Ultra-deep Sequencing of HIV primary infection: plasma
Retro-transcription was carried out with pan-subtype oligonucleotides. Next-generation sequencing of the near-full-length HIV genome was performed on the Illumina platform by fragmentation and sequencing of two long amplicons of 5.5 kilobases (kb) and 3.7 kb generated using pan-subtype primers. Genome reconstruction was obtained with a resequencing strategy using an ad hoc workflow built on the CLC workbench software (Qiagen). HIV variants in the capsid p24 protein (CA) and gp120 coding regions were examined, using the HXB2 amino acid sequence as a reference.