Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus

Abstract

SARS-CoV-2 has infected >40% of the world’s population (Collaborators 2022) resulting in a devastating loss of life. As the SARS-CoV-2 pandemic enters its endemic phase (Meng, Irwin et al. 2023, Pilz and Ioannidis 2023), multiple new variants continue to circulate. Since its initial spread, the rapid adaptation of the virus to selective pressures continues to produce variants of concern (VoC), of which the omicron variants presently account for over 90% of current SARS-CoV-2 infections (www.cdc.gov). SARS-CoV-2 displays three structural proteins that are potential targets for therapeutic intervention, but the primary focal point of vaccine development and many therapeutic strategies is the spike surface glycoprotein, which the virus uses to gain cell entry by attaching to the host cell angiotensinconverting enzyme 2 (ACE2) receptor (Jackson, Anderson et al. 2020, Krammer 2020, Letko, Marzi et al. 2020, Polack, Thomas et al. 2020). The spike protein trimer consists of three domains: the receptor binding domain (RBD) on S1 that binds ACE2, the S1 Nterminal domain (NTD) that has a poorly defined function, and the S2 domain that is involved in virus-host cell membrane fusion (Walls, Park et al. 2020, Jackson, Farzan et al. 2022). Glycosylation is most extensive on the NTD and the S2 domain, whereas the RBD is largely glycan free (Watanabe, Allen et al. 2020, Zhao, Praissman et al. 2020). Consequently, it is unsurprising that the most antigenic domain on spike is the RBD, where the vast majority of neutralizing antibodies have been shown to bind.