Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples.

Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance program. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimise data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: RNeasy PowerSoil Total RNA kit (PS), RNeasy PowerMicrobiome Kit (PMB), and MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modification, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.

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© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.