Discovery of Anti-SARS-CoV-2 XBB.1.5 and JN.1 Variant-Specific Monoclonal Single-Domain Antibodies from a Synthetic Library

Authors

Isamu Tsuji¹, Kumiko Okada², Benjamin Kroppen³, Tetsufumi Katta², Kaori Yamamura², Takeshi Nishihama², Ayako Miura¹, Hansjörg Götzke³, Eric Crampon¹ and Andrea Bertolotti-Ciarlet¹

Organizations

1. Vaccine Bioanalytical Development, Vaccine Business Unit, Takeda Pharmaceutical Company Ltd., Cambridge, MA 02139, USA
2. Vaccine MS&T Japan, Global Vaccine Business Unit, Takeda Pharmaceutical Company Ltd., Hikari 743-8502, Japan
3. NanoTag Biotechnologies GmbH, 37079 Göttingen, Germany

Abstract

Background/Objective

The SARS-CoV-2 virus frequently undergoes mutations to evade the human immune system. Vaccines for new strains are developed each season, and an identification test confirming the specific strain is essential for vaccine quality control, as stated by the U.S. Food and Drug Administration. However, a shorter timeline of antibody discovery was required to adjust vaccine development schedules. Therefore, anti-SARS-CoV-2 strain-specific, single-domain antibodies (sdAbs) for SARS-CoV-2 vaccines were discovered using alpaca synthetic libraries without animal immunization.

Methods

A synthetic sdAb library was developed based on conserved alpaca sdAb frameworks, with a degree of freedom in the three complementarity-determining regions. Specific and high-affinity sdAb clones were selected from the library by one ribosomal display round, followed by two phage display selections using a biotinylated strain-specific SARS-CoV-2 receptor-binding domain (RBD) of the spike protein as bait and non-biotinylated RBD variants to block. The sdAbs clones were applied to the identification test using Western blotting. The binding epitopes were determined by hydrogen–deuterium exchange mass spectrometry.

Results

Five clones of XBB.1.5 and two clones of JN.1-specific sdAbs were discovered. Anti-JN.1 sdAb clone 1B9 detected JN.1 vaccine products but no other previously produced vaccine strains, Wuhan, BA.5 and XBB.1.5, by WB for vaccine identification test. Four binding epitopes for anti-JN.1 sdAb clone 1B9 were identified, including the L455S mutation, a critical amino acid to evade neutralizing antibodies for the JN.1 strain. Conclusions: Anti-XBB.1.5 and JN.1-specific sdAbs were discovered from a synthetic single-domain antibody library within 8–9 weeks, and these sdAbs were applied to vaccine identification testing.

Keywords

SARS-CoV-2; monoclonal antibody; single-domain antibody; JN.1 strain; vaccine identification test; neutralizing antibody

CovalX Technology Used

Epitope Mapping
HDX-MS