Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Xiao, Amy; Wu, Fuqing; Bushman, Mary; Zhang, Jianbo; Imakaev, Maxim; Chai, Peter R.; Duvallet, Claire; Endo, Noriko; Erickson, Timothy; Armas, Federica; Arnold, Brian J.; Chen, Hongjie; Chandra, Franciscus; Ghaeli, Newsha; Gu, Xiaoqiong; Hanage, William P.; Lee, Wei Lin; Matus, Mariana; McElroy, Kyle A.; Moniz, Katya; Rhode, Steven F; Thompson, Janelle R.; Alm, Eric J.

doi:10.1101/2021.06.10.21258580

Cited by 17 publications

(19 citation statements)

References 42 publications

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“…It is thus conceivable that the signal captured by the WWI differs more significantly from the incidence rate during that period because the two indicators monitored different populations by that time than at the second peak of the epidemic. Such a change in the demographic of the pandemic has already been reported in the state of Massachusetts [19] and is shown in Figure 7. The correlation is still good between the two compared signals (>0.85 for every WWTP except Nancy), which is consistent with the results of [1,9,12,25,26,27,28].…”

Section: Seine Moréesupporting

confidence: 68%

Mathematical modeling and adequate environmental sampling plans are essential for the public health assessment of COVID-19 pandemics : development of a monitoring indicator for SARS-CoV-2 in wastewater

Cluzel¹,

Courbariaux²,

Wang³

et al. 2021

Preprint

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Since many infected people experience no or few symptoms, the SARS-CoV-2 epidemic is frequently monitored through massive virus testing of the population, an approach that may be biased and may be difficult to sustain in low-income countries. Since SARS-CoV-2 RNA can be detected in stool samples, quantifying SARS-CoV-2 genome by RT-qPCR in WWTPs has been proposed as an alternative tool to monitor virus circulation among human populations. However, measuring SARS-CoV-2 viral load in WWTPs can be affected by many experimental and environmental factors. To circumvent these limits, we propose here a novel indicator WWI that partly reduces and corrects the noise associated with the SARS-CoV-2 genome quantification in wastewater. This method has been successfully applied in the context of Obepine, a French national network that has been quantifying SARS-CoV-2 genome in a representative sample of French WWTPs since March 5th 2020. On August 26th, 2021, 168 WWTPs were monitored twice a week in the metropolitan and overseas territories of France. We detail the process of elaboration of this indicator, show that it is strongly correlated to the incidence rate and that the optimal time lag between these two signals is only a few days, making our indicator an efficient complement or even a credible alternative to the incidence rate. This alternative approach may be especially important to evaluate SARS-CoV-2 dynamics in human populations when the testing rate is low.

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Section: Seine Moréesupporting

confidence: 68%

Mathematical modeling and adequate environmental sampling plans are essential for the public health assessment of COVID-19 pandemics : development of a monitoring indicator for SARS-CoV-2 in wastewater

Cluzel¹,

Courbariaux²,

Wang³

et al. 2021

Preprint

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“…This section introduces the WCR metric to demonstrate the versatility of the QTA approach and constitutes Part 2 of 2 of the model QTA report. Here we adopt the interpretations provided by Xiao et al, 2021 [8] within the QTA framework and this is provided in Figure 5 and Tables 8 − 11 for the TAB sewershed longer-term QTA.…”

Section: Resultsmentioning

confidence: 99%

“…The wastewater to cases ratio (WCR) [8] was also considered and integrated as part of an extension to the base QTA report intended to demonstrate the versatility of the QTA methodology to integrate new metrics for additional trend analysis and insight. Table 3 provides an integration of the PHAC and WC recommended interpretations intended to supplement the CCC and WVS trend interpretations [10,11].…”

Section: Integrated Interpretationsmentioning

confidence: 99%

“…Additionally it was recommended that the magnitude and range of the WC ratio be established for each sewershed to assess a population baseline where sufficient public health testing capacity indicated a relatively constant WC ratio. Furthermore the WCR was recommended as a useful metric to better detect short-term trends of asymptomatic disease transmission compared to the wastewater and clinical data independently [8].…”

Section: Introductionmentioning

confidence: 99%

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Quantitative Trend Analysis of SARS-CoV-2 RNA in Municipal Wastewater Exemplified with Sewershed-Specific COVID-19 Clinical Case Counts

