tetano
Editor, Senior Moderator
J Clin Virol
. 2025 Jul 28:180:105845.
doi: 10.1016/j.jcv.2025.105845. Online ahead of print. SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing
Keith Farrugia[SUP] 1 [/SUP], Zain Khalil[SUP] 1 [/SUP], Adriana van de Guchte[SUP] 1 [/SUP], Bremy Alburquerque[SUP] 1 [/SUP], Daniel Floda[SUP] 1 [/SUP]; PSP Study Group; Komal Srivastava[SUP] 2 [/SUP], Luz H Patiño[SUP] 3 [/SUP], Juan David Ramirez[SUP] 3 [/SUP], Alberto E Paniz-Mondolfi[SUP] 4 [/SUP], Emilia Mia Sordillo[SUP] 4 [/SUP], Viviana Simon[SUP] 5 [/SUP], Ana S Gonzalez-Reiche[SUP] 6 [/SUP], Harm van Bakel[SUP] 7 [/SUP]
Affiliations
Background: 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.
Methods: 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.
Results: 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.
Conclusions: 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.
Keywords: Genotyping; Long-read sequencing; Molecular surveillance; SARS-CoV-2; Spike; Virus evolution; Virus variants.
. 2025 Jul 28:180:105845.
doi: 10.1016/j.jcv.2025.105845. Online ahead of print. SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing
Keith Farrugia[SUP] 1 [/SUP], Zain Khalil[SUP] 1 [/SUP], Adriana van de Guchte[SUP] 1 [/SUP], Bremy Alburquerque[SUP] 1 [/SUP], Daniel Floda[SUP] 1 [/SUP]; PSP Study Group; Komal Srivastava[SUP] 2 [/SUP], Luz H Patiño[SUP] 3 [/SUP], Juan David Ramirez[SUP] 3 [/SUP], Alberto E Paniz-Mondolfi[SUP] 4 [/SUP], Emilia Mia Sordillo[SUP] 4 [/SUP], Viviana Simon[SUP] 5 [/SUP], Ana S Gonzalez-Reiche[SUP] 6 [/SUP], Harm van Bakel[SUP] 7 [/SUP]
Affiliations
- PMID: 40774230
- DOI: 10.1016/j.jcv.2025.105845
Background: 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.
Methods: 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.
Results: 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.
Conclusions: 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.
Keywords: Genotyping; Long-read sequencing; Molecular surveillance; SARS-CoV-2; Spike; Virus evolution; Virus variants.