Rapid identification of SARS CoV-2 omicron sub-variant JN.1 (BA.2.86.1.1) with mass spectrometry

Abstract

Objective: The rapid detection and differentiation of strains of the BA.2.86 lineage including the new sub-variant JN.1 (BA.2.86.1.1) is demonstrated employing selected ion monitoring (SIM) and high resolution mass spectrometry. Methods: A study of a preliminary set of BA.2.86 lineage positive specimens, identified BA.2.86 and BA.2.86.1.1 peptide markers in 62.5 % and 29.1 % of samples. Results: Peptide-specific markers in the surface spike protein associated with the L455S mutation are confidently detected with high sensitivity in protein and virus digests.The virus was thus confidently assigned in over 91 % of positive specimens. Conclusions: A rise in the global prevalence of the JN.1 (BA.2.86.1.1) immune evasive sub-variant, that emerged in late 2023, requires that new strategies and protocols to detect such strains in human specimens are accelerated and implemented.

Keywords

• SARS CoV-2
• Coronavirus
• Omicron
• JN.1
• Mass spectrometry