Decoding Omicron's Dynamics: Nirmatrelvir Efficacy in K18-hACE2 Mice

The persistent evolution of SARS-CoV-2, driven by the intrinsic infidelity of its RNA-dependent RNA polymerase, continues to pose challenges for global health management. The emergence of antigenically distinct Omicron subvariants—including recent dominant strains like JN.1, KP.3.1.1, and LB.1—has diminished the effectiveness of antibody-based strategies, underscoring the critical need for conserved, direct-acting antivirals. A recent study utilizing the K18-hACE2 transgenic mouse model (expresses human ACE2 controlled by the human keratin 18 (K18) promoter) examined the infection kinetics and therapeutic susceptibility of these emerging subvariants relative to the ancestral WA1/2020 strain (early 2020 U.S. isolate of the virus), offering valuable preclinical insights.

Altered Viral Replication and Milder Pathogenesis

Vijeta Sharma and colleagues from David Perlin’s lab at the Center for Discovery and Innovation in Nutley revealed a notable temporal shift in lung infection kinetics exhibited by the Omicron subvariants compared to WA1/2020. The parental WA1/2020 strain exhibited a sustained and robust replication profile, reaching peak lung viral titers (~8.5 Log PFU) late in the observation period, specifically at 4 days post-infection (dpi). In contrast, the Omicron subvariants displayed accelerated kinetics, achieving an early peak in lung viral titer (~7–8 Log PFU) at 2 dpi, followed by a marked decline to 1–3 Log PFU by 4 dpi, indicating accelerated lung viral clearance.

This attenuated viral replication phenotype in the lower respiratory tract correlates with milder clinical outcomes. While WA1/2020 infection resulted in a progressive decline in body weight, reaching an average loss of approximately 10% by 4 dpi, mice infected with the Omicron subvariants maintained near-baseline weights throughout the observation period.

Early and Enhanced Immune Activation

The distinct viral kinetics corresponded to divergent host pulmonary immune responses. Mice infected with Omicron subvariants mounted an earlier and more pronounced immune activation compared to WA1/2020-infected mice. Proinflammatory cytokines and chemokines showed an earlier increase in subvariant-infected mice. For instance, at 2 dpi, KP.3.1.1 induced significantly higher GM-CSF levels compared to WA1/2020, reflecting accelerated early immune activation. This rapid immune response aligns with the reported upper respiratory tract tropism of the Omicron lineage, suggesting efficient triggering of innate immune sensing, which leads to rapid cytokine production. The faster clearance of the virus in Omicron cases was accompanied by a transient inflammatory profile that generally subsided by 4 dpi. In contrast, WA1/2020 displayed a more gradual and sustained inflammatory response, consistent with its more robust lower respiratory tract tropism.

Broad and Potent Antiviral Efficacy of Nirmatrelvir

Despite the extensive mutations in the spike protein that facilitate immune evasion, the conserved nature of the SARS-CoV-2 main protease (Mpro), the target of Nirmatrelvir, was key to maintaining therapeutic efficacy. Importantly, Omicron subvariants JN.1, KP.3.1.1, and LB.1 all share the conserved P132H mutation in Mpro, but biochemical studies confirm this mutation does not compromise Nirmatrelvir’s binding affinity or catalytic function.

In the K18-hACE2 model, early Nirmatrelvir treatment (1000 mg/kg orally, twice daily, starting 12 hours post-infection) resulted in significant reductions in viral load across all variants. Notably, the antiviral efficacy was significantly more pronounced against the Omicron subvariants compared to the parent WA1/2020 strain. Treatment nearly completely suppressed infectious virus in the lungs of JN.1 and LB.1 infected mice, with mean Log PFU reductions of 4.267 and 3.467, respectively, substantially surpassing the 1.413 Log PFU reduction observed in WA1/2020-infected mice.

Beyond viral reduction, Nirmatrelvir treatment was also associated with the attenuation of several key inflammatory mediators likely secondary to the reduction in viral burden.

Collectively, these findings reinforce that small-molecule antivirals targeting conserved viral elements, such as the Mpro inhibitor Nirmatrelvir, remain critical pillars of SARS-CoV-2 management, even as the virus continues to rapidly diversify. The study validates the continued utility of the K18-hACE2 transgenic mouse model as a robust platform for the timely evaluation of countermeasures against emerging variants.

Sharma V, Dolgov E, Tillery T, Mendez Romero C, Rojas-Triana A, Villalba Guzman DM, Goldgirsh K, Rasheed R, Gonzalez-Jimenez I, Alvarez N, Park S, Murugan M, Nelson AM, Perlin DS. Omicron Subvariants Infection Kinetics and Nirmatrelvir Efficacy in Transgenic K18-hACE2 Mice. Int J Mol Sci. 2025 Sep 29;26(19):9509. doi: 10.3390/ijms26199509. PMID: 41096776; PMCID: PMC12524663.  https://www.mdpi.com/1422-0067/26/19/9509