Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater

Abstract

The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence the recovered concentrations of target nucleic acid, including membrane types, homogenization instruments, speed and duration, and lysis buffer. In this study, 42 different AE workflows that varied these components were compared to determine the optimal workflow by quantifying endogenous SARS-CoV-2, human adenovirus 40/41 (HAdV 40/41), and a bacterial marker gene of fecal contamination (Bacteroides HF183). Our findings suggest that the workflow chosen had a significant impact on SARS-CoV-2 concentrations, whereas it had minimal impact on HF183 and no effect on HAdV 40/41 concentrations. When comparing individual components in a workflow, such as membrane type (MF-Millipore^™ 0.45 μm MCE vs. Isopore^™ 0.40 μm), we found that they had no impact on SARS-CoV-2, HAdV 40/41, and HF183 concentrations. This suggests that at least some consumables and equipment are interchangeable. Buffer PM1 + TRIzol-based workflows yielded higher concentrations of SARS-CoV-2 than other workflows. HF183 concentrations were higher in workflows without chloroform. Similarly, higher homogenization speeds (5000-10,000 rpm) led to increased concentrations of SARS-CoV-2 and HF183 but had no effect on HAdV 40/41. Our findings indicate that minor enhancements to the AE workflow can improve the recovery of viruses and bacteria from the wastewater, leading to improved outcomes from wastewater surveillance efforts.

Keywords: Adsorption-extraction; Centrifugation; HAdV 40/41; HF183; SARS-CoV-2; WBE.

Fig. 1.

Adsorption-extraction (AE) workflows used in this study for qPCR/RT-qPCR quantification of SARS-CoV-2, HAdV 40/41 and Bacteroides HF183.

Fig. 2.

Mean concentrations (log₁₀ GC/50 mL) of endogenous SARS-CoV-2 in wastewater samples collected from WWTPs A, B, and C using 42 AE-workflows. Error bars represent the standard deviation for RT-qPCR replicates. The asterisk (*) represents the workflow that resulted in the highest mean concentration of GC/50 mL.

Fig. 3.

Mean concentrations (log₁₀ GC/50 mL) of endogenous HAdV 40/41 in wastewater samples collected from WWTPs A, B, and C using 42 AE-workflows. Error bars represent the standard deviation for RT-qPCR replicates. The asterisk (*) represents the workflow that resulted in the highest mean concentration of GC/50 mL.

Fig. 4.

Mean concentrations (log₁₀ GC/50 mL) of endogenous HF183 in wastewater samples collected from WWTPs A, B, and C using 42 AE-workflows. Error bars represent the standard deviation for RT-qPCR replicates. The asterisk (*) represents the workflow that resulted in the highest mean concentration of GC/50 mL.