Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples

Alekseenko, Alisa; Barrett, Donal; Pareja-Sanchez, Yerma; Howard, Rebecca J.; Strandback, Emilia; Ampah-Korsah, Henry; Rovšnik, Urška; Zuniga-Veliz, Silvia; Klenov, Alexander; Malloo, Jayshna; Ye, Shenglong; Liu, Xiyang; Reinius, Björn; Elsässer, Simon J.; Nyman, Tomas; Sandh, Gustaf; Yin, Xiushan; Pelechano, Vicent

RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.