dPCR vs RT-qPCR: Battle for the Sewers
Additional Funding Sources
The project described was supported by a subgrant from the Idaho Department of Health and Welfare through the Epidemiology and Laboratory Capacity Enhancing Detection Through Coronavirus Response and Relief (CRR) Supplemental Funds (Grant 6 NU50CK000544-02) from the Centers for Disease Control and Prevention. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Department or Centers for Disease Control and Prevention. Hampikian Laboratory, Boise State University 07.15.22.
Abstract
Wastewater based epidemiology (WBE) is an important tool in predicting infection rates among a population. Viral concentration trends in wastewater give public officials the ability to forecast potential hospitalizations. Early in the COVID-19 Pandemic, a protocol utilizing Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) machinery provided a method for quantifying SARS-CoV-2. While RT-qPCR does accurately predict trends in hospitalizations due to SARS-CoV-2, quantifying particles is inhibited by fecal carbohydrates. In order to circumvent the effects of inhibition on data collection, a new protocol involving Digital Polymerase Chain Reaction (dPCR) machinery is coming into common use, which is more sensitive to differences in viral concentration. This project aims to verify previous findings and determine if the new protocol is preferable to the old protocol. Areas of interest include efficiency of time and labor as well as reduced variance between partitions. In order to determine this, the old and new protocols were conducted simultaneously or using the same samples while running respective protocols on different days. Data suggests that dPCR is more efficient in terms of time and labor. Additionally, dPCR shows less variance in virus concentration between collection sites, as well as duplicates, which may be attributed to increased sensitivity to inhibitory effects.
dPCR vs RT-qPCR: Battle for the Sewers
Wastewater based epidemiology (WBE) is an important tool in predicting infection rates among a population. Viral concentration trends in wastewater give public officials the ability to forecast potential hospitalizations. Early in the COVID-19 Pandemic, a protocol utilizing Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) machinery provided a method for quantifying SARS-CoV-2. While RT-qPCR does accurately predict trends in hospitalizations due to SARS-CoV-2, quantifying particles is inhibited by fecal carbohydrates. In order to circumvent the effects of inhibition on data collection, a new protocol involving Digital Polymerase Chain Reaction (dPCR) machinery is coming into common use, which is more sensitive to differences in viral concentration. This project aims to verify previous findings and determine if the new protocol is preferable to the old protocol. Areas of interest include efficiency of time and labor as well as reduced variance between partitions. In order to determine this, the old and new protocols were conducted simultaneously or using the same samples while running respective protocols on different days. Data suggests that dPCR is more efficient in terms of time and labor. Additionally, dPCR shows less variance in virus concentration between collection sites, as well as duplicates, which may be attributed to increased sensitivity to inhibitory effects.