Journal
ACS ES&T WATER
Volume -, Issue -, Pages -Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acsestwater.1c00387
Keywords
COVID-19; SARS-CoV-2; wastewater surveillance; RT-qPCR; dPCR
Categories
Funding
- NSF [2027752]
- Queensland Health
- CSIRO
- Directorate For Engineering
- Div Of Chem, Bioeng, Env, & Transp Sys [2027752] Funding Source: National Science Foundation
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This study compared the performance of RT-qPCR and RT-dPCR platforms in detecting SARS-CoV-2 RNA in low-prevalence locations in Queensland, Australia. The results showed that RT-dPCR had a lower limit of detection and a higher detection rate than RT-qPCR in both eluate and pellet samples.
We compared reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and RT digital PCR (RTdPCR) platforms for the trace detection of SARS-CoV-2 RNA in low-prevalence COVID-19 locations in Queensland, Australia, using CDC N1 and CDC N2 assays. The assay limit of detection (ALOD), PCR inhibition rates, and performance characteristics of each assay, along with the positivity rates with the RT-qPCR and RT-dPCR platforms, were evaluated by seeding known concentrations of exogenous SARS-CoV-2 in wastewater. The ALODs using RT-dPCR were approximately 2-5 times lower than those using RT-qPCR. During sample processing, the endogenous (n = 96) and exogenous (n = 24) SARS-CoV-2 wastewater samples were separated, and RNA was extracted from both wastewater eluates and pellets (solids). The RT-dPCR platform demonstrated a detection rate significantly greater than that of RT-qPCR for the CDC N1 and CDC N2 assays in the eluate (N1, p = 0.0029; N2, p = 0.0003) and pellet (N1, p = 0.0015; N2, p = 0.0067) samples. The positivity results also indicated that for the analysis of SARS-CoV-2 RNA in wastewater, including the eluate and pellet samples may further increase the detection sensitivity using RT-dPCR.
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