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Table 2 Details of PCR primer combinations

From: Frequency of subtype B and F1 dual infection in HIV-1 positive, Brazilian men who have sex with men

N0.

Primer

Combinations of Primers

Fragment amplified

PCR type

sequence (5’-3’)

Primer Position3

Product size bp

1

DPSH-O-Fwd1

1+2

pol-IN

Outer

ATAAGGCACAGGAGGAACATGAAAAATATCACAAC

4246-4280

266

2

DPLINF-O-Rev2

   

TTTTTTTTTCTGCTGGGATAACTTCTGCTTCTAGG

4512-4478

 

3

DPSH-N-Fwd

3+4

 

Nested

AGGAGGAACATGAAAAATATCACAAC

4255-4280

248

4

DPINF-N-Rev

   

CTGCTGGGATAACTTCTGCTTCTAGG

4503-4478

 

5

DPINF-O-Fwd

5+2

L-pol

Outer

TTTTTTTTTTTCTGATAAATGGACAGTGCAGCCTATACAAT

3247-3285

1265

6

DPINF-N-Fwd

6+4

 

Nested

CTGATAAATGGACAGTGCAGCCTATACAAT

3256-3285

1247

7

B01-Fwd

7+2

M-pol

Outer

TGGGTTATGAACTCCATCCTG

3238-3258

1274

8

B02-Fwd

8+4

 

Nested

CTGGATTCCTGAGTGGGAGTT

3776-3796

727

  1. The underlined nucleotides (non-HIV-1 specific sequences) are tails at the 5’ end of the outer reverse primers and were added to enhance the nested amplification with inner reverse primers.
  2. 1 Fwd: Forward, 2 Rev: Reverse.
  3. 3 Nucleotide position of the primer according to the HXB2 sequence (K03455) numbering.