CD4 and infection: Consistently, there was no correlation (r = 0.1683, p = 0.1827) between basal T/F LTR transcriptional activity and CD4 T cell count (S3E Fig), while consensus and autologous Tat-mediated T/F LTR transcription activity exhibited significant negative correlation (r = -0.3341, p = 0.0331 and r = -0.4413, p = 0.0065 respectively) with CD4 T cell count (S3F-S3G Fig) at one year post infection.