Fig. 5: STIP-Seq identifies clones responsible for viremia under ART and upon treatment interruption. | Nature Communications

Fig. 5: STIP-Seq identifies clones responsible for viremia under ART and upon treatment interruption.

From: In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Fig. 5

a–c Maximum-likelihood phylogenetic trees for three participants that underwent an analytical treatment interruption. The trees include V1–V3 env plasma sequences from before (T1) and during (T2, T3, and T4) the treatment interruption (P6, P7, and P8), as well as STIP-Seq, MIP-Seq and FLIPS sequences (T1) that were trimmed to the V1–V3 env region (P6, P7). Intact and defective proviruses are represented by circles and squares respectively, while V1-V3 plasma sequences are represented by triangles. Each assay is color-coded. Clones displaying a match between defective and intact STIP-Seq sequences and plasma sequences are indicated by red and green frames, respectively. HXB2 subtype B HIV-1 reference genome, NFL near full length, STIP-Seq simultaneous TCR, Integration site and Provirus sequencing, MIP-Seq Matched Integration site and Provirus sequencing, FLIPS Full-Length Individual Provirus Sequencing.

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