Are there any kits that allow direct Q-PCR from nasopharyngeal swabs without going through RNA purification that could be used universally (example for CFX96 instrument from bio-rad) ?
Cells-to-Signal kit can be used for this. Sensitivity for all "lysis" approaches (skipping RNA purification, direct qPCR) are lower vs "gold standard" approaches though (eg MagMax kit)
The SeeGene kit apparently works pretty well for this (https://www.biorxiv.org/content/10.1101/2020.04.06.028902v1).
The Tjian+Darzacq lab has found that for any approaches skipping an RNA extraction step, it is critical that swab samples are stored in UTM and inactivated by heat (75C, 30 min) and not by the addition of RNAshield, which inhibits downstream reactions. I hope this is helpful to you!
Agreeing with Alexander’s answer, Ct scores are higher (about 3-6) for ”direct lysis” methods.
Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 Institut Pasteur, Paris This protocol describes procedures for the detection of SARS-CoV-2 for two RdRp targets (IP2 and IP4). Based on the first sequences of SARS-CoV-2 made available on the GISAID database on January 11, 2020, primers and probes (nCoV_IP2 and nCoV_IP4) were designed to target the RdRp gene spanning nt 12621-12727 and 14010-14116 (positions according SARS-CoV, NC_004718). As a confirmatory assay, we used the E gene assay from the Charité protocol1
Hello Zouhaier, yes indeed, it works just fine directly with SeeGene (following heat inactivation) if swabs are in water or in UTM. It can work using other kits or other media, however you may need to dilute samples, depending on the medium in which the swabs have been stored.
We found good success using the QuickExtract-RNA -Kit (https://www.lucigen.com/QuickExtract-RNA-Extraction-Kit/) on other RNA virus not specifically for SARS-CoV-2. Hope this is helpful.