21 out of 396 RT-qPCR-positive samples could not be confirmed as SARS-CoV-2 positive through genetic validation. However, Orf1ab CRISPR DETECTR assay confirmed most samples, and amplicon sequencing was used to verify results. The study demonstrates the effectiveness of a multi-tiered approach for detecting SARS-CoV-2 in wastewater using RT-qPCR, amplicon sequencing, and CRISPR DETECTR assay.