RNA-HTA pro1 probe design and its use with protease variants. (A) Mutations engineered in the protease subtype B consensus sequence. Targeted codons are shown in capital letters. Six primary and six accessory drug resistance mutations were targeted by nucleotide insertion and substitutions, respectively (underlined). (B) RNA-HTA using protease variants from three different isolates (pNL, NIHRF, and PCPXM variants). The protease variants used in each lane correspond to the sequence numbers in panel C. The gel is shown from the loading wells to the DNA homoduplexes. (C) Alignment of the subtype B consensus, UHG-pro1 probe, and protease variants of pNL, NIHRF, and PCPXM used in panel B. Drug resistance codons targeted by the UHG-pro1 probe are underlined.