Persistent SARS-CoV-2 infection in SCID rats reflects immune vulnerability of the upper airway and trachea

In immunocompromised patients, persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection carries the risk of prolonged viral shedding and emergence of new variants. To reproduce the key features of persistent SARS-CoV-2 infection and evaluate its transmissibility, mouse-passaged SARS-CoV-2 was administered intranasally to severe combined immunodeficiency (SCID) rats deficient in Rag2 and Il2rg genes. The virus replicated in SCID rats for at least 6 weeks without causing severe symptoms. The main replication sites were the nasal cavity and trachea, and replicating viruses were barely detectable in the lungs. Infected areas within the nasal cavity and trachea showed minimal infiltration of neutrophils and M2 macrophages; however, a strong inflammatory response was observed in the lungs. Serial sequencing of the viral genome revealed accumulation of persistent mutations, predominantly in regions encoding nonstructural proteins. The persistently shed virus retained its infectivity, enabling its transmission to uninfected SCID rats. This model provides new insights into the immunological and tissue-associated features of persistent SARS-CoV-2 infection and offers a practical research platform for developing therapeutic interventions.

IMPORTANCE

Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in immunocompromised individuals promotes viral evolution and ongoing transmission, yet mechanistic studies have been limited by the absence of appropriate animal models. Existing mouse systems do not support longitudinal sampling or evaluate transmission, leaving critical questions unanswered. We established an SCID rat model that enables repeated noninvasive sampling from the same individuals, allowing longitudinal analysis of viral dynamics during prolonged infection. This approach revealed the emergence, disappearance, and fixation of viral mutations over time. Persistently infected rats also retained infectious and transmitted virus to naïve SCID rats, providing experimental evidence that prolonged infection preserves the transmission potential in this model. Persistent viral replication localized to the nasal cavity and trachea may be relevant to the upper-airway persistence reported in some immunocompromised patients. By capturing selected features of persistent SARS-CoV-2 infection under profoundly immunodeficient conditions, this model provides a valuable platform for investigating viral persistence, evolution, and transmission.