SARS-CoV-2 Detection: Fast and Cost-Effective Sample Processing Prior to RT-PCR

Abstract

The pandemic COVID-19 needs a rapid microbiological diagnostic from Clinical Microbiology Units. Due to the fact that it is done by using a reverse transcription polymerase chain reaction (rRT-PCR) previous RNA extraction and automated equipment and reagents for RNA extraction represent an economic increase to the diagnosis, we describe an easy, cost-effective and fast alternative extraction-free SARS-CoV-2. Samples were treated with proteinase K for 10 minutes at 55°C. Then, there is a heat-process for 5 minutes at 98°C and finally, 3 minutes at -20°C before a commercial-commonly-used rRT-PCR procedure. The RNA automated-extraction was also performed with QIAsymphony RNA Kit (Qiagen) equipment. A total of 220 nasopharyngeal and oropharyngeal swabs were analyzed. 113 samples were tested positive whereas 106 samples were tested negative with RNA automated-extraction and extraction-free method, for an agreement of 99%. A total of one discordant sample was noted in which no amplified result (gene ORF1ab and N) were observed by RNA automated-extraction and gene ORF1ab (Ct 39) and gene N (Ct 37) by extraction-free. Thus, results were comparable with automated-extraction. This method is not only clinically acceptable but also confers an easy, fast, and cost-effective alternative to automated-extraction. Therefore, microbiological laboratories, with low economics resources and/or without automated-extraction equipment, could incorporate it.