Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern

Zelyas, Nathan; Wong, Anita; Croxen, Matthew A.; Lynch, Tarah; Buss, Emily; Murphy, Stephanie A.; Shokoples, Sandy; Kanji, Jamil N

doi:10.1016/j.jviromet.2022.114553

Cited by 10 publications

(10 citation statements)

References 35 publications

(31 reference statements)

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“…A total of 897 wastewater samples collected were tested using the Beta-specific RT-qPCR assay but none of the samples tested positive for this VOC. Beta was undetectable by RT-qPCR in wastewater despite confirmed clinical cases of Beta being reported between January 2021 and July 2021 [ 26 , 27 ], corresponding from the end of 2nd to the beginning of 4th wave. The non-detection of Beta in wastewater was most likely because of a scant number of Beta cases in the province that reached a transient maximum detection rate of 5% until the end of July 2021 [ 26 ].…”

Section: Resultsmentioning

confidence: 99%

Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19

Hasing

Lee

Gao

et al. 2023

Emerging Microbes & Infections

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Wastewater-based surveillance is a valuable approach for monitoring COVID-19 at community level. Monitoring SARS-CoV-2 variants of concern (VOC) in wastewater has become increasingly relevant when clinical testing capacity and case-based surveillance are limited. In this study, we ascertained the turnover of six VOC in Alberta wastewater from May 2020 to May 2022. Wastewater samples from nine wastewater treatment plants across Alberta were analysed using VOC-specific RT-qPCR assays. The performance of the RT-qPCR assays in identifying VOC in wastewater was evaluated against next generation sequencing. The relative abundance of each VOC in wastewater was compared to positivity rate in COVID-19 testing. VOC-specific RT-qPCR assays performed comparatively well against next generation sequencing; concordance rates ranged from 89% to 98% for detection of Alpha, Beta, Gamma, Omicron BA.1 and Omicron BA.2, with a slightly lower rate of 85% for Delta ( p < 0.01). Elevated relative abundance of Alpha, Delta, Omicron BA.1 and BA.2 were each associated with increased COVID-19 positivity rate. Alpha, Delta and Omicron BA.2 reached 90% relative abundance in wastewater within 80, 111 and 62 days after their initial detection, respectively. Omicron BA.1 increased more rapidly, reaching a 90% relative abundance in wastewater after 35 days. Our results from VOC surveillance in wastewater correspond with clinical observations that Omicron is the VOC with highest disease burden over the shortest period in Alberta to date. The findings suggest that changes in relative abundance of a VOC in wastewater can be used as a supplementary indicator to track and perhaps predict COVID-19 burden in a population.

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Section: Resultsmentioning

confidence: 99%

Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19

Hasing

Lee

Gao

et al. 2023

Emerging Microbes & Infections

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“…To detect and identify variants of concern, a few studies reported multiple RT-qPCR assays. − Most studies identified a partial list of variants such as Alpha and Delta, Delta, or Omicron . Only one study reported a two-reaction multiplex RT-qPCR genotyping assay to differentiate five variants by examining six different mutations simultaneously.…”

Section: Discussionmentioning

confidence: 99%

Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples

et al. 2023

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The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/ 70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4−16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May−June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.

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“…We collected data on cases linked to outbreaks in childcare facilities using Alberta Health’s COVID-19 dataset that integrates data elements from several systems to provide a comprehensive COVID-19 cases and outbreak dataset. The Provincial Surveillance information system is a laboratory surveillance system that receives results for all notifiable diseases from laboratory surveillance conducted by Alberta Precision Labs (( 24 , 25 )). The communicable disease reporting system and the Communicable Disease Outbreak Management system contain information on COVID-19 cases and the data integration and measurement reporting system contains up-to-date information on people admitted and discharged from hospitals in Alberta (including for cases of multisystem inflammatory syndrome in children [MIS-C]).…”

Section: Methodsmentioning

confidence: 99%

Description of COVID-19 outbreaks in childcare facilities in Alberta, March 2020 to December 31, 2021

Geary¹,

Rudko²,

Scott³

2023

CCDR

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Background Children attending childcare are vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and mitigation measures such as masking, distancing, enhanced hygiene are not feasible for this population. Describing outbreak growth during the coronavirus disease 2019 (COVID-19) pandemic in childcare centres may provide insight into how to best mitigate the risks of COVID-19 and other infectious diseases in these settings. This article describes the childcare outbreaks and associated cases in Alberta at different time periods throughout the pandemic. Methods Our observational analysis used data on outbreaks and associated cases tracked through the Alberta Health Services Communicable Disease Outbreak Management database. We included all COVID-19 outbreaks opened in childcare facilities (March 2020 to December 31, 2021). We compared the characteristics of outbreaks and cases during each wave of the pandemic. Results There were a total of 841 childcare outbreaks, including 4,613 cases (70.2% in children and 29.8% adults). Many characteristics of outbreaks and cases varied across pandemic waves, including attack rates (12.1%–28.7% in adults and 5.8%–16.3% in children), percent of cases in children (56.4%–77.3%), and percent of outbreaks with a child index case (34.0%–70.1%). The overall average cases/outbreak was 5.5 (range: 1–68), and case examples of large outbreaks showed that delaying testing and attending daycare while symptomatic seemed to drive higher transmission. Conclusion Waves had different outbreak and case characteristics, for both adults and children. Transmission may happen more readily among adults and among children than between those two groups. Measures shown to be effective to reduce transmission in other settings can be implemented here, such as vaccination, strictly enforcing the exclusion of those symptomatic, and facilitating rapid testing.

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Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern

Cited by 10 publications

References 35 publications

Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19

Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19

Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples

Description of COVID-19 outbreaks in childcare facilities in Alberta, March 2020 to December 31, 2021

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