Nivetha Srikanthan


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A comparative analysis of the partitioning behaviour of SARS-CoV-2 RNA in liquid and solid fractions of wastewater
Patrick R. Breadner, Hadi A. Dhiyebi, Azar Fattahi, Nivetha Srikanthan, Samina Hayat, Marc G. Aucoin, Scott Joseph Boegel, Leslie M. Bragg, Paul M. Craig, Yuwei Xie, John P. Giesy, Mark R. Servos
Science of The Total Environment, Volume 895

As fragments of SARS-CoV-2 RNA can be quantified and measured temporally in wastewater, surveillance of concentrations of SARS-CoV-2 in wastewater has become a vital resource for tracking the spread of COVID-19 in and among communities. However, the absence of standardized methods has affected the interpretation of data for public health efforts. In particular, analyzing either the liquid or solid fraction has implications for the interpretation of how viral RNA is quantified. Characterizing how SARS-CoV-2 or its RNA fragments partition in wastewater is a central part of understanding fate and behaviour in wastewater. In this study, partitioning of SARS-CoV-2 was investigated by use of centrifugation with varied durations of spin and centrifugal force, polyethylene glycol (PEG) precipitation followed by centrifugation, and ultrafiltration of wastewater. Partitioning of the endogenous pepper mild mottled virus (PMMoV), used to normalize the SARS-CoV-2 signal for fecal load in trend analysis, was also examined. Additionally, two surrogates for coronavirus, human coronavirus 229E and murine hepatitis virus, were analyzed as process controls. Even though SARS-CoV-2 has an affinity for solids, the total RNA copies of SARS-CoV-2 per wastewater sample, after centrifugation (12,000 g, 1.5 h, no brake), were partitioned evenly between the liquid and solid fractions. Centrifugation at greater speeds for longer durations resulted in a shift in partitioning for all viruses toward the solid fraction except for PMMoV, which remained mostly in the liquid fraction. The surrogates more closely reflected the partitioning of SARS-CoV-2 under high centrifugation speed and duration while PMMoV did not. Interestingly, ultrafiltration devices were inconsistent in estimating RNA copies in wastewater, which can influence the interpretation of partitioning. Developing a better understanding of the fate of SARS-CoV-2 in wastewater and creating a foundation of best practices is the key to supporting the current pandemic response and preparing for future potential infectious diseases.

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Assessment of seasonality and normalization techniques for wastewater-based surveillance in Ontario, Canada
Hadi A. Dhiyebi, Jad Farah, Heather Ikert, Nivetha Srikanthan, Samina Hayat, Leslie M. Bragg, Asim Qasim, Mark Payne, Linda Kaleis, Caitlyn Paget, Dominika Celmer‐Repin, Arianne M. Folkema, Sarah Drew, Robert Delatolla, John P. Giesy, Mark R. Servos
Frontiers in Public Health, Volume 11

Introduction Wastewater-based surveillance is at the forefront of monitoring for community prevalence of COVID-19, however, continued uncertainty exists regarding the use of fecal indicators for normalization of the SARS-CoV-2 virus in wastewater. Using three communities in Ontario, sampled from 2021–2023, the seasonality of a viral fecal indicator (pepper mild mottle virus, PMMoV) and the utility of normalization of data to improve correlations with clinical cases was examined. Methods Wastewater samples from Warden, the Humber Air Management Facility (AMF), and Kitchener were analyzed for SARS-CoV-2, PMMoV, and crAssphage. The seasonality of PMMoV and flow rates were examined and compared by Season-Trend-Loess decomposition analysis. The effects of normalization using PMMoV, crAssphage, and flow rates were analyzed by comparing the correlations to clinical cases by episode date (CBED) during 2021. Results Seasonal analysis demonstrated that PMMoV had similar trends at Humber AMF and Kitchener with peaks in January and April 2022 and low concentrations (troughs) in the summer months. Warden had similar trends but was more sporadic between the peaks and troughs for PMMoV concentrations. Flow demonstrated similar trends but was not correlated to PMMoV concentrations at Humber AMF and was very weak at Kitchener ( r = 0.12). Despite the differences among the sewersheds, unnormalized SARS-CoV-2 (raw N1–N2) concentration in wastewater ( n = 99–191) was strongly correlated to the CBED in the communities ( r = 0.620–0.854) during 2021. Additionally, normalization with PMMoV did not improve the correlations at Warden and significantly reduced the correlations at Humber AMF and Kitchener. Flow normalization ( n = 99–191) at Humber AMF and Kitchener and crAssphage normalization ( n = 29–57) correlations at all three sites were not significantly different from raw N1–N2 correlations with CBED. Discussion Differences in seasonal trends in viral biomarkers caused by differences in sewershed characteristics (flow, input, etc.) may play a role in determining how effective normalization may be for improving correlations (or not). This study highlights the importance of assessing the influence of viral fecal indicators on normalized SARS-CoV-2 or other viruses of concern. Fecal indicators used to normalize the target of interest may help or hinder establishing trends with clinical outcomes of interest in wastewater-based surveillance and needs to be considered carefully across seasons and sites.

