TY - JOUR
T1 - Co-quantification of crAssphage increases confidence in wastewater-based epidemiology for SARS-CoV-2 in low prevalence areas
AU - Wilder, Maxwell L.
AU - Middleton, Frank
AU - Larsen, David A.
AU - Du, Qian
AU - Fenty, Ariana
AU - Zeng, Teng
AU - Insaf, Tabassum
AU - Kilaru, Pruthvi
AU - Collins, Mary
AU - Kmush, Brittany
AU - Green, Hyatt C.
N1 - Funding Information:
This work would not have been possible without seed funding from Syracuse University, the Environmental Data Science Initiative at SUNY-ESF, and the SUNY Discovery Fund. Additional funding was provided by Cooperative agreement EH171702 (Enhancing Innovation and Capabilities of the Environmental Public Health Tracking Network) through the Centers for Disease Control and Prevention.
Funding Information:
We are grateful to the staff at Onondaga County Water Environment Protection, Cortland Wastewater Treatment Facility, Water Pollution Control Plant in Auburn, New York, both wastewater treatment plants in Oswego, NY, the Ithaca Area Wastewater Treatment Facility, the Tompkins County Department of Health, and the Warren County Water and Sewer Department for sample collection, sample transport, and provision of supporting data. We also thank Abigail Stamm for her contribution to linking epidemiological and wastewater data, Dustin Hill for contributions to spatial data analysis, Joshua Powell for his technical advice on ultracentrifugation and the sucrose cushion technique, Emma Harnett for her role in sample processing, and David Uhlig for contributions to processing setup and troubleshooting.
Publisher Copyright:
© 2021 The Authors
PY - 2021/5/1
Y1 - 2021/5/1
N2 - Wastewater surveillance of SARS-CoV-2 RNA is increasingly being incorporated into public health efforts to respond to the COVID-19 pandemic. In order to obtain the maximum benefit from these efforts, approaches to wastewater monitoring need to be rapid, sensitive, and relatable to relevant epidemiological parameters. In this study, we present an ultracentrifugation-based method for the concentration of SARS-CoV-2 wastewater RNA and use crAssphage, a bacteriophage specific to the human gut, to help account for RNA loss during transit in the wastewater system and sample processing. With these methods, we were able to detect, and sometimes quantify, SARS-CoV-2 RNA from 20 mL wastewater samples within as little as 4.5 hours. Using known concentrations of bovine coronavirus RNA and deactivated SARS-CoV-2, we estimate recovery rates of approximately 7-12% of viral RNA using our method. Results from 24 sewersheds across Upstate New York during the spring and summer of 2020 suggested that stronger signals of SARS-CoV-2 RNA from wastewater may be indicative of greater COVID-19 incidence in the represented service area approximately one week in advance. SARS-CoV-2 wastewater RNA was quantifiable in some service areas with daily positives tests of less than 1 per 10,000 people or when weekly positive test rates within a sewershed were as low as 1.7%. crAssphage DNA concentrations were significantly lower during periods of high flow in almost all areas studied. After accounting for flow rate and population served, crAssphage levels per capita were estimated to be about 1.35 × 1011 and 2.42 × 108 genome copies per day for DNA and RNA, respectively. A negative relationship between per capita crAssphage RNA and service area size was also observed likely reflecting degradation of RNA over long transit times. Our results reinforce the potential for wastewater surveillance to be used as a tool to supplement understanding of infectious disease transmission obtained by traditional testing and highlight the potential for crAssphage co-detection to improve interpretations of wastewater surveillance data.
AB - Wastewater surveillance of SARS-CoV-2 RNA is increasingly being incorporated into public health efforts to respond to the COVID-19 pandemic. In order to obtain the maximum benefit from these efforts, approaches to wastewater monitoring need to be rapid, sensitive, and relatable to relevant epidemiological parameters. In this study, we present an ultracentrifugation-based method for the concentration of SARS-CoV-2 wastewater RNA and use crAssphage, a bacteriophage specific to the human gut, to help account for RNA loss during transit in the wastewater system and sample processing. With these methods, we were able to detect, and sometimes quantify, SARS-CoV-2 RNA from 20 mL wastewater samples within as little as 4.5 hours. Using known concentrations of bovine coronavirus RNA and deactivated SARS-CoV-2, we estimate recovery rates of approximately 7-12% of viral RNA using our method. Results from 24 sewersheds across Upstate New York during the spring and summer of 2020 suggested that stronger signals of SARS-CoV-2 RNA from wastewater may be indicative of greater COVID-19 incidence in the represented service area approximately one week in advance. SARS-CoV-2 wastewater RNA was quantifiable in some service areas with daily positives tests of less than 1 per 10,000 people or when weekly positive test rates within a sewershed were as low as 1.7%. crAssphage DNA concentrations were significantly lower during periods of high flow in almost all areas studied. After accounting for flow rate and population served, crAssphage levels per capita were estimated to be about 1.35 × 1011 and 2.42 × 108 genome copies per day for DNA and RNA, respectively. A negative relationship between per capita crAssphage RNA and service area size was also observed likely reflecting degradation of RNA over long transit times. Our results reinforce the potential for wastewater surveillance to be used as a tool to supplement understanding of infectious disease transmission obtained by traditional testing and highlight the potential for crAssphage co-detection to improve interpretations of wastewater surveillance data.
KW - Cross-assembly phage
KW - SARS-CoV-2
KW - Viral concentration
KW - Wastewater-based epidemiology
UR - http://www.scopus.com/inward/record.url?scp=85104107651&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85104107651&partnerID=8YFLogxK
U2 - 10.1016/j.wroa.2021.100100
DO - 10.1016/j.wroa.2021.100100
M3 - Article
AN - SCOPUS:85104107651
SN - 2589-9147
VL - 11
JO - Water Research X
JF - Water Research X
M1 - 100100
ER -