Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay

Erster, Oran; Mendelson, Ella; Kabat, Areej; Levy, Virginia; Mannasse, Batya; Assraf, Hadar; Azar, Roberto; Ali, Yaniv; Bucris, Efrat; Bar-Ilan, Dana; Elul, Michal; Mandelboim, Michal; Sofer, Danit; Fleishon, Shay; Zuckerman, Neta S.; Bar-Or, Itay

doi:10.1128/spectrum.02176-21

Cited by 12 publications

(6 citation statements)

References 27 publications

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“…While sequencing provides complete information on the examined sample, it is expensive, not readily amendable for high throughput, and it is limited by the sample quality. We recently demonstrated that variant-specific PCR can determine SC-2 variant identity in cases of poor sample quality where sequencing fails [41]. Here, we show that variant-specific PCR can be a valuable tool to rapidly identify variant dynamics in WW in a cost-effective manner, which in turn enables a large-scale screening of WW samples to obtain important epidemiological information.…”

Section: Discussionmentioning

confidence: 83%

National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel

Bar-Or

Indenbaum

Weil

et al. 2022

Viruses

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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 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 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 by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, 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, BA.2) and other variants.

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Section: Discussionmentioning

confidence: 83%

National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel

Bar-Or

Indenbaum

Weil

et al. 2022

Viruses

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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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“…The majority of the WWS studies (66/80, 82.5%) included in this review were conducted in resource-rich countries in Europe and North America (Figure 3). Out of the total of 80 studies, 38 (47.5%) were in Europe [4,9,18,23,28,, 28 (35.0%) in North America (20 studies in the US [11,[84][85][86][87][88][89][90][91][92][93][94][95][96][97][98][99][100][101], and 8 studies in Canada [102][103][104][105][106][107][108][109]), 10 studies (12.5%) in Asia [110][111][112][113][114][115][116][117], 2 studies in South America [118,119], and 1 study each were conducted in Africa [120] and Australia [121] (Table S1).…”

Section: Geospatial Distributionmentioning

confidence: 99%

Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

Tiwari

Adhikari

Zhang

et al. 2023

Water

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The emergence of new variants of SARS-CoV-2 associated with varying infectivity, pathogenicity, diagnosis, and effectiveness against treatments challenged the overall management of the COVID-19 pandemic. Wastewater surveillance (WWS), i.e., monitoring COVID-19 infections in communities through detecting viruses in wastewater, was applied to track the emergence and spread of SARS-CoV-2 variants globally. However, there is a lack of comprehensive understanding of the use and effectiveness of WWS for new SARS-CoV-2 variants. Here we systematically reviewed published articles reporting monitoring of different SARS-CoV-2 variants in wastewater by following the PRISMA guidelines and provided the current state of the art of this study area. A total of 80 WWS studies were found that reported different monitoring variants of SARS-CoV-2 until November 2022. Most of these studies (66 out of the total 80, 82.5%) were conducted in Europe and North America, i.e., resource-rich countries. There was a high variation in WWS sampling strategy around the world, with composite sampling (50/66 total studies, 76%) as the primary method in resource-rich countries. In contrast, grab sampling was more common (8/14 total studies, 57%) in resource-limited countries. Among detection methods, the reverse transcriptase polymerase chain reaction (RT-PCR)-based sequencing method and quantitative RT-PCR method were commonly used for monitoring SARS-CoV-2 variants in wastewater. Among different variants, the B1.1.7 (Alpha) variant that appeared earlier in the pandemic was the most reported (48/80 total studies), followed by B.1.617.2 (Delta), B.1.351 (Beta), P.1 (Gamma), and others in wastewater. All variants reported in WWS studies followed the same pattern as the clinical reporting within the same timeline, demonstrating that WWS tracked all variants in a timely way when the variants emerged. Thus, wastewater monitoring may be utilized to identify the presence or absence of SARS-CoV-2 and follow the development and transmission of existing and emerging variants. Routine wastewater monitoring is a powerful infectious disease surveillance tool when implemented globally.

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Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay

Cited by 12 publications

References 27 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

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

Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

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