Detection of SARS-CoV-2 Variants by Multiple Diagnostic Assays Second RESUBMISSION JCV-D-21-00675R2

Abstract

Introduction: The emergence of SARS-CoV-2 Variants of Concern (VOC) and Variants Being Monitored (VBM) have presented additional clinical and public health concerns regarding potential virus transmissibility, disease severity, and immune evasion. It is imperative that diagnostic assays can detect all such variants, and since commercial oligo sequences are commonly not available, empirical testing may be necessary to confirm this. To confirm the sensitivity of the SARS-CoV-2 assays used at the Wadsworth Center for the detection of VOC and VBM, relevant specimens were selected from the specimen archive and tested in the various platforms.

Materials and methods: Patient respiratory specimens submitted from clinal laboratories across the state were selected; three samples per variant were chosen to account for inter assay and variant reproducibility. The four molecular diagnostic platforms for SARS-CoV-2 currently in use at our facility were examined.

Results: A total of 64 specimens were tested, representing 2 VOC, 8 VBM and 4 other variants circulating in New York State. For certain samples, original Ct values provided by sample submitters were much higher, or lower, than those obtained from this study. The investigation of submitter testing platforms, with consideration of the assay's viral targets, confirmed the differences in Ct were not variant specific.

Conclusions: It was demonstrated that the diagnostic methods investigated in this study detected all the variants tested. Because of the continual evolution of the virus, it is vital to monitor new variants as they emerge for the ability of molecular diagnostic methods to detect them with acceptable sensitivity.

Keywords: Molecular diagnosis; SARS-CoV-2; Variant Being Monitored; Variant of Concern.

Fig. 1

The figure shows a variant stacked plot indicating the distribution of SARS-CoV-2 variants detected in New York State from December 2020 to December 2021. Sequencing was performed in the Advanced Genomics Technology Core at the Wadsworth Center, on samples submitted from clinical laboratories throughout New York State. Sequence analysis was performed by the Bioinformatics Core.