Pathology and viral evolutionary dynamics in a hamster model of persistent SARS-CoV-2 infection

SARS-CoV-2 infection typically resolves within weeks, but rare cases of prolonged replication-sometimes exceeding a year-have been documented, particularly in immunocompromised individuals. These persistent infections pose health risks and may give rise to highly divergent variants, yet the underlying biology remains poorly understood. Here, we describe a model of SARS-CoV-2 persistence using transgenic Syrian hamsters (males) lacking the interleukin-2 receptor gamma subunit (IL2rg). Infection with the XBB.1.16 variant led to efficient viral replication in respiratory tissues by two weeks after infection, with dissemination to other sites, including the intestinal tract. Viral titers remained high in multiple tissues at 100 days after infection. Longitudinal oral swab sequencing revealed dynamic shifts in intrahost single-nucleotide variant (iSNV) frequencies, with constellations of iSNVs rising and falling together, consistent with strong genetic linkage. Synonymous and nonsynonymous mutations accumulated at similar rates, suggesting genetic drift as the dominant evolutionary force. Tissue- and swab-derived sequences revealed extensive within-host diversity and hinted at tissue-specific evolutionary trajectories. This model enables detailed investigation of SARS-CoV-2 persistence and within-host viral evolution and provides a controlled system to study how long-term replication in tissue reservoirs may contribute to viral diversification.