Viral RNA extraction protocols from wastewater samples

The dataset was obtained with four RNA extraction protocols applied on 5 mL of raw wastewater (influent) samples. The protocols used were : - Protocol Z = commercial kit, based on silica column, and specific to wastewater samples. - Protocol NS1 = commercial kit, based on silica beads, and non specific to wastewater samples. - Protocol NS2 = Protocol NS1 with a neutral phenol chloroform treatment applied just after the lysis step. - Protocol SB = homemade protocol, based on silica beads, developed fo wastewater samples. Two kinds of analyses were performed on the samples: the quantification of the SARS-CoV-2 genome by targeting the E gene, the detection of RT-qPCR inhibitors by the quantification of F-specific RNA phages of genogroup II (FRNAPH-II). The delta Cq value between undiluted and diluted samples was used to detect the presence of RT-qPCR inhibitors. The analyses were carried out in three laboratories, with each comparing the Z protocol to one of the three other protocols (NS1, NS2 or SB). Each lab analysed influent samples collected in three wastewater treatment plant (WWTPs) with three distinct samples per WWTPs (n=9 per laboratory). Each sample was analyzed five times, giving 45 data points per laboratory. The dataset allows the comparison of the RNA extraction protocols for both RNA concentrations (SARS-CoV-2) and removal of RT-qPCR inhibitors (FRNAPH-II), for an effective optimisation of viral RNA extraction from complex matrices and high-quality downstream molecular analyses.