Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant

Abstract

The emergence of the B.1.617.2 (Delta) variant of the severe acute syndrome coronavirus (SARS-CoV-2) that emerged in 2019 (COVID-19), resulted in a surge of cases in India and has expanded and been detected across the world, including in the United States. The B.1.617.2 (Delta) variant has been seen to be twice more transmissible coupled with potential increases in disease severity and immune escape. As a result, case numbers and hospitalisations are once again on the rise in the USA. On 16 July 2021, the Centers for Disease Control and Prevention (CDC) reported a 7-day average 69.3% increase in new cases and a 35% increase in hospitalisations. Although the gold standard for SARS-CoV-2 variants identification remains genomic sequencing, this approach is not accessible to many clinical laboratories. The main goal of this study was to validate and implement the detection of the B.1.617.2 (Delta) variant utilising an open reverse transcription polymerase chain reaction (RT-PCR) platform by explicitly detecting the S-gene target failure (SGTF) corresponding to the deletion of two amino acids (ΔE156/ΔF157) characteristic of B.1.617.2 (Delta) variant. This approach was conceived as a rapid screening of B.1.617.2 (Delta) variant in conjunction with CDC's recommended N1 (nucleocapsid gene), N2, and RP (human RNase P) genes, as a pre-screening tool prior to viral genomic sequencing. We assessed 4,937 samples from 5 July to 5 September 2021. We identified the B.1.617.2 (Delta) variant in 435 of 495 positive samples (87.8%); the additional positive samples (7 samples, 1.4%) were found to belong to the B.1.1.7 (Alpha, UK) lineage and the remaining 53 samples (10.7%) were reported as 'other' lineages. Whole genome sequencing of 46 randomly selected samples validated the strains identified as positive and negative for the B.1.617.2 (Delta) variant and confirmed the S gene deletion in addition to B.1.617.2 characteristic mutations including L452R, T478K, P681R and D950N located in the spike protein. This modality has been used as routine testing at the Riverside University System Health (RUHS) Medical Center as a method for detection of B.1.617.2 (Delta) to pre-screen samples before genome sequencing. The assay can be easily implemented in clinical laboratories, most notably those with limited economic resources and access to genomic platforms.

Keywords: Delta COVID-19 variant; RT-PCR test; SARS-CoV-2.

Fig. 1

Primers and probes used to detect the SARS-CoV-2 SGTF. Regions targeted corresponding to variants B.1.1.7 (Alpha: upper set) and B.1.617.2 (Delta: lower set) are shown including specific forward/reverse primers and probes used on the open platform RT-PCR. Protein sequence shows the respective deletions (marked in blue).

Fig. 2

Sequence alignments of representative full genome sequencing of variants detected by real-time RT-PCR in samples from RUHS patient samples; genome reference NC_045512.2. Arrows indicate the deletion on the Spike protein at nucleotide positions 22029/71 (ΔE156/ΔF157), and representative mutations at positions 22917 (L452R), 22995 (T478K) and 24410 (D950N) of B.1.617.2 (Delta) variant (A), and the corresponding deletion and mutations corresponding to B.1.1.7 (Alpha) variant (B).