Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution

Abstract

In keeping with the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 causative agent, PCR assays have been developed to rapidly detect SARS-CoV-2 variants, which have emerged since the first (Alpha) variant was identified. Based on specific assortment of SARS-CoV-2 spike-protein mutations (ΔH69/V70, E484K, N501Y, W152C, L452R, K417N, and K417T) among the major variants known to date, Seegene Allplex SARS-CoV-2 Variants I and Variants II assays have been available since a few months before the last (Omicron) variant became predominant. Using S gene next-generation sequencing (NGS) as the SARS-CoV-2 variant identification reference method, we assessed the results of SARS-CoV-2-positive nasopharyngeal swab samples from two testing periods, before (n = 288, using only Variants I) and after (n = 77, using both Variants I and Variants II) the appearance of Omicron. The Variants I assay allowed correct identification for Alpha (37/37), Beta/Gamma (28/30), or Delta (220/221) variant-positive samples. The combination of the Variants I and Variants II assays allowed correct identification for 61/77 Omicron variant-positive samples. While 16 samples had the K417N mutation undetected with the Variants II assay, 74/77 samples had both ΔH69/V70 and N501Y mutations detected with the Variants I assay. If considering only the results by the Variants I assay, 6 (2 Beta variant positive, 1 Delta variant positive, and 3 Omicron variant positive) of 365 samples tested in total provided incorrect identification. We showed that the Variants I assay alone might be more suitable than both the Variants I and Variants II assays to identify currently circulating SARS-CoV-2 variants. Inclusion of additional variant-specific mutations should be expected in the development of future assays. IMPORTANCE Omicron variants of SARS-CoV-2 pose more important public health concerns than the previously circulating Alpha or Delta variants, particularly regarding the efficacy of anti-SARS-CoV-2 vaccines and therapeutics. Precise identification of these variants highly requires performant PCR-based assays that allow us to reduce the reliance on NGS-based assays, which remain the reference method in this topic. While the current epidemiological SARS-CoV-2 pandemic context suggests that PCR assays such as the Seegene Variants II may be dispensable, we took advantage of NGS data obtained in this study to show that the array of SARS-CoV-2 spike protein mutations in the Seegene Variants II assay may be suboptimal. This reinforces the concept that initially developed PCR assays for SARS-CoV-2 variant detection could be no longer helpful if the SARS-CoV-2 pandemic evolves to newly emerging variants.

Keywords: PCR assay; SARS-CoV-2; amino acid mutation; next-generation sequencing; spike protein; variant detection.

FIG 1

SARS-CoV-2 VOC or non-VOC identification scheme by PCR assays (A) based on the detection of seven amino acid mutations in the SARS-CoV-2 spike (S) protein (B). The Seegene Allplex Variants I assay (here named the Seegene Variants I assay) detects the SARS-CoV-2 RdRP gene in addition to the indicated mutations. The Seegene Allplex Variants II assay (here named the Seegene Variants II assay) detects four mutations, including W152C, which is specific for the Epsilon variant (which is not a VOC according to the WHO). The S protein mutation position is shown, with E484K and N501Y involving RBD ACE2 contact amino acid residues.

FIG 2

Next-generation sequencing results for SARS-CoV-2-positive NPS samples showing amino acid mutations in the SARS-CoV-2 spike (S) gene-encoded protein. Sample results are shown according to the type of SARS-CoV-2 variant (Alpha, Beta, Gamma, Delta, or Omicron) identified. In each graph, colors allow grouping of S protein mutations according to whether (red) or not (black) they define the indicated SARS-CoV-2 variant.