TABLE 1.

PCR amplification strategy for the second set of 43 samples

Target-specific primeraDirectionHXB2 fragment (nt)bAmino acidsc
CCTCAGATCACTCTTTGGCSense2253→2271PR1→PR7
ACTYTTGGVCCATCCATTCCAntisense2611→2592RT15→RT21
ATTTTCCCATTAGTCCTATTGSense2545→2565PR98→RT6
ACTAGGTATGGTAAATGCAGAntisense2951→2932RT128→RT134
CTRGATGTGGGTGATGCASense2874→2891RT109→RT114
CNYTATAGGCTGTACTGTCCAntisense3284→3265RT239→RT245
  • a Each primer also comprised one of two adaptor sequences from the 454 Life Sciences platform (GCCTCCCTCGCGCCATCAG and GCCTCCCTCGCGCCATCAG) and one 4-nucleotide barcode (ACTT, ATCA, TCTG, TACT, CTCT, or CTCA) in the following 5′ to 3′ orientation: 454 adaptor-barcode-primer. Thus, a total of 48 (3 × 2 × 8) primers were used to encompass protease and 5′ RT and to enable pooling of eight samples.

  • b nt, nucleotide.

  • c PR, protease.