Fig. 1: Study Scheme.
The study scheme shows the infection times, treatment details, plasma collection, RNA isolation, Reverse Transcription PCR amplification, and subsequent sequencing assays and data analysis. In this study, humanized mice were either infected with HIV-1NL4-3 or HIV-1ADA and were subsequently divided into four treatment subgroups: 1- no treatment; 2- LA ART treatment consisting of NMDTG and NRPV at 45 mg/kg and NMABC and NM3TC at 40 mg/kg, administered via intramuscular injection two weeks post-infection (WPI) and ceased at 6 WPI; 3- CRISPR-Cas9 treatment at 7/8 WPI; or 4- sequential LA ART and CRISPR-Cas9 treatment with viral rebound. Plasma-derived viral RNA was isolated from all groups at designated time points, and three independent PCR-amplified HIV-1-regions (gag, pol, env) were sequenced and analyzed using Sanger sequencing. Amplicons of the pol regions were further sequenced and analyzed through the Illumina MiSeq platform. Sequences of interest, including the guide RNA targeting region, protease (PR), reverse transcriptase (RT), and integrase (IN) regions, env variable loop, and CD4 binding loop region, were analyzed using the bioinformatic pipeline. The crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core is downloaded from the RCSB Protein Data Bank (https://www.rcsb.org/). Fig. 1 is created using the Biorender software.
