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

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

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


In this report, we describe the development of a reverse transcription-quantitative PCR (RT-qPCR) assay, termed Alpha-Delta assay, which can detect all severe acute respiratory syndrome coronavirus 2 (SC-2) variants and distinguish between the Alpha (B.1.1.7) and Delta (B.1.617.2) variants. The Alpha- and Delta-specific reactions in the assay target mutations that are strongly linked to the target variant. The Alpha reaction targets the D3L substitution in the N gene, and the Delta reaction targets the spike gene 156 to 158 mutations. Additionally, we describe a second Delta-specific assay that we use as a confirmatory test for the Alpha-Delta assay that targets the 119 to 120 deletion in the Orf8 gene. Both reactions have similar sensitivities of 15 to 25 copies per reaction, similar to the sensitivity of commercial SC-2 detection tests. The Alpha-Delta assay and the Orf8119del assay were successfully used to classify clinical samples that were subsequently analyzed by whole-genome sequencing. Lastly, the capability of the Alpha-Delta assay and Orf8119del assay to identify correctly the presence of Delta RNA in wastewater samples was demonstrated. This study provides a rapid, sensitive, and cost-effective tool for detecting and classifying two worldwide dominant SC-2 variants. It also highlights the importance of a timely diagnostic response to the emergence of new SC-2 variants with significant consequences on global health.

Original languageEnglish
JournalMicrobiology spectrum
Issue number2
StatePublished - 27 Apr 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
Copyright © 2022 Erster et al.


  • Alpha (B.1.1.7)
  • Delta (B.1.617.2)
  • RT-qPCR
  • SARS-COV-2
  • SC-2 surveillance
  • classification
  • diagnostic assay


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