Elizabeth Renouf’s research while affiliated with University of Ottawa and other places

The recent global resurgence of measles in 2023–2024, despite vaccine preventability, underscores a critical public health issue, largely due to reduced vaccination coverage during the SARS-CoV-2 pandemic. In response, Ottawa Public Health intensified vaccination efforts in 2023 and 2024. Additionally, a research initiative began in April 2024 to monitor Ottawa wastewater for measles virus (MeV) using established wastewater and environmental surveillance (WES) protocols. Unexpected positive MeV detections through RT-qPCR in Ottawa wastewater—despite no active regional cases—prompted genotypic and retrospective analyses of archived RNA samples dating back to 2020. The genotypic analysis identified positive detection to belong to genotype A, the progenitor strain of the viral vaccines, marking the first report of MeV vaccine RNA in a large catchment area. Linear regression analysis revealed detections aligned with intensified vaccination efforts by Ottawa Public Health. These findings emphasize the importance of integrating genotypic analysis into WES practices to mitigate possible confounding factors, such as vaccine shedding into wastewater. Additionally, this research highlights potential public health applications using MeV WES as a complementary tool. Implementing the findings of this study for MeV WES, and for other re-emerging viruses, could improve public health response and resource allocation.

Background The emergence of COVID-19 in Canada prompted extensive efforts in population-wide surveillance, including wastewater-based surveillance (WBS). WBS offers insights into the prevalence of infectious disease burden, however, reasons for poor correlation between hospital admissions and wastewater viral signal in some locations across Ontario remain unclear, while others demonstrate remarkable correlations. This study aims to elucidate the parameters influencing hospitalization-WBS correlation quality to guide infectious disease research and surveillance.Figure 1:Geographic overview of sampling locations in Ontario, Canada Methods Wastewater viral signals and daily hospital admissions geospatially linked with the surveyed sewersheds, were obtained from the Ontario Wastewater Surveillance Initiative. The study included 94 sampling sites (Figure 1), excluding those with inadequate sampling frequency. Spearman’s rank correlation coefficient (ρ) was calculated between hospital admissions and wastewater signals for all included sites during the Omicron BA.1 and BA.2 waves from Nov. 1st,2021 to Jun. 30th, 2022. Regression trees were constructed using the R packages “rpart” and “rpart.plot” to identify factors influencing hospitalization-WBS ρ, including population size, hospital admissions range, proportion of zero admissions, and site isolation status.Figure 2:Regression trees representing a classification model for evaluating the correlation quality between hospitalizations and wastewater signal during the Omicron BA.1 wave – coinciding with a period of waned vaccination immunity (A) and the Omicron BA.2 wave – coinciding with a period of significant vaccination immunity (B). Results Regression tree analysis identified critical population size thresholds influencing hospitalization-WBS ρ: populations under 66,000 exhibited weaker ρ (ρ > 0.650) during Omicron BA.1, and under 187,000 during the BA.2 wave (Figure 3). Larger population areas exhibited stronger hospitalization-WBS ρ, suggesting both are reliable infectious disease burden indicators, influenced by differences in community immunity dynamics between the two waves. Conclusion Populations under 66,000 during a period of waned vaccine immunity and under 187,000 during a period of significant vaccine immunity exhibit distinct relationship between hospital admissions and wastewater signals. These thresholds mark key sizes of communities where the efficacy of wastewater surveillance becomes more pronounced, emphasizing its utility in smaller populations where clinical surveillance of infectious diseases may be limited. Disclosures All Authors: No reported disclosures

Background Coronavirus disease (COVID-19) quickly spread around the world after its initial identification in Wuhan, China in 2019 and became a global public health crisis. COVID-19 related hospitalizations and deaths as important disease outcomes have been investigated by many studies while less attention has been given to the relationship between these two outcomes at a public health unit level. In this study, we aim to establish the relationship of counts of deaths and hospitalizations caused by COVID-19 over time across 34 public health units in Ontario, Canada, taking demographic, geographic, socio-economic, and vaccination variables into account. Methods We analyzed daily data of the 34 health units in Ontario between March 1, 2020 and June 30, 2022. Associations between numbers of COVID-19 related deaths and hospitalizations were explored over three subperiods according to the availability of vaccines and the dominance of the Omicron variant in Ontario. A generalized additive model (GAM) was fit in each subperiod. Heterogeneity across public health units was formulated via a random intercept in each of the models. Results Mean daily COVID-19 deaths increased quickly as daily hospitalizations increased, particularly when daily hospitalizations were less than 20. In all the subperiods, mean daily deaths of a public health unit was significantly associated with its population size and the proportion of confirmed cases in subjects over 60 years old. The proportion of fully vaccinated (2 doses of primary series) people in the 60 + age group was a significant factor after the availability of the COVID-19 vaccines. The deprivation index, a measure of poverty, had a significantly positive effect on COVID-19 mortality after the dominance of the Omicron variant in Ontario. Quantification of these effects was provided, including effects related to public health units. Conclusions The differences in COVID-19 mortality across health units decreased over time, after adjustment for other covariates. In the last subperiod when most public health protections were released and the Omicron variant dominated, the least advantaged group might suffer higher COVID-19 mortality. Interventions such as paid sick days and cleaner indoor air should be made available to counter lifting of health protections.

