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

Abstract

The global shortage of reagents and kits for nucleic acid extraction and molecular detection of SARS-CoV-2, requires new cost-effective strategies for the diagnosis of suspected COVID-19 cases, especially in countries that need to increase detection capacity. Pooled nucleic acid testing has been extensively used as a cost-effective strategy for HIV, HepB, HepC and influenza. Also, protocols dispensing of RNA extraction appears as an attractive option for detection of SARS-CoV-2. In this study we found that pooling of 5 samples showed that Ct variation were in the range of 1.0-4.5 units with less likehood of false negative results. Results of the sample without nucleic acid extraction was unsatisfactory with a significative increase in Ct values and thus, for a false negative result. In conclusion, pooling nasopharyngeal  samples with both automated and manual extraction proved reliable, and thus a potential efficient alternative for the diagnosis of suspected COVID-19 in developing countries.