Table 1. Primers used for amplicon generation.

Amplicon	HxB2 position	HIV specific primer (5′-3′)
Prot	2136–2164	TCAGAGCAGACCAGAGCCAACAGCCCCA
	2621–2650	AATGCTTTTATTTTTTCTTCTGTCAATGGC
RT11		-
		-
RT2	2706–2734	GAAAATCCATACAATACTCCAGTATTTGC
	3119–3145	CTATGCTGCCCTATTTCTAAGTCAGAT
RT32	2874–2891	CTRGATGTGGGTGATGCA
	3265–3284	CNYTATAGGCTGTACTGTCC

Note that forward and reverse primers are linked to primer A and B (454 Life Sciences; Roche) respectively and contain the TCAG key. To distinguish each sample in the multiplexed UDPS, nine unique sequence tags (MID1 to 9, according Roche's protocol) were inserted between the adaptor A or B and the gene specific primer.

¹RT1: primers under patent process

²Primers from Mitzuya's paper [29]