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Community Surveillance of Omicron in Ontario: Wastewater-based Epidemiology Comes of Age.
Authors presented in alphabetical order: | Jos Arts | R. Stephen Brown | David Bulir | Trevor C. Charles | Christopher T. DeGroot | Robert Delatolla | Jean‐Paul Desaulniers | Elizabeth A. Edwards | Meghan Fuzzen | Kimberley Gilbride | Jodi Gilchrist | Lawrence Goodridge | Tyson E. Graber | Marc Habash | Peter Jüni | Andrea E. Kirkwood | James Knockleby | Christopher J. Kyle | Chrystal Landgraff | Chand S. Mangat | Douglas Manuel | R. Michael L. McKay | Edgard M. Mejia | Aleksandra Mloszewska | Banu Örmeci | Claire J. Oswald | Sarah Jane Payne | Hui Peng | Shelley Peterson | Art F. Y. Poon | Mark R. Servos | Denina Simmons | Jianxian Sun | Minqing Ivy Yang | Gustavo Ybazeta

Abstract Wastewater-based surveillance of SARS-CoV-2 RNA has been implemented at building, neighbourhood, and city levels throughout the world. Implementation strategies and analysis methods differ, but they all aim to provide rapid and reliable information about community COVID-19 health states. A viable and sustainable SARS-CoV-2 surveillance network must not only provide reliable and timely information about COVID-19 trends, but also provide for scalability as well as accurate detection of known or unknown emerging variants. Emergence of the SARS-CoV-2 variant of concern Omicron in late Fall 2021 presented an excellent opportunity to benchmark individual and aggregated data outputs of the Ontario Wastewater Surveillance Initiative in Canada; this public health-integrated surveillance network monitors wastewaters from over 10 million people across major population centres of the province. We demonstrate that this coordinated approach provides excellent situational awareness, comparing favourably with traditional clinical surveillance measures. Thus, aggregated datasets compiled from multiple wastewater-based surveillance nodes can provide sufficient sensitivity (i.e., early indication of increasing and decreasing incidence of SARS-CoV-2) and specificity (i.e., allele frequency estimation of emerging variants) with which to make informed public health decisions at regional- and state-levels.

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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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Emergence and Spread of the SARS-CoV-2 Omicron Variant in Alberta Communities Revealed by Wastewater Monitoring
Casey R.J. Hubert | Nicole Acosta | Barbara Waddell | Maria E. Hasing | Yuanyuan Qiu | Meghan Fuzzen | Nathanael B.J. Harper | María A. Bautista | Tiejun Gao | Chloe Papparis | Jenn Van Doorn | Kristine Du | Kevin Xiang | Leslie Chan | Laura Vivas | Puja Pradhan | Janine McCalder | Kashtin Low | Whitney England | John Conly | M. Cathryn Ryan | Gopal Achari | Jia Hu | Jason Cabaj | Chris Sikora | Larry Svenson | Nathan Zelyas | Mark R. Servos | Jon Meddings | Steve E. Hrudey | Kevin J. Frankowski | Michael D. Parkins | Xiaoli Pang | Bonita E. Lee

Abstract Wastewater monitoring of SARS-CoV-2 allows for early detection and monitoring of COVID-19 burden in communities and can track specific variants of concern. Targeted assays enabled relative proportions of SARS-CoV-2 Omicron and Delta variants to be determined across 30 municipalities covering >75% of the province of Alberta (pop. 4.5M) in Canada, from November 2021 to January 2022. Larger cities like Calgary and Edmonton exhibited a more rapid emergence of Omicron relative to smaller and more remote municipalities. Notable exceptions were Banff, a small international resort town, and Fort McMurray, a more remote northern city with a large fly-in worker population. The integrated wastewater signal revealed that the Omicron variant represented close to 100% of SARS-CoV-2 burden prior to the observed increase in newly diagnosed clinical cases throughout Alberta, which peaked two weeks later. These findings demonstrate that wastewater monitoring offers early and reliable population-level results for establishing the extent and spread of emerging pathogens including SARS-CoV-2 variants.