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Omicron COVID-19 Case Estimates Based on Previous SARS-CoV-2 Wastewater Load, Regional Municipality of Peel, Ontario, Canada
Lydia Cheng, Hadi A. Dhiyebi, Monali Varia, Kyle Atanas, Nivetha Srikanthan, Samina Hayat, Heather Ikert, Meghan Fuzzen, Carly Sing-Judge, Yash Badlani, Eli Zeeb, Leslie M. Bragg, Robert Delatolla, John P. Giesy, Elaine Gilliland, Mark R. Servos
Emerging Infectious Diseases, Volume 29, Issue 8

We determined correlations between SARS-CoV-2 load in untreated water and COVID-19 cases and patient hospitalizations before the Omicron variant (September 2020-November 2021) at 2 wastewater treatment plants in the Regional Municipality of Peel, Ontario, Canada. Using pre-Omicron correlations, we estimated incident COVID-19 cases during Omicron outbreaks (November 2021-June 2022). The strongest correlation between wastewater SARS-CoV-2 load and COVID-19 cases occurred 1 day after sampling (r = 0.911). The strongest correlation between wastewater load and COVID-19 patient hospitalizations occurred 4 days after sampling (r = 0.819). At the peak of the Omicron BA.2 outbreak in April 2022, reported COVID-19 cases were underestimated 19-fold because of changes in clinical testing. Wastewater data provided information for local decision-making and are a useful component of COVID-19 surveillance systems.

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An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays
Meghan Fuzzen, Nathanael B.J. Harper, Hadi A. Dhiyebi, Nivetha Srikanthan, Samina Hayat, Leslie M. Bragg, Shelley Peterson, Ivy Yang, Jianxian Sun, Elizabeth Edwards, John P. Giesy, Chand S. Mangat, Tyson E. Graber, Robert Delatolla, Mark R. Servos
Science of The Total Environment, Volume 881

Wastewater-based surveillance has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription polymerase chain reaction (RT-PCR) or whole genome sequencing (WGS). Rapid, reliable RT-PCR assays continue to be needed to determine the relative frequencies of VOCs and sub-lineages in wastewater-based surveillance programs. The presence of multiple mutations in a single region of the N-gene allowed for the design of a single amplicon, multiple probe assay, that can distinguish among several VOCs in wastewater RNA extracts. This approach which multiplexes probes designed to target mutations associated with specific VOC's along with an intra-amplicon universal probe (non-mutated region) was validated in singleplex and multiplex. The prevalence of each mutation (i.e. VOC) is estimated by comparing the abundance of the targeted mutation with a non-mutated and highly conserved region within the same amplicon. This is advantageous for the accurate and rapid estimation of variant frequencies in wastewater. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from several communities in Ontario, Canada in near real time from November 28, 2021 to January 4, 2022. This includes the period of the rapid replacement of the Delta variant with the introduction of the Omicron variant in these Ontario communities in early December 2021. The frequency estimates using this assay were highly reflective of clinical WGS estimates for the same communities. This style of qPCR assay, which simultaneously measures signal from a non-mutated comparator probe and multiple mutation-specific probes contained within a single qPCR amplicon, can be applied to future assay development for rapid and accurate estimations of variant frequencies.

