Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification

Novel Workflows for Separate Isolation of Pathogen RNA or DNA from Wastewater: Detection by Innovative and Conventional qPCR

Wastewater-based surveillance (WBS) can provide a wealth of information regarding the health status of communities from measurements of nucleic acids found in wastewater. Processing workflows for WBS typically include sample collection, a primary concentration step, and lysis of the microbes to release nucleic acids, followed by nucleic acid purification and molecular-based quantification. This manuscript provides workflows from beginning to end with an emphasis on filtration-based concentration approaches coupled with specific lysis and nucleic acid extraction processes. Here, two WBS processing approaches are presented, one focusing on RNA-specific pathogens and the other focused on DNA-specific pathogens found within wastewater: 1) The RNA-specific approach, employed for analyzing RNA viruses like severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) couples electronegative filtration of wastewater with the placement of the filter within a lysis buffer followed by direct RNA extraction. 2) The DNA-specific approach, employed for analyzing DNA pathogens like Candida auris, uses size selection membranes during filtration, subsequently followed by a lysis buffer, bead-beating, and DNA extraction. Separate workflows for RNA versus DNA isolations have the advantage of improving the detection of the target pathogen. A novel aspect of the RNA-specific workflow is the direct extraction of nucleic acids from filter lysates, which shows enhanced recoveries, whereas the DNA-specific approach requires bead beating prior to extraction. Novelty is also provided in a new qPCR approach called Volcano 2nd Generation (V2G), which uses a polymerase capable of using RNA as a template, bypassing the reverse transcriptase step normally required for qPCR. Key features • Membrane filtration approaches for concentrating suspended solids from wastewater. After concentration, workflows are optimized for separate recovery of RNA and DNA. • Unique polymerase utilized to perform qPCR analysis, foregoing reverse transcription, for RNA. • Sample products for use with other molecular techniques (e.g., sequencing) as workflow approaches generate high-quality, concentrated nucleic acid extracts with minimal inhibitors. • Validated through COVID-19 surveillance where >1,000 samples of wastewater and >3,000 filter concentrates produced from these samples have been created and analyzed, with published results. This complete protocol was used in: J Biomol Tech (2023), DOI: 10.7171/3fc1f5fe.dfa8d906.

Wastewater Based Measures of COVID-19 and Associations with Children's Absenteeism at Grade Schools

During the COVID-19 pandemic schools closed due to concerns over disease spread resulting in lost learning opportunities. One approach for documenting disease spread includes wastewater (WW) surveillance of the virus that causes COVID-19 (Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2) and other infectious pathogens. The objective of this study was to evaluate whether wastewater can be used to track children's health at grade schools in an underserved community, which was vulnerable due to limited health-based data and difficulties in implementing mitigation measures. The 18-month study was initiated during January 2022 at 9 grade schools (3 high, 2 middle, and 4 elementary schools) characterized as low income. Children's health was evaluated through absenteeism due to difficulties in attaining representative clinical diagnoses through school-based clinics. Wastewater measurements of SARS-CoV-2 were available weekly through grab sample collection and RNA extraction followed by quantification using qPCR. The average absenteeism rate was 7.1%, ranging from 4.6% to 12.5% per school. Fraction of WW samples positive for SARS-CoV-2 was 38% with SARS-Cov-2 levels ranging from detection limits (100 gc/L) to a maximum of 10.2 million gc/L. When data were aggregated across all schools, a statistically significant association was observed between weekly absenteeism rates and WW SARS-CoV-2 with a one percent increase in the loge WW SARS-CoV-2 associated with a 1.4% increase in student absence (p < 0.05). When evaluating the data by individual school, this association was strongest at schools with enclosed architecture characterized by limited natural ventilation. For schools with limited resources for clinical diagnosis of illnesses, school absenteeism coupled with wastewater-based monitoring should be utilized for assessing overall health of student populations. Strategies to maintain schools open during pandemics should include consideration of school architecture along with appropriate messaging of WW monitoring results to inform administrators and families.

Wastewater based surveillance can be used to reduce clinical testing intensity on a university campus

Clinical testing has been a vital part of the response to and suppression of the COVID-19 pandemic; however, testing imposes significant burdens on a population. College students had to contend with clinical testing while simultaneously dealing with health risks and the academic pressures brought on by quarantines, changes to virtual platforms, and other disruptions to daily life. The objective of this study was to analyze whether wastewater surveillance can be used to decrease the intensity of clinical testing while maintaining reliable measurements of diseases incidence on campus. Twelve months of human health and wastewater surveillance data for eight residential buildings on a university campus were analyzed to establish how SARS-CoV-2 levels in the wastewater can be used to minimize clinical testing burden on students. Wastewater SARS-CoV-2 levels were used to create multiple scenarios, each with differing levels of testing intensity, which were compared to the actual testing volumes implemented by the university. We found that scenarios in which testing intensity fluctuations matched rise and falls in SARS-CoV-2 wastewater levels had stronger correlations between SARS-CoV-2 levels and recorded clinical positives. In addition to stronger correlations, most scenarios resulted in overall fewer weekly clinical tests performed. We suggest the use of wastewater surveillance to guide COVID-19 testing as it can significantly increase the efficacy of COVID-19 surveillance while reducing the burden placed on college students during a pandemic. Future efforts should be made to integrate wastewater surveillance into clinical testing strategies implemented on college campuses.