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Early and late cyanobacterial bloomers in a shallow, eutrophic lake
Kristin J. Painter | Jason J. Venkiteswaran | Dana F. Simon | Sung Vo Duy | Sébastien Sauvé | Helen M. Baulch

Cyanobacterial blooms present challenges for water treatment, especially in regions like the Canadian prairies where poor water quality intensifies water treatment issues. Buoyant cyanobacteria that resist sedimentation present a challenge as water treatment operators attempt to balance pre-treatment and toxic disinfection by-products. Here, we used microscopy to identify and describe the succession of cyanobacterial species in Buffalo Pound Lake, a key drinking water supply. We used indicator species analysis to identify temporal grouping structures throughout two sampling seasons from May to October 2018 and 2019. Our findings highlight two key cyanobacterial bloom phases - a mid-summer diazotrophic bloom of Dolichospermum spp. and an autumn Planktothrix agardhii bloom. Dolichospermum crassa and Woronichinia compacta served as indicators of the mid-summer and autumn bloom phases, respectively. Different cyanobacterial metabolites were associated with the distinct bloom phases in both years: toxic microcystins were associated with the mid-summer Dolichospermum bloom and some newly monitored cyanopeptides (anabaenopeptin A and B) with the autumn Planktothrix bloom. Despite forming a significant proportion of the autumn phytoplankton biomass (>60%), the Planktothrix bloom had previously not been detected by sensor or laboratory-derived chlorophyll-a. Our results demonstrate the power of targeted taxonomic identification of key species as a tool for managers of bloom-prone systems. Moreover, we describe an autumn Planktothrix agardhii bloom that has the potential to disrupt water treatment due to its evasion of detection. Our findings highlight the importance of identifying this autumn bloom given the expectation that warmer temperatures and a longer ice-free season will become the norm.

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Challenges in hydrologic-land surface modelling of permafrost signatures - Impacts of parameterization on model fidelity under the uncertainty of forcing
Mohamed S. Abdelhamed | Mohamed Elshamy | Saman Razavi | H. S. Wheater

Permafrost plays an important role in the hydrology of arctic/subarctic regions. However, permafrost thaw/degradation has been observed over recent decades in the Northern Hemisphere and is projected to accelerate. Hence, understanding the evolution of permafrost areas is urgently needed. Land surface models (LSMs) are well-suited for predicting permafrost dynamics due to their physical basis and large-scale applicability. However, LSM application is challenging because of the large number of model parameters and the complex memory of state variables. Significant interactions among the underlying processes and the paucity of observations of thermal/hydraulic regimes add further difficulty. This study addresses the challenges of LSM application by evaluating the uncertainty due to meteorological forcing, assessing the sensitivity of simulated permafrost dynamics to LSM parameters, and highlighting issues of parameter identifiability. Modelling experiments are implemented using the MESH-CLASS framework. The VARS sensitivity analysis and traditional threshold-based identifiability analysis are used to assess various aspects of permafrost dynamics for three regions within the Mackenzie River Basin. The study shows that the modeller may face significant trade-offs when choosing a forcing dataset as some datasets enable the representation of some aspects of permafrost dynamics, while being inadequate for others. The results also emphasize the high sensitivity of various aspects of permafrost simulation to parameters controlling surface insulation and soil texture; a detailed list of influential parameters is presented. Identifiability analysis reveals that many of the most influential parameters for permafrost simulation are unidentifiable. These conclusions will hopefully inform future efforts in data collection and model parametrization.

