Raw data of "A Comparative Analysis of Near-Full-Length HIV-1 DNA Genomes in Divergent Virologic Response Groups Reveals Significant Genetic Variations in Low-Level Viremia"

The unclear molecular mechanism underlying low-level viremia (LLV) in HIV-1-infected individuals remains a key unsolved issue in HIV research. High-throughput sequencing studies have characterized HIV-1 DNA quasispecies in LLV individuals but relied on partitioned PCR primers, which prevented analysis of entire intact or defective genomes. To overcome these limitations, we employed single-genome amplification (SGA) and near-full-length genome (NFLG) primers to amplify whole HIV-1 DNA, followed by in-silico genomic analysis. A total of 41 individuals with divergent virologic responses—virologic suppression (VS), LLV, virologic failure (VF)—after at least 12 months of antiretroviral therapy (ART) were enrolled. CD4+ T cells were isolated via magnetic beads separation, after which near-full-length HIV-1 DNA was amplified and sequenced. Genomic integrity was verified using the HIV Database Quality Control tool and manual inspection. Genetic diversity was calculated using MEGA software. Genotypic drug resistance and co-receptor tropism were detected via the HIVdb Program and Geno2pheno (coreceptor). Among 196 analyzable non-hypermutated NFLGs, intact HIV-1 DNA correlated significantly with virologic responses (p < 0.0001). NFLG divergence followed the order LLV > VF > VS (p < 0.05), with CRF01_AE showing greater divergence than CRF07_BC (p < 0.05). LLV individuals exhibited more diverse drug-resistant HIV-1 DNA. CXCR4-tropic HIV-1 DNA was significantly more frequent in CRF01_AE (85.9%, p < 0.0001) than in CRF07_BC (9.8%). In conclusion, LLV exhibits greater complexity and clinical relevance, as evidenced by higher mutation rates and more diverse drug resistance compared to VF and VS.