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Intersex manifestation in the rainbow darter (Etheostoma caeruleum): Are adult male fish susceptible to developing and recovering from intersex after exposure to endocrine active compounds?
Keegan A. Hicks, Meghan Fuzzen, Hadi A. Dhiyebi, Leslie M. Bragg, Patricija Marjan, Jessie Cunningham, Mark E. McMaster, Nivetha Srikanthan, Kirsten E. Nikel, Maricor J. Arlos, Mark R. Servos
Aquatic Toxicology, Volume 261

For over a decade, intersex has been observed in rainbow darter (RD) (Etheostoma caeruleum) populations living downstream wastewater treatment plants (WWTPs) in the Grand River, Ontario, Canada. To further our understanding of intersex development in adult male fish, the current study addressed three objectives: i) can intersex be induced in adult male fish, ii) is there a specific window of exposure when adult male fish are more susceptible to developing intersex, and iii) can pre-exposed adult male fish recover from intersex? To assess intersex induction in adult male fish, wild male RD were exposed in the laboratory for 22 weeks (during periods of spawning, gonadal regression, and gonadal recrudescence) to environmentally relevant concentrations of 17α-ethinylestradiol (EE2) including nominal 0, 1, and 10 ng/L. Intersex rates and severity at 10 ng/L EE2 were similar to those observed historically in adult male populations living downstream WWTPs in the Grand River and confirmed previous predictions that 1–10 ng/L EE2 would cause these adverse effects. To assess a window of sensitivity in developing intersex, male RD were exposed to nominal 0, 1 or 10 ng/L EE2 for 4 weeks during three different periods of gonadal development, including (i) spawning, (ii) early recrudescence and (iii) late recrudescence. These short-term exposures revealed that intersex incidence and severity were greater when RD were exposed while gonads were fully developed (during spawning) compared to periods of recrudescence. To assess if RD recover from intersex, wild fish were collected downstream WWTPs in the Grand River and assessed for intersex both before and after a 22-week recovery period in clean water that included gonadal regression and recrudescence. Results showed that fish did not recover from intersex, with intersex rates and severity similar to those both before and after the transition to clean water. This study further advances our knowledge on intersex manifestation in adult male fish including their sensitivity to endocrine active compounds during different periods of their annual reproductive cycle and their limited ability to recover from intersex after onset of the condition.


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Multiplex RT-qPCR assay (N200) to detect and estimate prevalence of multiple SARS-CoV-2 Variants of Concern in wastewater
Meghan Fuzzen, Nathanael B.J. Harper, Hadi A. Dhiyebi, Nivetha Srikanthan, Samina Hayat, Shelley Peterson, Ivy Yang, Jianxian Sun, Elizabeth A. Edwards, John P. Giesy, Chand S. Mangat, Tyson E. Graber, Robert Delatolla, Mark R. Servos

Abstract Wastewater-based surveillance (WBS) has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Quantities of viral fragments of SARS-CoV-2 in wastewater are related to numbers of clinical cases of COVID-19 reported within the corresponding sewershed. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) or sequencing. A multiplex RT-qPCR assay to detect and estimate the prevalence of multiple VOCs, including Omicron/Alpha, Beta, Gamma, and Delta, in wastewater RNA extracts was developed and validated. The probe-based multiplex assay, named “N200” focuses on amino acids 199-202, a region of the N gene that contains several mutations that are associated with variants of SARS- CoV-2 within a single amplicon. Each of the probes in the N200 assay are specific to the targeted mutations and worked equally well in single- and multi-plex modes. To estimate prevalence of each VOC, the abundance of the targeted mutation was compared with a non- mutated region within the same amplified region. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from six sewersheds in Ontario, Canada collected between December 1, 2021, and January 4, 2022. Using the N200 assay, the replacement of the Delta variant along with the introduction and rapid dominance of the Omicron variant were monitored in near real-time, as they occurred nearly simultaneously at all six locations. The N200 assay is robust and efficient for wastewater surveillance can be adopted into VOC monitoring programs or replace more laborious assays currently being used to monitor SARS- CoV-2 and its VOCs.

