Differential Gene Expression and Transcriptomics Reveal High M‐Gene Expression in JN.1 and KP.1/2 Omicron Sub‐Variants of SARS‐CoV‐2: Implications for Developing More Sensitive Diagnostic Tests

ABSTRACT SARS‐CoV‐2, a positive‐strand RNA virus, utilizes both genomic replication and subgenomic mRNA transcription. Whole genome sequencing (WGS) from clinical samples can estimate viral gene expression levels. WGS was conducted on 529 SARS‐CoV‐2 positive clinical samples from Assam and northeastern India to track viral emergence and assess gene expression patterns. The results reveal differential expression across structural, non‐structural, and accessory genes, with notable upregulation of the M gene, especially in the Omicron variant, followed by E and ORF6. The mean transcript per million (TPM) expression levels of the M gene were significantly higher in Omicron variants (175 611 ± 46 921), peaking in the KP.1/KP.2 sublineage (220 493 ± 34 917), compared to the Delta variant (129 717 ± 33 773). The relative fold change of M gene expression between Delta and Omicron 2024 subvariants showed a 1.6‐fold change. Variant‐wise gene expression analysis suggests a correlation between gene expression and viral mutation, impacting replication. As anticipated, the expression levels of genes surge with the increase in the virus mutation. The Chi‐square trend for average substitution count versus average TPM of the M gene was highly significant (72.78., p < 0.0001). The M gene's high expression and low mutation rate make it an ideal target for designing a real‐time RT‐PCR kit assay. These findings highlight the need for continuous surveillance and understanding of viral gene expression dynamics for effective COVID‐19 management. Further studies are necessary to elucidate the significance of these observations in viral pathogenesis and transmission dynamics.