AACCca��conserving the translation. Also an AccIII restriction site at position 308 was modified to CCCGGA for cloning purposes. 5.2. Synthetic production of the HIV-1 subtype C backbone. The final design of the subtype C sequence was 2. Viral RNA extraction Viral RNA extraction of plasma and virus stocks was carried out on an EasyMAG according to the guidelines of the manufacturer, starting with 600 ml input material and eluting in 25 ml. If the samples were processed for viral load determination on the EasyQ, EasyQ calibrator was added along with the magnetic silica according to the guidelines of 17785458 the manufacturer. 3. GPRT amplification and gel analysis A One-Step RT-PCR amplification was used to generate a 2.3 kb HIV-1 fragment ) using the ��39-RT�� and ��59-OUT�� primers. RNA input was 10 ml, final volume 35 ml. Subsequently, a nested PCR was performed using the ��39-In�� and ��59-In�� primers generating a 1.8 kb GPRT fragment for homologous recombination with the subtype B backbone, or the ��59-Infusion�� and ��39-Infusion�� primers generating a 1.7 kb GPRT-fragment adapted for ��In-Fusion��cloning in the subtype C backbone. The In-Fusion amplicon is shorter. In contrast to homologous recombination, where the overlaps are preferably as long as possible, the overlapping sequences must be exactly 15 bases long in the In-Fusion assay. Both nested amplicons 
encode roughly the same region of the 39-end of GAG but contain the same coding sequences for protease and reverse transcriptase. To ensure identical mutation profiles, all virus stocks were sequenced to ascertain that no other non-subtypespecific mutations might influence the resistance profile. 4. Amplicon purification Gel extraction of the 1.7 kb GPRT-In-Fusion amplicons was performed using the QIAquick Gel Extraction Kit, following the manufacturer’s instructions. The 1.8 kb GPRT amplicons, used for homologous recombination, were purified prior to gel analysis, using the QIAquick PCR Purification Kit, following the manufacturer’s instructions. 5. Design and construction of the HIV-1 subtype C backbone for In-Fusion-cloning 5.1. Initial sequence design, synthesis and construction of the HIV-1 subtype C backbone. The in silico design of the HIV-1 subtype C backbone was based on the subtype C sequence divided into 4 fragments, three of which were destined for synthesis. The synthesis of the 3 DNA fragments was performed at Centocor, CA, USA as follows: padded sequences were get SR2516 parsed into contiguous segments of equal length on both the forward and reverse strands; each segment was chemically synthesized as an oligonucleotide using GENEW RITERTM instrumentation and purified by reversed phase HPLC; purified oligonucleotides were assembled using proprietary gene assembly technology using EcoRI and BamHI. Vector Fragment-I contained an EcoRI-BamHI flanking fragment of HIV-1 59-LTR and GAG, as well as an inserted BstEII restriction site and a small downstream part of POL. Vector Fragment-II contained an EcoRI-BamHI flanking fragment of HIV-1 GAG, as well as an inserted BstEII restriction site, the 39 part of POL, a fragment of ENV and the 39-LTR. Vector Fragment-III contained an EcoRI-BamHI flanking fragment of the complete HIV-1 ENV and the upstream part of the 39LTR. While the V3 envelope region of AB023804 was predicted to be R5-tropic according to the Geno2Pheno prediction tool and Position Specific Scoring Matrices, an R4-tropic virus was needed for the transfection assay in MT4 host cells. An envelo