Cobas taqman 48

We constituted pools of plasma from all participants and performed two pooling strategies as previously described.^16–18 (link) First, we used mini-pools of five samples each (generating 234 mini-pools) and then 10 × 10 matrix pools of mini-pool samples above the threshold (VL >200 copies/mL) only. VF for an individual sample was defined as VL ≥1000 copies/mL and this translated to a VL of ≥200 copies/mL to define a positive mini-pool and ≥100 copies/mL for a positive matrix pool. From the 234 mini-pools, 120 pools (600 samples) had a VL of ≥200 copies/mL; these samples were arranged in six 10 × 10 matrix pools, each with 100 samples. We resolved the matrix pools as previously described.^16–18 (link) Briefly, we used results of column and row pools to guide on which individual sample to test first, thus minimizing the number of individual tests and costs. We used the Cobas^®AmpliPrep/Cobas^®TaqMan 48 system with a detection range of 20–100000000 copies/mL to perform all VL tests. The mini-pool platform was used for initial screening as we hypothesized that it had a higher sensitivity and NPV than a 10 × 10 matrix pool. We addressed the issue of false negatives by testing 21 randomly selected ‘negatives’ from each pooling strategy, thus determining their NPV. Our negatives were samples with a VL <1000 copies/mL and the positives were samples with a VL ≥1000 copies/mL.

Plasma HIV viral load was measured by COBAS TaqMan 48 (Roche, France), as
previously reported.⁴ The lower limit of HIV RNA detection was 20 copies/mL.