Pileggi

Shurgold

Sun

et al. 2022

Preprint

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We present and demonstrate a quantitative statistical linear trend analysis (QTA) approach to analyze and interpret SARS-CoV-2 RNA wastewater surveillance results concurrently with clinical case data. This demonstration is based on the work completed under the Ontario (Canada) Wastewater Surveillance Initiative (WSI) by two laboratories in four large sewersheds within the Toronto Public Health (TPH) jurisdiction. The sewersheds were sampled over a 9-month period and data were uploaded to the Ontario Wastewater Surveillance Data and Visualization Hub (Ontario Dashboard) along with clinical case counts, both on a sewershed-specific basis. The data from the last 5-months, representing a range of high and low cases, was used for this demonstration. The QTA was conducted on a sewershed specific approach using the recommendations for public health interpretation and use of wastewater surveillance data by the United States Centers for Disease Control and Prevention (US CDC). The interpretation of the QTA results was based on the integration of both clinical and wastewater virus signals using an integration matrix in an interim draft guide by the Public Health Agency of Canada (PHAC). The key steps in the QTA consisted of (i) the calculation of Pepper Mild Mottle Virus (PMMoV), flow and flow-PMMoV-normalized virus loads; (ii) computation of the linear trends including interval estimation to identify the key inflection points using a segmented linear regression method and (iii) integrated interpretations based on consideration of both the cases and wastewater signals, as well as end user actionability. This approach is considered a complementary tool to commonly used qualitative analyses of SARS-CoV-2 RNA in wastewater and is intended to directly support public health decisions using a systematic quantitative approach.

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“…Wastewater (WW) surveillance has emerged as a method to track SARS-CoV-2 variants in a manner that is complementary to sequencing clinical samples. Wastewater-based epidemiology has the potential to variant lineages earlier than clinical sampling and provides valuable insights about the viral spread in the population (Bibby et al 2021;Xiao et al 2021). This is because wastewater sampling can catch asymptomatic cases that would otherwise not present for a nasal swab sample, but that do excrete viral RNA in stool (Bibby et al 2021;Jones et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada

N’Guessan

Tsitouras

Sanchez-Quete

et al. 2022

Preprint

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Wastewater-based epidemiology has emerged as a promising tool to monitor pathogens in a population, particularly when clinical diagnostic capacities become overwhelmed. During the ongoing COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), several jurisdictions have tracked viral concentrations in wastewater to inform public health authorities. While some studies have also sequenced SARS-CoV-2 genomes from wastewater, there have been relatively few direct comparisons between viral genetic diversity in wastewater and matched clinical samples from the same region and time period. Here we report sequencing and inference of SARS-CoV-2 mutations and variant lineages (including variants of concern) in 936 wastewater samples and thousands of matched clinical sequences collected between March 2020 and July 2021 in the cities of Montreal, Quebec City, and Laval, representing almost half the population of the Canadian province of Quebec. We benchmarked our sequencing and variant-calling methods on known viral genome sequences to establish thresholds for inferring variants in wastewater with confidence. We found that variant frequency estimates in wastewater and clinical samples are correlated over time in each city, with similar dates of first detection. Across all variant lineages, wastewater detection is more concordant with targeted outbreak sequencing than with semi-random clinical swab sampling. Most variants were first observed in clinical and outbreak data due to higher sequencing rate. However, wastewater sequencing is highly efficient, detecting more variants for a given sampling effort. This shows the potential for wastewater sequencing to provide useful public health data, especially at places or times when sufficient clinical sampling is infrequent or infeasible.

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Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Cited by 17 publications

References 42 publications

Mathematical modeling and adequate environmental sampling plans are essential for the public health assessment of COVID-19 pandemics : development of a monitoring indicator for SARS-CoV-2 in wastewater

Mathematical modeling and adequate environmental sampling plans are essential for the public health assessment of COVID-19 pandemics : development of a monitoring indicator for SARS-CoV-2 in wastewater

Quantitative Trend Analysis of SARS-CoV-2 RNA in Municipal Wastewater Exemplified with Sewershed-Specific COVID-19 Clinical Case Counts

Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada

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