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Design and Validation of Sample Splitting Protocol for Comparison of SARS-CoV-2 Quantification in Wastewater
Alex H. S. Chik, Jane J. Y. Ho, Nivetha Srikanthan, Hadi A. Dhiyebi, Mark R. Servos
Journal of Environmental Engineering, Volume 148, Issue 8

Evaluations of analytical performance through interlaboratory comparisons and proficiency tests are underway globally for biomolecular-based methods [e.g., reverse-transcription quantitative polymerase chain reaction (RT-qPCR)] used in the surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. These evaluations often rely on sharing a common reference wastewater sample that is split among participating laboratories. A known quantity of recovery surrogates can be introduced to the wastewater matrix by the coordinating laboratory as an exogenous control in a spike-and-recovery approach; however, split-sample comparisons are increasingly performed to evaluate in situ quantities of SARS-CoV-2 genetic signal native to the sample due to the lack of a universally accepted recovery surrogate of SARS-CoV-2. A reproducible procedure that minimizes the variability of SARS-CoV-2 genetic signal among split wastewater aliquots is therefore necessary to facilitate the method comparisons, especially when a large number of aliquots are required. Emerging literature has suggested that SARS-CoV-2 genetic signal in wastewater is linked to the solids fraction. Accordingly, a protocol that allows for equal distribution of solids content evenly among wastewater aliquots was also likely to facilitate even distribution of the SARS-CoV-2 genetic signal. Based on this premise, we reviewed existing sample splitting apparatus and approaches used for solids-based parameters in environmental samples. A portable batch reactor was designed, comprised of readily accessible materials and equipment. This design was validated through splitting of real wastewater samples collected from a municipal wastewater treatment facility serving a population with reported cases of COVID-19. This work applies well-established solid-liquid mixing theory and concepts that are likely unfamiliar to molecular microbiologists and laboratory analysts, providing (1) a prototype adaptable for a range of sample quantities, aliquot sizes, microbial targets, and water matrices; and (2) a pragmatic demonstration of critical considerations for design and validation of a reproducible and effective sample splitting protocol.


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Comparison of approaches to quantify SARS-CoV-2 in wastewater using RT-qPCR: Results and implications from a collaborative inter-laboratory study in Canada
Alex H. S. Chik, Melissa B. Glier, Mark R. Servos, Chand S. Mangat, Xiaoli Pang, Yuanyuan Qiu, Patrick M. D’Aoust, Jean-Baptiste Burnet, Robert Delatolla, Sarah Dorner, Qiudi Geng, John P. Giesy, R. Michael L. McKay, Michael R. Mulvey, Natalie Prystajecky, Nivetha Srikanthan, Yuwei Xie, Bernadette Conant, Steve E. Hrudey
Journal of Environmental Sciences, Volume 107

Detection of SARS-CoV-2 RNA in wastewater is a promising tool for informing public health decisions during the COVID-19 pandemic. However, approaches for its analysis by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) are still far from standardized globally. To characterize inter- and intra-laboratory variability among results when using various methods deployed across Canada, aliquots from a real wastewater sample were spiked with surrogates of SARS-CoV-2 (gamma-radiation inactivated SARS-CoV-2 and human coronavirus strain 229E [HCoV-229E]) at low and high levels then provided "blind" to eight laboratories. Concentration estimates reported by individual laboratories were consistently within a 1.0-log10 range for aliquots of the same spiked condition. All laboratories distinguished between low- and high-spikes for both surrogates. As expected, greater variability was observed in the results amongst laboratories than within individual laboratories, but SARS-CoV-2 RNA concentration estimates for each spiked condition remained mostly within 1.0-log10 ranges. The no-spike wastewater aliquots provided yielded non-detects or trace levels (<20 gene copies/mL) of SARS-CoV-2 RNA. Detections appear linked to methods that included or focused on the solids fraction of the wastewater matrix and might represent in-situ SARS-CoV-2 to the wastewater sample. HCoV-229E RNA was not detected in the no-spike aliquots. Overall, all methods yielded comparable results at the conditions tested. Partitioning behavior of SARS-CoV-2 and spiked surrogates in wastewater should be considered to evaluate method effectiveness. A consistent method and laboratory to explore wastewater SARS-CoV-2 temporal trends for a given system, with appropriate quality control protocols and documented in adequate detail should succeed.

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Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations
Patrick M. D’Aoust, Tyson E. Graber, Élisabeth Mercier, Danika Montpetit, Ilya Alexandrov, Nafisa Neault, Aiman Tariq Baig, Janice Mayne, Xu Zhang, Tommy Alain, Mark R. Servos, Nivetha Srikanthan, Malcolm R. MacKenzie, Daniel Figeys, Manuel Dujovny, Peter Jüni, Alex MacKenzie, Robert Delatolla
Science of The Total Environment, Volume 770

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 non-discriminating surveillance tool. However, their efficacy in prospectively capturing resurgences 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 h 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 h. 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.