key: cord-0870118-cqlzph10
authors: Hubert, C. R.; Acosta, N.; Waddell, B. J.; Hasing, M. E.; Qiu, Y.; Fuzzen, M.; Harper, N. B.; Bautista, M. A.; Gao, T.; Papparis, C.; Van Doorn, J.; Du, K.; Xiang, K.; Chan, L.; Vivas, L.; Pradhan, P.; McCalder, J.; Low, K.; England, W. E.; Conly, J.; Ryan, M. C.; Achari, G.; Hu, J.; Cabaj, J. L.; Sikora, C.; Svenson, L.; Zelyas, N.; Servos, M.; Meddings, J.; Hrudey, S. E.; Frankowski, K.; Parkins, M. D.; Pang, X.; Lee, B. E.
title: Emergence and Spread of the SARS-CoV-2 Omicron Variant in Alberta Communities Revealed by Wastewater Monitoring
date: 2022-03-10
journal: nan
DOI: 10.1101/2022.03.07.22272055
sha: f04f2862e474bcad302550b05f4616ce80f8c6ee
doc_id: 870118
cord_uid: cqlzph10

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.

The COVID-19 pandemic has led to rapid scientific progress in wastewater-based surveillance Medema et al. 2020; Nemudryi et al. 2020; Randazzo et al. 2020) . Sampling, testing 75 and rapidly reporting wastewater virus RNA levels provides early warning of the population-wide 76 disease burden to policy makers, health officials and the public, enabling evidence-based 77 decision making for preparedness and disease control.

On November 24, 2021, South Africa first reported the emergence of a novel SARS-CoV-2 80 variant associated with rapid community transmission in the Gauteng province (WHO, 2021) . By

November 26 th the World Health Organization had labelled Omicron as a new variant of concern 82 (VOC). Omicron was subsequently rapidly identified in countries around the world, including in 83 Canada where on November 28 th cases were detected in inbound international travellers.

Alberta's first case of Omicron from clinical specimen testing was confirmed on November 30.

By December and into January this virus had spread rapidly throughout large and smaller 86 communities, prompting re-introduction of public health restrictions.

Wastewater testing can also differentiate changes in disease burden caused by different VOCs 89 in communities (Lee et al. 2021 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 qPCR screening of RNA extracted from wastewater that can provide accurate data on VOCs at 98 a fraction of the cost, and in near-real time. In Alberta wastewater is sampled, processed and 99 analyzed in university laboratories in Calgary and Edmonton, and reported to health officials and 100 online to the public two days after sampling. In this study, variant-specific PCR assays were 101 employed to assess the emergence and temporal change in prevalence of the Omicron and 

Wastewater was collected from municipal WWTPs across the province as 24-h composite 111 samples up to 3 times per week. RNA was isolated from wastewater using either affinity binding Omicron-to-Delta ratio to be estimated in each wastewater sample using the Omicron signal 128 (R203K-G204R assay) and the Delta signal (R203M assay). This allowed the emergence and 129 prevalence of Omicron to be tracked at the population level throughout the province.

The daily number of new cases of COVID-19 clinically diagnosed across the province were 132 collected from Data Analytics of Alberta Health Services, and are reported using a 7-day rolling 133 average.

Wastewater separation, identification and quantification of SARS-CoV-2 is intrinsically more 138 complicated than conducting the same PCR strategy on clinical samples (i.e., nasopharyngeal 139 swabs). It is not normally recommended that results be directly compared between different 140 WWTPs, due to intrinsic heterogeneities, e.g., physiochemical differences manifesting different 141 PCR inhibition potential, different proportions of urban, industrial and agricultural inputs, and 142 different flow rates and distances impacting signal degradation (Pecson et al. 2021) . While 143 these limitations apply to total SARS-CoV-2 quantification, they are mitigated when determining 144 Omicron-to-Delta ratios within the same multiplex RT-qPCR reaction, since RNA genomes 145 derived from either variant are expected to react similarly to the factors mentioned above. Table S1 ). In Calgary, four 150 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101/2022.03.07.22272055 doi: medRxiv preprint consecutive samples collected during December 5-9 revealed the sustained presence of 3-9%

Omicron (compared to >90% Delta) among infected individuals contributing to the sewershed in 152 this cosmopolitan city of 1.3 million people. Omicron was first detected in wastewater in the 153 capital city of Edmonton (pop. 1.1 million) on December 10 th (15% Omicron; 85% Delta). The 154 rate of increase of Omicron in the international resort town of Banff was higher than in larger 155 cities such as Calgary and Edmonton (Fig. 1) and surpassed 80% in thrice weekly samples 156 taken during December 20-23. By this time, Calgary and Edmonton had just surpassed 50%, 157 and the proportion of Omicron infections was growing in smaller bedroom communities adjacent 158 to these two large urban centres (e.g., Okotoks, High River, Strathmore and especially Airdrie, 159 which are all <70 km away from Calgary; Fig. 1, Fig. S2 ). Communities that experienced the 160 most delayed emergence of Omicron were smaller and more remote, with Brooks (pop. 14,451; 

More remote communities located a greater distance away from Alberta's large international 181 airports exhibited later emergence of the Omicron variant ( Fig. 1; Fig. S2 ). The Calgary 

Wastewater results also demonstrate that the emergence of Omicron was the driver of clinical 197 cases increasing in December and January during Alberta's 5 th wave (grey shaded area in Fig.   198 1A, B). During this time COVID-19 public health surveillance shifted to focus PCR testing on 199 patients at risk for severe illness and eligible for early treatment, patients presenting to 200 emergency wards with more serious illness, and essential workers (AHS, 2022) . This resulted in 201 PCR testing dramatically underestimating total disease burden in the population as a whole 202 relative to earlier waves. Clinical cases that were reported still show a steep increase after the 203 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 10, 2022. 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101/2022.03.07.22272055 doi: medRxiv preprint 256 b wastewater samples processed using the ultrafiltration method 257 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 258 259 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 267 268 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

Alberta Health (2022) Covid-19 Alberta Statistics. Government of Alberta 305 https://www.alberta.ca/stats/covid-19-alberta-statistics.htm#variants-of-concern. Accessed 306 February, 2022.

Banff (2022) 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101/2022.03.07.22272055 doi: medRxiv preprint

Near 335 real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in 336 wastewater using an allele-specific primer extension PCR strategy

Evaluating social and spatial inequalities of large scale rapid lateral flow 341

SARS-CoV-2 antigen testing in COVID-19 management: An observational study of 342

The Lancet Regional Health Europe

1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR

Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic 353 Variants of SARS-CoV-2 in Municipal Wastewater

Coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the 357 early stage of the epidemic in the Netherlands

Show us 362 the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps

Temporal detection and phylogenetic assessment of 367 SARS-CoV-2 in municipal wastewater

Reproducibility and sensitivity of 36 372 methods toquantify the SARS-CoV-2 genetic signal in rawwastewater: findings from an 373 interlaboratorymethods evaluation in the U

Spatial and temporal 378 distribution of SARS-CoV-2 diversity circulating in wastewater

CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 associated with variants of concern in Canadian wastewater samples. 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted March 10, 2022. ; https://doi.org/10.1101/2022.03.07.22272055 doi: medRxiv preprint