Table 2. Primers used in the optimized in-house assay.
Primer name | Sequence (5′→3′) | Location(based on HXB2) | Purpose |
PRTM-F1* | F1a-TGAARGAITGYACTGARAGRCAGGCTAATF1b-ACTGARAGRCAGGCTAATTTTTTAG | 2057–20852068–2092 | RT-PCR, one of mixture componentsRT-PCR, one of mixture components |
PRTM2-F1 | TAGGGA RAATYTGGCCTTCC | 2090–2109 | Rescue RT-PCR primer |
RT-R1 | ATCCCTGCATAAATCTGACTTGC | 3370–3348 | RT-PCR |
PRT-F2 | CTTTARCTTCCCTCARATCACTCT | 2243–2266 | Nested PCR & sequencing |
RT-R2 | CTTCTGTATGTCATTGACAGTCC | 3326–3304 | Nested PCR & sequencing |
SeqF3 | AGTCCTATTGARACTGTRCCAG | 2556–2577 | Sequencing |
SeqR3 | TTTYTCTTCTGTCAATGGCCA | 2639–2619 | Sequencing |
SeqF4 | CAGTACTGGATGTGGGRGAYG | 2869–2889 | Sequencing |
SeqR4 | TACTAGGTATGGTAAATGCAGT | 2952–2931 | Sequencing |
*: PRTM-F1 is a mixture of primers F1a and F1b at a ratio of 1:1 (w/w).