New discovery of high-affinity SARS-CoV-2 spike S2 protein binding peptide selected by PhIP-Seq

•A peptide Spep-1 targeting S2 of SARS-CoV-2 spike protein was selected by PhIP-Seq.•Spep-1 showed nanomolar affinity and high specificity to spike protein.•S-1 based immunoassay can detect femtomolar spike antigen in spiked serum samples.•Spep-1 can be used in future on S2 recognition, virus tracing and drug delivery.