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Significant underestimation of peatland permafrost along the Labrador Sea coastline
Yifeng Wang | Robert G. Way | Jordan Beer | Anika Forget | Rosamond Tutton | Meredith C. Purcell

Abstract. Northern peatlands cover approximately four million km2, and about half of these peatlands are estimated to contain permafrost and periglacial landforms, like palsas and peat plateaux. In northeastern Canada, peatland permafrost is predicted to be spatially concentrated in the western interior of Labrador and largely absent along the Labrador Sea and Gulf of St. Lawrence coastline. However, the paucity of observations of peatland permafrost in the interior coupled with ongoing use of perennially frozen peatlands along the coast by Labrador Inuit and Innu cast doubt on the reliability of existing maps of peatland permafrost distribution in the region. In this study, we develop a multi-stage consensus-based inventory of peatland permafrost complexes in coastal Labrador and adjacent parts of Quebec using high-resolution satellite imagery and validate it with extensive field visits and low-altitude aerial photography and videography. A total of 1885 wetland complexes were inventoried, of which 1023 were interpreted as likely containing peatland permafrost. Likely peatland permafrost complexes were mostly found in lowlands within 40 km of the coastline where mean annual air temperatures of up to +1.2 °C are recorded. Evaluation of the geographic distribution of peatland permafrost complexes reveals a clear gradient from the outer coasts, where peatland permafrost is more abundant, to inland peatlands, where permafrost is generally absent. This coastal gradient may be attributed to a combination of climatic and geomorphological influences which lead to lower insolation, thinner snowpacks, and more frost-susceptible materials along the coast. The results of this study also suggest that existing maps of permafrost distribution for southeastern Labrador require adjustment to better reflect the abundance of peatland permafrost complexes which are located to the south of the regional sporadic discontinuous permafrost limit. This study constitutes the first dedicated peatland permafrost inventory for Labrador, and our results provide an important baseline for future mapping, modelling, and climate change adaptation strategy development in the region.

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Evaluating a reservoir parametrisation in the vector-based global routing model mizuRoute (v2.0.1) for Earth System Model coupling
Inne Vanderkelen | Shervan Gharari | Naoki Mizukami | Martyn P. Clark | David M. Lawrence | Sean Swenson | Yadu Pokhrel | Naota Hanasaki | Ann van Griensven | Wim Thiery

Abstract. Human-controlled reservoirs have a large influence on the global water cycle. While global hydrological models use generic parametrisations to model human dam operations, the representation of reservoir regulation is often still lacking in Earth System Models. Here we implement and evaluate a widely used reservoir parametrisation in the global river routing model mizuRoute, which operates on a vector-based river network resolving individual lakes and reservoirs, and which is currently being coupled to an Earth System Model. We develop an approach to determine the downstream area over which to aggregate irrigation water demand per reservoir. The implementation of managed reservoirs is evaluated by comparing to simulations ignoring inland waters, and simulations with reservoirs represented as natural lakes, using (i) local simulations for 26 individual reservoirs driven by observed inflows, and (ii) global-scale simulations driven by runoff from the Community Land Model. The local simulations show a clear added value of the reservoir parametrisation, especially for simulating storage for large reservoirs with a multi-year storage capacity. In the global-scale application, the implementation of reservoirs shows an improvement in outflow and storage compared to the no-reservoir simulation, but compared to the natural lake parametrisation, an overall similar performance is found. This lack of impact could be attributed to biases in simulated river discharge, mainly originating from biases in simulated runoff from the Community Land Model. Finally, the comparison of modelled monthly streamflow indices against observations highlights that the inclusion of dam operations improves the streamflow simulation compared to ignoring lakes and reservoirs. This study overall underlines the need to further develop and test water management parametrisations, as well as to improve runoff simulations for advancing the representation of anthropogenic interference with the terrestrial water cycle in Earth System Models.

