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).