Omicron Subvariants Infection Kinetics and Nirmatrelvir Efficacy in Transgenic K18-hACE2 Mice

Abstract

The persistent evolution of SARS-CoV-2 has led to the emergence of antigenically distinct Omicron subvariants exhibiting increased transmissibility, immune evasion, and altered pathogenicity. Among these, recent subvariants like JN.1, KP.3.1.1, and LB.1 possess unique antigenic and virological features, underscoring the need for continued surveillance and therapeutic evaluation. As vaccines and commercial monoclonal antibodies show reduced effectiveness against these variants, the role of direct-acting antivirals, such as Nirmatrelvir, targeting conserved viral elements like the main protease inhibitor, becomes increasingly crucial. In this study, we investigated the replication kinetics, host immune responses, and therapeutic susceptibility of three recently circulating Omicron subvariants in the K18-hACE2 transgenic mouse model, using the SARS-CoV-2 parent WA1/2020 strain as a reference. Omicron subvariants exhibited a marked temporal shift in viral infection kinetics characterized by an early lung viral titer peak ([~]7-8 Log PFU) at 2 days post-infection (dpi), followed by a decline (1-3 Log PFU) by 4 dpi. Pulmonary cytokine and chemokine responses (GM-CSF, TNF-, IL-1{beta}, IL-6) showed an earlier increase in subvariant-infected mice compared to a gradual response in WA1/2020 infection. Notably, Nirmatrelvir treatment led to significant reduction in lung viral titers in subvariant-infected mice than in WA1/2020, surpassing its efficacy against the parent strain. These findings highlight that Omicron subvariants infection yields a broad dynamic range in viral burden with minimum variability, while retaining a prominent therapeutic response to Nirmatrelvir. This study provides insights to the emerging subvariants pathogenesis and therapeutic responsiveness, reinforcing the importance of continued variant monitoring and the development of effective countermeasures. ImportanceThe emergence of SARS-CoV-2 Omicron subvariants still poses a significant public health challenge due to their antigenic drift, altered pathogenesis, and immune evasion capabilities. This study comprehensively highlights the distinct replication kinetics, immune responses, and therapeutic susceptibility of the recently circulating Omicron subvariants JN.1, KP.3.1.1, and LB.1 using the K18-hACE2 mouse model. We demonstrate that while these subvariants exhibit altered virological profiles and immune activation patterns compared to the parent WA1/2020 strain, they remain susceptible to Nirmatrelvir which is a direct-acting main protease inhibitor. Notably, Nirmatrelvir demonstrated greater in vivo antiviral efficacy in Omicron subvariant infections than in the ancestral WA1/2020 strain. These findings underscore the enduring therapeutic value of protease-targeting antivirals and emphasize the critical need for ongoing variant-specific preclinical assessments.