Table 1.

Methodologies for the detection of HIV drug resistance-associated mutations

	Advantages	Disadvantages
Sanger or population sequencing	Well-established, standardised and scientifically validated; highly reproducible; widely available	Inability to detect minority viral variants occurring at a frequency < 15–20% in a patient’s sample; labour intensive and time consuming
Next-generation ultradeep sequencinga	Able to detect low abundance viral variants occurring at a frequency between ~ 2% and 15%; capable of quantifying the relative frequency of each variant; high throughput and low cost per sample	Financial, infrastructural and logistical challenges impede widespread adoption; generates large amount of data and complex bioinformatic methodology is required for interpretation; uncertain clinical significance of variants detected at low frequency

^aTypically using the Illumina sequencing technology