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

• Published in: International journal of infectious diseases Vol. 109; pp. 315 - 320
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Canada Elsevier Ltd 01.08.2021; The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases; Elsevier
• Subjects: COVID-19; COVID-19 Testing; Heat shock; Heat-Shock Response; Humans; Pandemics; Real-Time Polymerase Chain Reaction; RNA extraction free; RNA, Viral - genetics; RT-qPCR; SARS-CoV-2; Sensitivity and Specificity; COVID-19; SARS-CoV-2; RT-qPCR; RNA extraction free; Heat shock
• ISSN: 1201-9712; 1878-3511
• DOI: 10.1016/j.ijid.2021.06.038

•Heat shock based SARS-CoV-2 RT-PCR diagnosis has a sensitivity up to 89.4%.•For 100.000 copies/mL LoD, the sensitivity is as high as 98.6%.•Heat shock based SARS-CoV-2 RT-PCR is a reliable tool for low resources settings. The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits. 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. 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) of 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. 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 at the time of testing. This affordable protocol can help 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.