key: cord-1053615-5mcgcnut authors: D'Aoust, P. M.; Graber, T. E.; Mercier, E.; Montpetit, D.; Alexandrov, I.; Neault, N.; Baig, A. T.; Mayne, J.; Zhang, X.; Alain, T.; Servos, M. R.; Srikanthan, N.; MacKenzie, M.; Figeys, D.; Manuel, D.; Juni, P.; MacKenzie, A. E.; Delatolla, R. title: Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 hours before COVID-19 clinical tests and 96 hours before hospitalizations date: 2020-11-23 journal: nan DOI: 10.1101/2020.11.22.20236554 sha: 7bc75be3d2f74de53a54ff052e53c78f567e3291 doc_id: 1053615 cord_uid: 5mcgcnut Curtailing the Spring 2020 COVID-19 surge required sweeping and stringent interventions by governments across the world. Wastewater-based COVID-19 epidemiology programs have been initiated in many countries to provide public health agencies with a complementary disease tracking metric and facile surveillance tool. However, their efficacy in prospectively capturing resurgence following a period of low prevalence is unclear. In this study, the SARS-CoV-2 viral signal was measured in primary clarified sludge harvested every two days at the City of Ottawa's water resource recovery facility during the summer of 2020, when clinical testing recorded daily percent positivity below 1%. In late July, increases of >400% in normalized SARS-CoV-2 RNA signal in wastewater were identified 48 hours prior to reported >300% increases in positive cases that were retrospectively attributed to community-acquired infections. During this resurgence period, SARS-CoV-2 RNA signal in wastewater preceded the reported >160% increase in community hospitalizations by approximately 96 hours. This study supports wastewater-based COVID-19 surveillance of populations in augmenting the efficacy of diagnostic testing, which can suffer from sampling biases or timely reporting as in the case of hospitalization census. The COVID-19 global pandemic has profound impacts on day-to-day life through sickness, death 42 and also the economic and social effects of lockdowns, closures and curfews put in place by local 43 governments to control and limit the community spread of the disease. COVID-19 surveillance 44 approaches invoked by nations around the world include case ascertainment of individual patients and 45 include nucleic acid-based tests, serological tests and contact tracing. The objective of this study is to 46 investigate early identification of COVID-19 infection resurgence in Ottawa (Ontario, Canada), using 47 SARS-CoV-2 viral RNA signal in primary sludge wastewater. Roda Husman, 2020), an understanding of the predictive ability of this epidemiological metric is 57 necessary for public health units to appropriately action this tool (Hart and Halden, 2020; Hill et al., 2020 ; 58 Thompson et al., 2020) . In particular, studies to date that demonstrate the potential for WBE to identify 59 the onset of community infection prior to clinical testing have largely been applied to identifying first wave 60 of the disease in community (Kaplan et resurgences. The objectives of this study are to establish a relationship between: i) increases in SARS-65 CoV-2 RNA signal in wastewater, ii) increases in the number of new COVID-19 positive patient cases in 66 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint 118 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint and epidemiological metrics, a student's t-test and Pearson's correlation analyses were performed, with a 120 p-value of 0.05 or lower signifying significance. 121 To evaluate if a lag existed between the appearance of increased SARS-CoV-2 RNA signal in 122 wastewater and epidemiological metrics, time-step analyses were also performed where the correlations 123 between viral RNA signal and epidemiological metrics were offset by a period of 1 to 7 days. The time-124 step analysis was performed across three discreet time-periods: i) pre-resurgence and resurgence, 125 ending after the resurgence (June 21 st to July 21 st ), ii) pre-resurgence and post-resurgence, extending to 126 the end of the data set (June 21 st to July 25 th ) and iii) full data period (June 21 st to August 4 th ). 127 Additionally, dilution tests demonstrated that the sample PCR was not inhibited. 139 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint wastewater was also shown to be low at the beginning of the study period through to the week of July 13 146 with both N1 and N2 regions below 1.00x10 -4 copies/copies PMMoV. There was a 450% relative increase 147 (p<0.05) in N1 and 440% increase (p<0.05) in N2 viral regions on July 17 to 19 compared to July 13 to 148 15. The absolute increase of 2.03x10 -4 and 3.01x10 -4 copies/copies PMMoV was reported during this 149 period of increase for N1 and N2 gene regions, respectively (Figure 2e ). The wastewater-based 150 epidemiological metric in this study was not corrected for recovery percentages. 151 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint 184 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. official testing strategies or media sentiment, and iv) provides an exit strategy/path forward for public 208 health units as something to eventually transition to once immunization is available, to cut down on 209 clinical testing costs, while maintaining broad surveillance capabilities. However, limitations to this WBE 210 approach includes the following: i) data obtained only gives high-altitude view of the situation in the 211 community, and it is currently not possible to correlate this data to an actual number of cases in the 212 community; ii) testing protocols must be optimized and retain sensitivity at very-low levels of disease 213 incidence to remain relevant; iii) widespread adoption of WBE requires scale-up of public health units' 214 current capabilities and/or partnership with private laboratories or research institutions, and iv) increases 215 in resolution (more localized, upstream of water resource recovery facilities, for example) of tests in 216 watersheds may lead to ethical questions for public health unit if it wishes to act upon the data, due to the 217 potential risk for identifying or singling out small subgroups of a population. It is noted however that these 218 issues are not dissimilar to other ethical issues currently existing with other COVID-19 public health 219 endeavors, such as COVID-19 potential exposure notification smartphone applications. 220 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted November 23, 2020. ; https://doi.org/10.1101/2020.11.22.20236554 doi: medRxiv preprint Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in 260 communities with low COVID-19 incidence and prevalence Case definition for coronavirus disease 2019 (COVID-19) Computational analysis of SARS-CoV-2/COVID-19 surveillance by 264 wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and 265 challenges SARS-CoV-2 known and 267 unknowns, implications for the water sector and wastewater-based epidemiology to support national 268 responses worldwide: early review of global experiences with the COVID-19 pandemic Indicators via an epidemic model: Application to hospital admissions and RNA detection in sewage 272 sludge First proof of the 274 capability of wastewater surveillance for COVID-19 in India through detection of genetic material of First detection of SARS-CoV-2 in untreated wastewaters in Italy Pretreatment with propidium 280 monoazide/sodium lauroyl sarcosinate improves discrimination of infectious waterborne virus by RT-of SARS-CoV-2: A rapid review SARS-CoV-2 in wastewater: potential health risk, but also 286 data source SARS-CoV-2 in stool than adults? Presence of SARS-Coronavirus-292 2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the 293 epidemic in the Netherlands Sewage analysis as a tool for the COVID-19 295 pandemic response and management: the urgent need for optimised protocols for SARS-CoV-2 296 detection and quantification Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics Making waves: Wastewater surveillance of SARS-CoV-2 for population-310 based health management Post-312 lockdown detection of SARS-CoV-2 RNA in the wastewater of Highly predictive regression model of active cases of COVID-19 in a population by screening 317 wastewater viral load 1-36 SARS-CoV-2 titers in wastewater are higher than expected from 321 clinically confirmed cases Prolonged viral shedding in feces of pediatric patients with coronavirus disease 325 2019 Characteristics of pediatric SARS-CoV-2 infection 328 and potential evidence for persistent fecal viral shedding