Summary of samples, HIV-1 levels, and sequencing depthsa

SubjectSample nameTime point (no. of days since fingerstick)Plasma HIV-1 load (copies/ml)CD4 count [cells/mm3 (%)]HIV-1 RNA copies/μlHIV-1 sequencing depth (mean)
First positiveLast negativePlasmaCVLPlasmaCVL
AD4476,300,000306 (30)382,50079,7502,735192
D11111430,000,000217 (23)538,50072,5501,835338
BD115445,000432 (40)5,686251,900372,328
D771213,000,000304 (41)50,63056,15050206
CD7711100,000,000208 (50)1,330,00064,1001,904424
  • a Plasma and CVL samples were selected during the first 2 weeks that viremia was detectable. For each sample, both the number of days since the first positive fingerstick test for HIV-1 and the number of days since the last negative fingerstick test are listed. Clinical measurements of the HIV-1 load in plasma and the CD4 count are shown, as well as the HIV-1 quantification in RNA extracted from both plasma and CVL using qRT-PCR. The mean depth of HIV-1 genome sequencing for each sample is shown, and the sequencing depth across the HIV-1 genome is shown in Fig. 4.