Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Transcriptional analysis reveals predicted dysfunctional responses in CD8+ T cells from UnTx individuals versus early Tx individuals.
  • Fig. S2. TCR clonotype dynamics in early Tx and UnTx HIV.
  • Fig. S3. Longitudinal characterization of HIV-specific CD8+ T cell responses in Tx and UnTx hyperacute HIV infection.
  • Table S1. Baseline characteristics of study participants.
  • Table S2. Effect of interval between treatment initiation and sample collection on immune parameters in Fiebig stages I and II and Fiebig stages III to V participants.
  • Table S3. Immunodominant responses measured by HLA class I tetramers in individuals Tx in Fiebig stages III to V and UnTx donors.
  • Legends for tables S4 to S7
  • Table S8. TCR╬▓ clonotype sequences.
  • Legend for table S9

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Other Supplementary Material for this manuscript includes the following:

  • Table S4 (Microsoft Excel format). Results from the RNA-seq differential expression tests in HIV-specific, CMV-specific, and total CD8+ T cells (excluding the tetramer-specific cells) between the time points assayed in Tx individuals.
  • Table S5 (Microsoft Excel format). Results from the RNA-seq differential expression tests in HIV-specific, CMV-specific, and total CD8+ T cells (excluding the tetramer-specific cells) between the time points assayed in UnTx individuals.
  • Table S6 (Microsoft Excel format). Results from the RNA-seq differential expression tests between CMV-specific and HIV-specific CD8+ T cells at the late and long-term time points and the difference between those cells between the two time points.
  • Table S7 (Microsoft Excel format). Results from the RNA-seq differential expression tests between HIV-specific CD8+ T cells from Tx and UnTx individuals at each time point.
  • Table S9 (Microsoft Excel format). Table contains alignment statistics and metadata on the RNA-seq samples in this study.
  • Data file S1 (Microsoft Excel format). Primary data.