Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities

Oloye, Femi Francis; Xie, Yuwei; Asadi, Mohsen; Cantin, Jenna; Challis, Jonathan K.; Brinkmann, Markus; McPhedran, Kerry N.; Kristian, Kevin; Keller, Mark P.; Sadowski, Mike; Jones, Paul D.; Landgraff, Chrystal; Mangat, Chand S.; Fuzzen, Meghan; Servos, Mark R.; Giesy, John P.

doi:10.1016/j.scitotenv.2022.156741

Cited by 33 publications

(22 citation statements)

References 40 publications

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“…Conversely, although this study observed a lower viral load during the Omicron wave as compared to the Delta wave, this has not been universally observed. For example, Oloye et al reported that the total viral load detected by RT-qPCR for 3 Canadian cities showed the Omicron VOC to be 2-fold greater than that observed for the Delta wave [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Johnson

Mangwana

Sharma

et al. 2022

The Journal of Infectious Diseases

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This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation exists between SARS-CoV-2 viral RNA in wastewater samples and clinical cases (r = 0.7749, p < 0.0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven 3rd wave, was significantly higher than during the Omicron-driven 4th wave, p < 0.005. Whole-genome sequencing confirmed the presence of Omicron lineage defining mutations in wastewater with the first occurrence reported on 23 November 2021 (BA.1 predominant). The variant rapidly spread, with the prevalence of Omicron positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sub-lineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. Taken together, these findings demonstrate the value of WBE to monitor the spatiotemporal spread and potential origination of new Omicron sub-lineages of SARS-CoV-2.

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Section: Discussionmentioning

confidence: 99%

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Johnson

Mangwana

Sharma

et al. 2022

The Journal of Infectious Diseases

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“…Furthermore, WBE capability has been recently investigated as an early warning system also for variants of concern (VOCs) occurrence inside a community. Indeed, VOCs are commonly characterized by high transmissibility and virulence/clinical disease presentation interfering with the implemented diagnostic assays and public health measures, as well as the effectiveness of vaccines and therapeutics ( Oloye et al, 2022 ; World Health Organization, 2022 ). When the sequencing capacity of all clinical cases is limited, the monitoring of SARS-CoV-2 infections through WBE could enhance the prompt identification and rapid estimation of virus load also in presence of VOCs complementing the national testing efforts.…”

Section: Side-by-side Comparison Between Covid-19 Surveillance Based ...mentioning

confidence: 99%

“…When the sequencing capacity of all clinical cases is limited, the monitoring of SARS-CoV-2 infections through WBE could enhance the prompt identification and rapid estimation of virus load also in presence of VOCs complementing the national testing efforts. Monitoring studies have pointed out the detection of a specific VOC (e.g., Omicron and Delta) in MWW prior to its recognition through clinical testing ( Chassalevris et al, 2022 ; Oloye et al, 2022 ; Reynolds et al, 2022 ). Specifically, WBE was able to identify the emergence of a variant (Omicron) inside a community (Thessaloniki, Greek city) earlier than its identification via routine surveillance based on clinical samples preceding the first declared Omicron case by approximately 7 days and highlighting the Delta-to-Omicron BA.1 transition patterns ( Chassalevris et al, 2022 ).…”

Section: Side-by-side Comparison Between Covid-19 Surveillance Based ...mentioning

confidence: 99%

Wastewater-based epidemiology approach: The learning lessons from COVID-19 pandemic and the development of novel guidelines for future pandemics

2023

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“…As SARS-CoV-2 mutates, it will have to be seen if WBE will still remain a highly effective tool for campuses, communities, etc. However, to date, WBE has been successful in the detection of many variants (Hrudey & Conant, 2022), including Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron (Hrudey & Conant, 2022;Kirby et al, 2022;Oloye et al, 2022;Sutton et al, 2022;Wolfe et al, 2022). Additionally, this type of wastewater surveillance program may be useful in other ways, namely, in detecting other pathogens and viruses in wastewater such as E. coli or salmonella.…”

Section: Conclusion and Recommendations For Future Workmentioning

confidence: 99%

Implementing wastewater surveillance for SARS‐CoV‐2 on a university campus: Lessons learned

Wartell

Proano

Bakalian

et al. 2022

Water Environment Research

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Wastewater surveillance, also known as wastewater‐based epidemiology (WBE), has been successfully used to detect SARS‐CoV‐2 and other viruses in sewage in many locations in the United States and globally. This includes implementation of the surveillance on college and university campuses. A two‐phase study was conducted during the 2020–2021 academic year to test the feasibility of a WBE system on campus and to supplement the clinical COVID‐19 testing performed for the student, staff, and faculty body. The primary objective during the Fall 2020 semester was to monitor a large portion of the on‐campus population and to obtain an understanding of the spreading of the SARS‐CoV‐2 virus. The Spring 2021 objective was focused on selected residence halls and groups of residents on campus, as this was more efficient and relevant for an effective follow‐up response. Logistical problems and planning oversights initially occurred but were corrected with improved communication and experience. Many lessons were learned, including effective mapping, site planning, communication, personnel organization, and equipment management, and obtained along the way, thereby paving an opportune guide for future planning efforts. Practitioner Points WBE was successful in the detection of many SARS‐CoV‐2 variants incl. Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron. Careful planning and contingencies were essential for a successful implementation of a SARS‐CoV‐2 monitoring program. A surveillance program may be important for detection and monitoring of other public health relevant targets in wastewater incl. bacteria, viruses, fungi and viruses. Diverse lessons were learned incl. effective mapping, site planning, communication, personnel organization, and equipment management, thereby providing a guide for future planning efforts.

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Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities

Cited by 33 publications

References 40 publications

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Wastewater-based epidemiology approach: The learning lessons from COVID-19 pandemic and the development of novel guidelines for future pandemics

Implementing wastewater surveillance for SARS‐CoV‐2 on a university campus: Lessons learned

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