-resistant minority variants when they are present below 20% of the total virus population. Next-generation sequencing (NGS) addresses this issue and is being introduced into diagnostic laboratories. This review gives an overview of the resistance tests currently used and explores the opportunities and challenges that NGS genotypic resistance tests will bring.
  
  
  RESULTS
  The technical challenges of NGS, such as PCR and sequence-related errors, are being addressed and various assays are currently undergoing technical validation for clinical use. Although not conclusive, the data seem to suggest that NGS will be valuable for low genetic barrier drugs and certain types of tests such as the HIV-1 tropism test. Clinical validation of the reporting and interpretation of minority variant results are essential when laboratories start reporting these results.
  
  
  CONCLUSIONS
  The first wave of NGS technology is being rolled out in diagnostic laboratories. Antiviral test benefits include increased sensitivity and eventually cheaper antiviral resistance tests. There is a risk that low percentage minority variants may be over interpreted. This could result in antiviral drugs, which may have been effective, being possibly denied to patients if proper clinical validation studies are not performed.
authors.affiliation: Public Health England, West Midlands Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham, UK.
authors.forename: Erasmus
authors.initials: E
authors.lastname: Smit
mesh_terms: D003362:Cost-Benefit Analysis; D003586:Cytomegalovirus Infections / Q000188:drug therapy*; D024882:Drug Resistance, Viral / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy*; D006509:Hepatitis B / Q000188:drug therapy*; D006526:Hepatitis C / Q000188:drug therapy*; D006801:Humans; D025202:Molecular Diagnostic Techniques; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D056189:Viral Tropism / Q000187:drug effects / Q000235:genetics*