SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) are characterized by distinct mutations in the S1 domain of the viral spike protein. This domain encompasses the N-terminal domain, the receptor-binding domain, and part of the cleavage site region. While mutations in other genomic regions of SARS-CoV-2 can impact VOC potential, the S1 domain holds particular importance for identifying variants and assessing antigenic evolution and immune escape potential.

We describe a rapid high-throughput sequencing-based assay, SpikeID, for the unbiased detection and identification of SARS-CoV-2 variants based on spike S1 amplicon sequencing. We benchmarked the SpikeID assay against Illumina whole-genome sequencing across 622 clinical biospecimens, representing lineages that circulated globally from October 2021 to January 2024.

SpikeID unambiguously detected 100 % of WHO-designated VOCs and identified PANGO lineages circulating at ≥1 % prevalence in the New York City (NYC) area with 93 % accuracy in comparison to whole-genome sequencing. This reduction in accuracy was largely due to PANGO lineages that are only distinguishable by mutations outside the S1 domain.

We demonstrate the utility and scalability of the SpikeID assay during the emergence and subsequent surge of Omicron and Omicron-derived lineages in New York City, and show that our approach enables cost-effective, reliable, and near-real-time detection of emerging lineages.