Quantitative detection of SARS-CoV-2 B.1.1.7 variant in wastewater by allele-specific RT-qPCR

Lee, Wei Lin; McElroy, Kyle A.; Armas, Federica; Imakaev, Maxim; Gu, Xiaoqiong; Duvallet, Claire; Chandra, Franciscus; Chen, Hongjie; Leifels, Mats; Mendola, Samuel; Sullivan, Roisin; Powell, Morgan M.; Wilson, Shane T.; Wu, Fuqing; Xiao, Amy; Moniz, Katya; Matus, Mariana; Ghaeli, Newsha; Thompson, Janelle R.; Alm, Eric J.

doi:10.1101/2021.03.28.21254404

Cited by 13 publications

(24 citation statements)

References 30 publications

(31 reference statements)

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“…First, the interpretation of the WC ratio relies on the assumption that the viral shedding rate did not drastically change over the course of the pandemic. While some variants of SARS-CoV-2 have been reported to have higher shedding rates or longer shedding duration (Frampton et al, 2021;Kissler et al, 2021), the B.1.1.7 variant did not make up a large proportion of wastewater viral titers in the Boston Area until March 2021, well past the periods in the summer where we described the notable peaks in the WC ratio (Lee et al, 2021). There have been mixed reports of the difference in shedding rate between symptomatic and asymptomatic people (Han et al, 2020;Van Vinh Chau et al, 2020;Zhou et al, 2020), but in any case, it is unlikely that the ratio of asymptomatic to symptomatic cases would swiftly change in a catchment of 2.25 million people.…”

Section: Discussionsupporting

confidence: 49%

“…However, the proportion of B.1.1.7 in the last week of January 2021, during the peak of the second wave, was estimated to make up only an average of ∼2.1% COVID-19 cases in the U.S (Washington et al, 2021). Furthermore, B.1.1.7 did not make up a large proportion of wastewater viral titers in the Boston Area until Feb-March 2021, towards the end of the second wave (Lee et al, 2021).…”

Section: Relationship Between Wastewater Data New Cases and Deaths Is Different In The First And Second Wavesmentioning

confidence: 94%

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Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Xiao

Bushman

et al. 2021

Preprint

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Wastewater surveillance has emerged as a useful tool in the public health response to the COVID-19 pandemic. While wastewater surveillance has been applied at various scales to monitor population-level COVID-19 dynamics, there is a need for quantitative metrics to interpret wastewater data in the context of public health trends. We collected 24-hour composite wastewater samples from March 2020 through May 2021 from a Massachusetts wastewater treatment plant and measured SARS-CoV-2 RNA concentrations using RT-qPCR. We show that the relationship between wastewater viral titers and COVID-19 clinical cases and deaths varies over time. We demonstrate the utility of three new metrics to monitor changes in COVID-19 epidemiology: (1) the ratio between wastewater viral titers and clinical cases (WC ratio), (2) the time lag between wastewater and clinical reporting, and (3) a transfer function between the wastewater and clinical case curves. We find that the WC ratio increases after key events, providing insight into the balance between disease spread and public health response. We also find that wastewater data preceded clinically reported cases in the first wave of the pandemic but did not serve as a leading indicator in the second wave, likely due to increased testing capacity. These three metrics could complement a framework for integrating wastewater surveillance into the public health response to the COVID-19 pandemic and future pandemics.

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Section: Discussionsupporting

confidence: 49%

Section: Relationship Between Wastewater Data New Cases and Deaths Is Different In The First And Second Wavesmentioning

confidence: 94%

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Xiao

Bushman

et al. 2021

Preprint

Self Cite

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“…Following the methodology established in our previous study demonstrating single nucleotide discrimination for mutations associated with the SARS-CoV-2 Alpha variant (Lee et al, 2021), we developed an Allele-Specific RT-qPCR (AS RT-qPCR) panel for tracking mutations indicative of the SARS-CoV-2 variants Delta (B.1.617.2), Delta plus ( B.1.617.2.1) , Kappa (B.1.617.1) and Beta (B.1.351) and validated this approach for synthetic mixtures of Beta and Kappa VOC RNA in a wastewater RNA matrix (Delta assay validation is currently in progress, subject to availability of commercial RNA standards). To design allele specific primers we screened a panel of primers targeting mutations characteristic of four variants -Delta, Delta plus, Kappa and Beta, and identified primers targeting five loci -T19R, D80A, K417N, T478K and E484Q as having optimal sensitivity and specificity.…”

Section: Resultsmentioning

confidence: 99%

“…We designed AS RT-qPCR reactions to detect five non-synonymous single nucleotide variants in the spike gene. Primers and probes were designed following our previous work (Lee et al, 2021) and using the Integrated DNA Technologies (IDT)'s PrimerQuest Tool.…”

Section: Assay Designmentioning

confidence: 99%

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Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR

Lee

Armas

et al. 2021

Preprint

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The Delta (B.1.617.2) variant has caused major devastation in India and other countries around the world. First detected in October 2020, it has now spread to more than 100 countries, prompting WHO to declare it as a global variant of concern (VOC). The Delta (B.1.617.2), Delta plus (B.1.617.2.1) and Kappa (B.1.617.1) variants are all sub-lineages of the original B.1.617 variant. Prior to the inception of B.1.617, vaccine rollout, safe-distancing and timely lockdowns greatly reduced COVID-19 hospitalizations and deaths. However, the Delta variant, allegedly more infectious and for which existing vaccines seemed less effective, has catalyzed the resurgence of cases. Therefore, there is an imperative need for increased surveillance of the B.1.617 variants. While the Beta variant is increasingly outpaced by the Delta variant, the spread of the Beta variant remains of concern due to its vaccine resistance. Efforts have been made to utilize wastewater-based surveillance for community-based tracking of SARS-CoV-2 variants, however wastewater with its low SARS-CoV-2 viral titers and mixtures of viral variants, requires assays to be variant-specific yet accurately quantitative for meaningful interpretation. Following on the design principles of our previous assays for the Alpha variant, here we report allele-specific and multiplex-compatible RT-qPCR assays targeting mutations T19R, D80A, K417N, T478K and E484Q, for quantitative detection and discrimination of the Delta, Delta plus, Kappa and Beta variants in wastewater. This method is open-sourced and can be implemented using commercially available RT-qPCR protocols, and would be an important tool for tracking the spread of B.1.617 and the Beta variants in communities.

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Surveillance for SARS‐CoV‐2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks

Acosta

Bautista

Waddell

et al. 2023

Journal of Medical Virology

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Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR.Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.

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Quantitative detection of SARS-CoV-2 B.1.1.7 variant in wastewater by allele-specific RT-qPCR

Cited by 13 publications

References 30 publications

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR

Surveillance for SARS‐CoV‐2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks

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