Detection of SARS-CoV-2 from wastewater samples utilizing the Bead Ruptor Elite™ Bead Mill Homogenizer and chemagic™ Prime™ instrument

Most wastewater surveillance programs are accomplished through regimented examination of filters put in sewage lines, or water samples acquired from wastewater treatment plants which are then prepared for nucleic acid extraction and RT-PCR amplification to detect the presence of known SARS-CoV-2 genetic targets. Standard methods for preparation of filters involve long processing times and incubations on ice which can be a burden to high-throughput workflows.

In this application note, we examine a streamlined methodology for filter homogenization utilizing the OMNI Bead Ruptor Elite™ Bead Mill Homogenizer followed by automated RNA extraction on the chemagic™ Prime™ instrument in preparation for RT-PCR detection of SARS-CoV-2 spiked wastewater samples. This high throughput methodology provides a robust and reliable workflow for detection of SARS-CoV-2 from wastewater samples.

Procedure of  SARS-CoV-2 detection from wastewater

The City of Houston (Houston, TX USA) Health Department provided the known SARS-CoV-2 positive wastewater samples for utilization in this workflow validation study. Nitrocellulose filters with known SARS-CoV-2 exposure were taken from city wastewater plants from December 2021 to February 2022 to evaluate for the detection of SARS-CoV-2 nucleocapsid genetic segments via RT-PCR.

Filter Processing on the Bead Ruptor Elite Bead Mill Homogenizer

Intact nitrocellulose filters with known SARS-CoV-2 positive wastewater exposure were placed into respective 2 mL Hard Tissue Homogenization Mix Tubes along with 600 µL of Lysis Buffer included with the chemagic Viral DNA/RNA 300 Kit. Samples were then placed onto the Bead Ruptor Elite Bead Mill Homogenizer utilizing the 48 Position 2 mL Tube Carriage, and homogenized at 6.0 m/s for 60 sec. The samples were then centrifuged at 12,500 rpm for 4 min and transferred to the chemagic Prime instrument  for automated RNA extraction.

Automated SARS-CoV-2 RNA Extraction

Precisely 300 µL of homogenate was loaded into a 96 well plate and processed on the chemagic Prime instrument  utilizing the chemagic Viral DNA/RNA 300 Kit per the manufacturer’s instructions.