Analytical and clinical evaluation of a heat shock SARS-CoV-2 diagnosis method without RNA extraction for N and E genes RT-qPCR.

Bruno, Alfredo; de Mora, Domenica; Freire-Paspuel, Byron; Rodriguez, Angel S.; Paredes-Espinosa, Maria Belen; Olmedo, Maritza; Sanchez, Martha; Romero, Jennifer; Paez, Michelle; Gonzalez, Manuel; Orlando, Alberto; Garcia-Bereguiain, Miguel Angel

BACKGROUND: : The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits. OBJECTIVE: : The aim of our study was to evaluate the clinical performance and analytical sensitivity of a simple SARS-CoV-2 diagnosis protocol based on heat shock without RNA extraction using both "CDC" (N gene) and "Charite" (E gene) RT-qPCR protocols. RESULTS: : 1,036 nasopharyngeal samples, 543 of them SARS-CoV-2 positive, were analyzed. The heat shock method correctly identified 68,8% (232/337) and 89.4% (202/226) SARS-CoV-2 positive samples for N gene and E gene, respectively. Analytical sensitivity was assessed for heat shock method using the CDC RT-qPCR protocol, obtaining sensitivity values of 98,6%, 93,3% and 84,8% for limit of detection of 100.000, 50.000 and 20.000 viral RNA copies/mL of sample. CONCLUSIONS: : Our findings show that a simple heat shock SARS-CoV-2 RT-qPCR diagnosis method without RNA extraction is a reliable alternative for potentially infectious SARS-CoV-2 positive patients. This affordable protocol can help to overcome the cost and supply shortages for SARS-CoV-2 diagnosis, especially in developing countries. In Ecuador, it has been used already by laboratories in the public health system for more than 100.000 specimens.