Enhanced RNA Extraction from Stool Samples Using Fe-MSN Nanoparticles: A Comparative Study with Magnetic Beads and Silica Columns

Background: The human digestive system is known as a diverse collection of microorganisms, which includes viruses. Several viral agents can cause gastroenteritis problems, such as rotavirus, enteroviruses, and coronaviruses like SARS-CoV-2. Reverse transcription polymerase chain reaction (RT-PCR) has been used to identify viral genetic elements in stool samples. An important challenge with stool RT-PCR testing is the difficulty in removing inhibitors present in fecal samples. Objectives: This study aims to systematically compare the efficiency of different RNA extraction methods and assess the advantages of using Fe-doped mesoporous silica nanoparticle column (Fe-MSN) nanoparticles for viral RNA isolation from stool samples. Methods: In this study, three extraction methods were used for collecting RNA: (1) Silica membrane column, (2) Fe-MSN, and (3) automated magnetic bead-based commercial extraction kit. The results were compared by evaluating the cycle threshold (Ct) in multiplex real-time PCR for the SARS-CoV-2 virus gene and RNase P gene. Results: The results demonstrated that Fe-MSN nanoparticles provide a more efficient extraction process, yielding higher RNA purity and lower Ct values in RT-PCR compared to conventional methods. A 5-fold decrease in the Ct value of different studied genes was observed after using the Fe-MSN column for RNA extraction compared to the commercial extraction kit. Conclusions: This research aimed to assess and determine the most dependable and precise technique for isolating total RNA from stool samples. The results of this study showed that the Fe-MSN column is the best choice for this purpose.