LTR Amplification of early HIV-1 subtype C
Library preparation was performed using the Qiagen FX DNA Library Preparation Kit (Qiagen, Germany). Dual index barcodes provided with platform-specific adapters were used for multiplexing. As the index barcodes were pre-integrated into the adapters, the PCR enrichment and indexing PCR steps were excluded during library preparation. Sequencing was performed on the Illumina NovaSeq system according to the manufacturers instructions