ABSTRACT
Molecular methods play an ever-expanding role in many areas of the clinical laboratory. Despite their growing familiarity, the application of diagnostic assays involving nucleic acid sequencing, amplification, or hybridization still presents unique challenges in the realm of clinical virology. The primary challenge in assay design arises from the potentially extreme genetic heterogeneity of viruses, not only among isolates infecting different human populations, but even within an individual. This chapter briefly reviews the biological basis for viral genetic heterogeneity, demonstrates the importance of matching assay technology to test objective, describes general methods for using viral genetic sequence data to direct assay design, and explores strategies for accommodating unavoidable sequence heterogeneity.
