Supplementary Materials

The PDF file includes:

  • Methods
  • Fig. S1. Inference and enumeration of TF viruses.
  • Fig. S2. HIV-1 quasispecies diversification over time.
  • Fig. S3. Determination of IFN-I IC50 values.
  • Fig. S4. IFN-I resistance of bulk and limiting dilution isolates from the same plasma samples.
  • Fig. S5. Correlation of IFNα2 and IFNβ IC50 values.
  • Fig. S6. Phylogenetic relationships of rebound isolates.
  • Fig. S7. Closely related rebound and post-ATI QVOA isolates from participant A08.
  • Table S1. Generation of HIV-1 isolates from plasma and PBMCs of 10 individuals sampled from acute infection throughout their clinical course.
  • Table S2. IFN-I resistance of plasma and QVOA isolates from longitudinally sampled study participants.
  • Table S3. Generation of viral isolates from ART-suppressed individuals with and without treatment interruption.
  • Table S4. IFN-I resistance of viral outgrowth and rebound isolates.

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (Microsoft Excel format). GenBank accession numbers.