Optimizing RT-PCR detection of SARS-CoV-2 for developing countries using pool testing

Mauricio J Farfan; Juan P Torres; Miguel ORyan; Mauricio Olivares; Pablo Gallardo; Carolina Salas

First, we prepared 6 pools of 5 samples subject to automated extraction (Table 1) For comparison between automated extraction, manual extraction and non-extraction, 5 new pools were prepared ( Table 2 ). Pools 8 to 11 include 4 negative samples and 1 positive sample with CT values of 23.5, 16.8, 26.8 and 35 respectively. Pool 7 included 5 negative samples. SARS-CoV-2 amplification was observed in pools 8, 9, and 10 using automated extraction, manual extraction, or adding the pool sample directly to the PCR mix. Similar CT values were observed using manual or automated extraction, but an increase of ~5 units was observed by adding 5 µl of non-extracted pool samples to the RT-PCR reaction (Figure 1 ). There was no amplification signal of SARS-CoV2 in pools 7 (all negative samples) and 11 (4 negative and one positive with a high Ct) for any extraction procedure.