RT-qPCR detection of SARS-CoV-2 mutations S 69–70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples

Peterson, Shelley; Lidder, Ravinder; Daigle, Jade; Wonitowy, Quinn; Dueck, Codey; Nagasawa, Audra; Mulvey, Michael R.; Mangat, Chand S.

doi:10.1016/j.scitotenv.2021.151283

Cited by 50 publications

(51 citation statements)

References 21 publications

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“…Some recent studies of SC-2 variants surveillance relied on the use of genomic sequencing or PCR detection of mutations that are not specific to a particular variant 31,32 . Other studies describe environmental surveillance using a combination of variant-specific and variant-nonspecific reactions 33,34 . Peterson et al 34 describe the use of six reactions to indicate the presence of alpha, beta (B.1.351) or gamma (P1) variant, but not distinguish between them.…”

Section: Discussionmentioning

confidence: 99%

“…Other studies describe environmental surveillance using a combination of variant-specific and variant-nonspecific reactions 33,34 . Peterson et al 34 describe the use of six reactions to indicate the presence of alpha, beta (B.1.351) or gamma (P1) variant, but not distinguish between them. The authors examined WW from five major cities, as well as rural communities, determining the prevalence of the three mutations in each site.…”

Section: Discussionmentioning

confidence: 99%

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National Scale Real-Time Surveillance of Sars-Cov-2 Variants Dynamics by Wastewater Monitoring in Israel

Bar-Or

Indenbaum

Weil³

et al. 2021

Preprint

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In this report, we describe a national-scale monitoring of the SARS-COV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of twelve wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December-2020 and March-2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021, and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February-March 2021. This study demonstrates the importance of monitoring SC-2 variant dynamics on a national scale through wastewater sampling. It also provides a proof-of-concept methodology for continuous surveillance by using a combination of inclusive and selective PCR tests, which is far more amendable for high throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1) variant.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

National Scale Real-Time Surveillance of Sars-Cov-2 Variants Dynamics by Wastewater Monitoring in Israel

Bar-Or

Indenbaum

Weil³

et al. 2021

Preprint

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“…Results from the PHAC-NML assay were consistent with the data produced by GeneXpert. As part of the laboratory-developed assay, information is also provided on the variants present in the wastewater sample ( 31 ). PHAC-NML reported B.1.1.7 (alpha variant) as the majority variant present in Yellowknife wastewater.…”

Section: Resultsmentioning

confidence: 99%

“…PHAC-NML has protocols to process both the supernatant and solid fractions of wastewater ( 31 ). Samples received from Northwest Territories and Vancouver underwent both the supernatant and solids processing methods, while only the solids were processed for samples received from Toronto, Montreal, Edmonton, and Halifax wastewater treatment plants as per the preferences of these communities.…”

Section: Methodsmentioning

confidence: 99%

A Sensitive and Rapid Wastewater Test for SARS-COV-2 and Its Use for the Early Detection of a Cluster of Cases in a Remote Community

Daigle

Racher

Hazenberg

et al. 2022

Appl Environ Microbiol

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Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories. Importance: Wastewater-based surveillance is a powerful tool that provides an unbiased measure of COVID-19 prevalence in a community. This work describes a sensitive wastewater rapid test for SARS-CoV-2 based on a widely distributed technology, the GeneXpert. The advantages of an easy-to-use wastewater test for SARS-CoV-2 are clear – it supports surveillance in remote communities, improves access to testing, and provides faster results allowing for an immediate public health response. The application of wastewater rapid testing in a remote community facilitated the detection of a COVID-19 cluster and triggered public health action, clearly demonstrating the utility of this technology. Wastewater surveillance will become increasingly important in the post-vaccination pandemic landscape as individuals with asymptomatic/mild infections continue transmitting SARS-CoV-2 but are unlikely to be tested.

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“…This bioanalytical approach was applied to IWW samples from different locations in Belgium to retrospectively monitor the emergence of each VOC at a population scale. To our knowledge, most pre-existing WBE applications on SARS-CoV-2 variants mainly focus on sequencing [ 29 , 34 , 35 , 36 , 37 ] and RT-qPCR [ 26 , 28 , 38 , 39 ]. Only a limited number of studies have applied dPCR to estimate the VOC circulation in IWW [ 25 , 27 , 40 , 41 ].…”

Section: Introductionmentioning

confidence: 99%

Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater

Boogaerts

Bogaert

Poelvoorde

et al. 2022

Viruses

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Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase chain reaction (dPCR) assay was optimized, validated and applied for the measurement of emerging SARS-CoV-2 variants of concern (VOC) in influent wastewater (IWW) samples. Key mutations were targeted in the different VOC strains, including SΔ69/70 deletion, N501Y, SΔ241 and SΔ157. The presented bioanalytical method was able to distinguish between SARS-CoV-2 RNA originating from the wild-type and B.1.1.7, B.1.351 and B.1.617.2 variants. The dPCR assay proved to be sensitive enough to detect low concentrations of SARS-CoV-2 RNA in IWW since the limit of detection of the different targets ranged between 0.3 and 2.9 copies/µL. This developed WBE approach was applied to IWW samples originating from different Belgian locations and was able to monitor spatio-temporal changes in the presence of targeted VOC strains in the investigated communities. The present dPCR assay developments were realized to bring added-value to the current national WBE of COVID-19 by also having the spatio-temporal proportions of the VoC in presence in the wastewaters.

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RT-qPCR detection of SARS-CoV-2 mutations S 69–70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples

Cited by 50 publications

References 21 publications

National Scale Real-Time Surveillance of Sars-Cov-2 Variants Dynamics by Wastewater Monitoring in Israel

National Scale Real-Time Surveillance of Sars-Cov-2 Variants Dynamics by Wastewater Monitoring in Israel

A Sensitive and Rapid Wastewater Test for SARS-COV-2 and Its Use for the Early Detection of a Cluster of Cases in a Remote Community

Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater

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