Direct RT-qPCR assay for SARS-CoV-2 variants of concern (Alpha, B.1.1.7 and Beta, B.1.351) detection and quantification in wastewater

Karin Yaniv, Eden Ozer, Marilou Shagan, Satish Lakkakula, Noam Plotkin, Nikhil Suresh Bhandarkar, Ariel Kushmaro

Research output: Contribution to journalArticlepeer-review

51 Scopus citations

Abstract

Less than a year following the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, variants of concern have emerged in the form of variant Alpha (B.1.1.7, the British variant) and Beta (B.1.351, the South Africa variant). Due to their high infectivity and morbidity, it has become clear that it is crucial to quickly and effectively detect these and other variants. Here, we report improved primers-probe sets for reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2 detection including a rapid, cost-effective, and direct RT-qPCR method for detection of the two variants of concern (Alpha, B.1.1.7 and Beta, B.1.351). All the developed primers-probe sets were fully characterized, demonstrating sensitive and specific detection. These primer-probe sets were also successfully employed on wastewater samples aimed at detecting and even quantifying new variants in a geographical area, even prior to the reports by the medical testing. The novel primers-probe sets presented here will enable proper responses for pandemic containment, particularly considering the emergence of variants of concern.

Original languageEnglish
Article number111653
JournalEnvironmental Research
Volume201
DOIs
StatePublished - 1 Oct 2021

Keywords

  • Molecular probes
  • Reverse transcriptase polymerase chain reaction
  • SARS-CoV-2
  • Variants of concern
  • Wastewater-based epidemiological monitoring

ASJC Scopus subject areas

  • Biochemistry
  • General Environmental Science

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