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Burned Area and Carbon Emissions Across Northwestern Boreal North America from 2001–2019
Stefano Potter | S. Cooperdock | Sander Veraverbeke | Xanthe J. Walker | Michelle C. Mack | Scott J. Goetz | Jennifer L. Baltzer | L. L. Bourgeau-Chavez | Arden Burrell | Catherine M. Dieleman | Nancy H. F. French | Stijn Hantson | Elizabeth Hoy | Liza K. Jenkins | Jill F. Johnstone | Evan S. Kane | Susan M. Natali | James T. Randerson | M. R. Turetsky | Ellen Whitman | Elizabeth B. Wiggins | Brendan M. Rogers

Abstract. Fire is the dominant disturbance agent in Alaskan and Canadian boreal ecosystems and releases large amounts of carbon into the atmosphere. Burned area and carbon emissions have been increasing with climate change, which have the potential to alter the carbon balance and shift the region from a historic sink to a source. It is therefore critically important to track the spatiotemporal changes in burned area and fire carbon emissions over time. Here we developed a new burned area detection algorithm between 2001–2019 across Alaska and Canada at 500 meters (m) resolution that utilizes finer-scale 30 m Landsat imagery to account for land cover unsuitable for burning. This method strictly balances omission and commission errors at 500 m to derive accurate landscape- and regional-scale burned area estimates. Using this new burned area product, we developed statistical models to predict burn depth and carbon combustion for the same period within the NASA Arctic-Boreal Vulnerability Experiment (ABoVE) core and extended domain. Statistical models were constrained using a database of field observations across the domain and were related to a variety of response variables including remotely-sensed indicators of fire severity, fire weather indices, local climate, soils, and topographic indicators. The burn depth and aboveground combustion models performed best, with poorer performance for belowground combustion. We estimate 2.37 million hectares (Mha) burned annually between 2001–2019 over the ABoVE domain (2.87 Mha across all of Alaska and Canada), emitting 79.3 +/- 27.96 (+/- 1 standard deviation) Teragrams of carbon (C) per year, with a mean combustion rate of 3.13 +/- 1.17 kilograms C m-2. Mean combustion and burn depth displayed a general gradient of higher severity in the northwestern portion of the domain to lower severity in the south and east. We also found larger fire years and later season burning were generally associated with greater mean combustion. Our estimates are generally consistent with previous efforts to quantify burned area, fire carbon emissions, and their drivers in regions within boreal North America; however, we generally estimate higher burned area and carbon emissions due to our use of Landsat imagery, greater availability of field observations, and improvements in modeling. The burned area and combustion data sets described here (the ABoVE Fire Emissions Database, or ABoVE-FED) can be used for local to continental-scale applications of boreal fire science.

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Mapping snow depth over lake ice in Canada’s sub-arctic using ground-penetrating radar
Alicia Pouw | Homa Kheyrollah Pour | A. A. MacLean

Abstract. Ice thickness across lake ice is influenced mainly by the presence of snow and its distribution, as it directly impacts the rate of lake ice growth. The spatial distribution of snow depth over lake ice varies and is driven by wind redistribution and snowpack metamorphism, creating variability in the lake ice thickness. The accuracy and consistency of snow depth measurement data on lake ice are challenging and sparse to obtain. However, high spatial resolution lake snow depth observations are necessary for the next generation of thermodynamic lake ice models. Such information is required to improve the knowledge and understanding of snow depth distribution over lake ice. This study maps snow depth distribution over lake ice using ground-penetrating radar (GPR) two-way travel-time (TWT) with ~9 cm spatial resolution along transects totalling ~44 km over four freshwater lakes in Canada’s sub-arctic. The accuracy of the snow depth retrieval is assessed using in situ snow depth observations (n =2,430). On average, the snow depth derived from GPR TWTs for the early winter season is estimated with a root mean square error (RMSE) of 1.58 cm and a mean bias error of -0.01 cm. For the late winter season on a deeper snowpack, the accuracy is estimated with RMSE of 2.86 cm and a mean bias error of 0.41 cm. The GPR-derived snow depths are interpolated to create 1 m spatial resolution snow depth maps. Overall, this study improved lake snow depth retrieval accuracy and introduced a fast and efficient method to obtain high spatial resolution snow depth information, which is essential for the lake ice modelling community.