@article {269, title = {Identification of environmental and methodological factors driving variability of Pepper Mild Mottle Virus (PMMoV) across three wastewater treatment plants in the City of Toronto.}, journal = {Sci Total Environ}, volume = {932}, year = {2024}, month = {2024 Jul 01}, pages = {172917}, abstract = {

PMMoV has been widely used to normalize the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, influenza, and respiratory syncytial virus (RSV) to account for variations in the fecal content of wastewater. PMMoV is also used as an internal RNA recovery control for wastewater-based epidemiology (WBE) tests. While potentially useful for the interpretation of WBE data, previous studies have suggested that PMMoV concentration can be affected by various physico-chemical characteristics of wastewater. There is also the possibility that laboratory methods, particularly the variability in centrifugation steps to remove supernatant from pellets can cause PMMoV variability. The goal of this study is to improve our understanding of the main drivers of PMMoV variability by assessing the relationship between PMMoV concentration, the physico-chemical characteristics of wastewater, and the methodological approach for concentrating wastewater samples. We analyzed 24-hour composite wastewater samples collected from the influent stream of three wastewater treatment plants (WWTPs) located in the City of Toronto, Ontario, Canada. Samples were collected 3 to 5 times per week starting from the beginning of March 2021 to mid-July 2023. The influent flow rate was used to partition the data into wet and dry weather conditions. Physico-chemical characteristics (e.g., total suspended solids (TSS), biological oxygen demand (BOD), alkalinity, electrical conductivity (EC), and ammonia (NH)) of the raw wastewater were measured, and PMMoV was quantified. Spatial and temporal variability of PMMoV was observed throughout the study period. PMMoV concentration was significantly higher during dry weather conditions. Multiple linear regression analysis demonstrates that the number and type of physico-chemical parameters that drive PMMoV variability are site-specific, but overall BOD and alkalinity were the most important predictors. Differences in PMMoV concentration for a single WWTP between two different laboratory methods, along with a weak correlation between pellet mass and TSS using one method may indicate that differences in sample concentration and subjective subsampling bias could alter viral recovery and introduce variability to the data.

}, keywords = {Environmental Monitoring, Ontario, Tobamovirus, Waste Disposal, Fluid, Wastewater}, issn = {1879-1026}, doi = {10.1016/j.scitotenv.2024.172917}, author = {Goitom, Eyerusalem and Ariano, Sarah and Gilbride, Kim and Yang, Minqing Ivy and Edwards, Elizabeth A and Peng, Hui and Dannah, Nora and Farahbakhsh, Farnaz and Hataley, Eden and Sarvi, Hooman and Sun, Jianxian and Waseem, Hassan and Oswald, Claire} } @article {270, title = {Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region.}, journal = {Water Res X}, volume = {22}, year = {2024}, month = {2024 Jan 01}, pages = {100221}, abstract = {

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between the two biomarkers has been noticed by independent studies using these methods since late 2021. The reason is presumed to be due to mutations in regions targeted by the N1 qPCR probe. In this study, we systematically investigated and unequivocally confirmed that the underlying reason for this discrepancy was mutations in the N1 probe target, and that a single mutation could cause a significant drop in signal. We first confirmed the proportion of related mutations in wastewater samples (Jan 2021-Dec 2022) using nested PCR and LC-MS. Based on relative proportions of N1 alleles, we separated the wastewater data into four time periods corresponding to different variant waves: Period I (Alpha and Delta waves with 0 mutation), Period II (BA.1/BA.2 waves with a single mutation found in all Omicron strains), Period III (BA.5.2* wave with two mutations), and Period IV (BQ.1* wave with two mutations). Significantly lower N1 copies relative to N2 copies in samples from Periods II-IV compared to those from Period I was observed in wastewater. To further pinpoint the extent to which each mutation impacted N1 quantification, we compared the qPCR response among different synthetic oligomers with corresponding mutations. This study highlighted the impact of even just one or two mutations on qPCR-based wastewater surveillance of SARS-CoV-2.

}, issn = {2589-9147}, doi = {10.1016/j.wroa.2024.100221}, author = {Sun, Jianxian and Yang, Minqing Ivy and Peng, Jiaxi and Khan, Ismail and Lopez, Jhoselyn Jaramillo and Chan, Ronny and Edwards, Elizabeth A and Peng, Hui} } @article {212, title = {Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities.}, journal = {Sci Total Environ}, year = {2022}, month = {2022 Sep 03}, pages = {158547}, abstract = {

Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-depth analysis and understanding of the metrics derived from WWS is required to interpret and utilize WWS-acquired data effectively (McClary-Gutierrez et al., 2021; O{\textquoteright}Keeffe, 2021). In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven cities in Canada over periods ranging from 8 to 21 months. This work demonstrates that significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing (resulting in a reduction to testing access and a reduction in the number of daily tests) in these communities, despite increases in the wastewater signal. Furthermore, the WC ratio decreased significantly in 6 of the 7 studied locations, serving as a potential signal of the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community (40-60 \% allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community (40-60 \% allelic proportion). Finally, a significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant{\textquoteright}s greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when community immunity was high. The WC ratio, used as an additional monitoring metric, could complement clinical case counts and wastewater signals as individual metrics in its potential ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.

}, issn = {1879-1026}, doi = {10.1016/j.scitotenv.2022.158547}, author = {D{\textquoteright}Aoust, Patrick M and Tian, Xin and Towhid, Syeda Tasneem and Xiao, Amy and Mercier, Elisabeth and Hegazy, Nada and Jia, Jian-Jun and Wan, Shen and Kabir, Md Pervez and Fang, Wanting and Fuzzen, Meghan and Hasing, Maria and Yang, Minqing Ivy and Sun, Jianxian and Plaza-Diaz, Julio and Zhang, Zhihao and Cowan, Aaron and Eid, Walaa and Stephenson, Sean and Servos, Mark R and Wade, Matthew J and MacKenzie, Alex E and Peng, Hui and Edwards, Elizabeth A and Pang, Xiao-Li and Alm, Eric J and Graber, Tyson E and Delatolla, Robert} }