Three new probe-based quantitative PCR assays were designed based on Chae et al . (2017), Pérez-Osorio et al. (2012), and Sales et al . (2012) to quantitate Mycobacterium tuberculosis complex (MTBC) species, M. tuberculosis (MTB), and M. bovis (MB) in wastewater targeting genomic regions rv0577, RD9, and the deletion of RD4, respectively. The assays were validated for specificity using four Mycobacterial species, including two MTBC species and two non-tuberculosis Mycobacteria species, and endogenous wastewater samples from Ottawa, Ontario, Canada, Mumbai, India, and a remote Northern Indigenous community in Nunangat with known ongoing tuberculosis cases or outbreaks. The three assays demonstrate high sensitivity and are suitable for use in wastewater. Partitioning experiments performed on endogenous MTBC and MTB in collected wastewaters from Mumbai, India with known tuberculosis outbreaks show that the targeted genomic regions of rv0577 (MTBC) and RD9 (MTB) used to quantitate human tuberculosis infection predominately partition to solids fraction of wastewaters. The partitioning results of this study, in combination with the presented probe-based PCR assays, provide guidance on how to best enrich wastewaters and rapidly and economically quantify tuberculosis with high specificity and sensitivity in wastewaters. GRAPHICAL ABSTRACT

The recent global resurgence of measles in 2023-2024, despite its preventability through vaccination, is a significant public health concern largely driven by decreased vaccination coverage during the SARS-CoV-2 pandemic. To address this resurgence and to restore vaccine coverage disrupted by the pandemic, Ottawa Public Health intensified vaccination efforts in 2023 and 2024. Additionally, a research initiative began in April 2024 to monitor Ottawa wastewater for measles virus (MeV) using established wastewater and environmental surveillance (WES) protocols. Given the absence of active measles cases in the Ottawa region, unexpected positive MeV detections through RT-qPCR prompted genotypic analysis as well as retrospective analysis of archived RNA samples dating back to 2020. The genotypic analysis identified positive detection to belong to genotype A, the progenitor strain of the viral vaccines, marking the first report of MeV RNA and MeV vaccine shedding in North American wastewater. Positive detections in both real-time and retrospectively analysed samples coincided with the increased vaccination efforts by Ottawa Public Health. These finding emphasize the importance of integrating genotypic analysis into WES practices to mitigate possible confounding factors, such as vaccine shedding into wastewater. Additionally, this research highlights the potential application of MeV WES for monitoring community immunization efforts in real time. Implementing the findings of this study for MeV WES, as well as for other re-emerging viruses, will enhance the accuracy of public health response and optimize resource allocation.

This study presents a comprehensive analysis of the decay patterns of endogenous SARS-CoV-2 and Pepper mild mottle virus (PMMoV) within wastewaters spiked with stool from infected patients expressing COVID-19 symptoms, and hence explores the decay of endogenous SARS-CoV-2 and PMMoV targets in wastewaters from source to collection of the sample. Stool samples from infected patients were used as endogenous viral material to more accurately mirror real-world decay processes compared to more traditionally used lab-propagated spike-ins. As such, this study includes data on early decay stages of endogenous viral targets in wastewaters that are typically overlooked when performing decay studies on wastewaters harvested from wastewater treatment plants that contain already-degraded endogenous material. The two distinct sewer transport conditions of dynamic suspended sewer transport and bed and near-bed sewer transport were simulated in this study at temperatures of 4°C, 12°C and 20°C to elucidate decay under these two dominant transport conditions within wastewater infrastructure. The dynamic suspended sewer transport was simulated over 35 hours, representing typical flow conditions, whereas bed and near-bed transport extended to 60 days to reflect the prolonged settling of solids in sewer systems during reduced flow periods. In dynamic suspended sewer transport, no decay was observed for SARS-CoV-2, PMMoV, or total RNA over the 35-hour period, and temperature ranging from 4°C to 20°C had no noticeable effect. Conversely, experiments simulating bed and near-bed transport conditions revealed significant decreases in SARS-CoV-2 and total RNA concentrations by day 2, and PMMoV concentrations by day 3. Only PMMoV exhibited a clear trend of increasing decay constant with higher temperatures, suggesting that while temperature influences decay dynamics, its impact may be less significant than previously assumed, particularly for endogenous RNA that is bound to dissolved organic matter in wastewater. First order decay models were inadequate for accurately fitting decay curves of SARS-CoV-2, PMMoV, and total RNA in bed and near-bed transport conditions. F-tests confirmed the superior fit of the two-phase decay model compared to first order decay models across temperatures of 4°C to 20°C. Finally, and most importantly, total RNA normalization emerged as an appropriate approach for correcting the time decay of SARS-CoV-2 exposed to bed and near-bed transport conditions. These findings highlight the importance of considering decay from the point of entry in the sewers, sewer transport conditions, and normalization strategies when assessing and modelling the impact of viral decay rates in wastewater systems. This study also emphasizes the need for ongoing research into the diverse and multifaceted factors that influence these decay rates, which is crucial for accurate public health monitoring and response strategies.