Table 1.

Primers used in this study

Primer_ID	Seq (5′→3′)	HXB2 position	Ref.
Amplification primers
F1Gag-Vpu
0682F	TCTCTCGACGCAGGACTCGGCTTGCTG	0682→0708	[4,21]
0776F	CTAGAAGGAGAGAGAGATGGGTGCGAG	0776→0800	[4]
6352R	GGTACCCCATAATAGACTGTRACCCACAA	6352→6324	[17]
6231R	CTCTCATTGCCACTGTCTTCTGCTC	6231→6207	[17]
F2Vif-3LTR
5550F	AGARGAYAGATGGAACAAGCCCCAG	5550→5574	[17]
5861F	TGGAAGCATCCRGGAAGTCAGCCT	5861→5884	[17]
9555R	TCTACCTAGAGAGACCCAGTACA	9555→9533	Present study
Sequencing primers
F1Gag-Vpu
0776F	CTAGAAGGAGAGAGAGATGGGTGCGAG	0776→0800	[4]
1231F	TCACCTAGAACTTTRAATGCATGGG	1231→1255	Present study
1817F	TAGAAGAAATGATGACAG	1817→1834	[22]
2586F	AAGCCAGGAATGGATGGCCCA	2586→2606	[23]
2713R	GGATTTTCAGGCCCAATTTTTG	2713→2692	Present study
3885R	CTGCTCCATCTACATAGAA	3885→3867	[24]
4350R	CACAGCTAGCTACTATTTCTTTTGC	4350→4326	[24]
4900F	GGGTTTATTACAGGGACAGCAGAG	4900→4923	[25]
5066R	ATCATCACCTGCCATCTGTTTTCCAT	5066→5041	[26]
6231R	CTCTCATTGCCACTGTCTTCTGCTC	6231→6207	[17]
F2Vif-3LTR
5861F	TGGAAGCATCCRGGAAGTCAGCCT	5861→5884	[17]
6559F	GGGATCAAAGCCTAAAGCCATGTGTAA	6559→6585	[22]
7002F	TTRTTAAATGGTAGTATAGC	7002→7021	Present study
7373R	GAAAAATTCTCCTCYACAATTAAA	7373→7350	Present study
7761F	GTGGGAATAGGAGCTGTGTTCCTTGGG	7761→7787	[22]
8445R	CTCTCTCTCCACCTTCTTCTTC	8445→8424	[22]
9555R	TCTACCTAGAGAGACCCAGTACA	9555→9533	Present study

Source of the primers are given. The primer IDs are changed from the original for the ease of identification. The numbering is as per HXB2 (K03455).