Background: Colorectal cancer (CRC) shows marked heterogeneity across anatomical sites, immune environments, and clinical outcomes. While studies well discussed about bacterial contributions to the tumor microenvironment, viral components remain less defined .Furthermore, the specific host cells of these viruses and how they are distributed across various cell types remain a subject of debate. So present study efforts shed a light on the question of viral footprint detection, and their distribution across cell types.
Methods: We developed a marker-independent computational framework to detect viral sequences from unmapped reads in single-cell RNA sequencing (scRNA-seq) datasets of colorectal tumors, matched controls, and healthy groups. Non-human reads were aligned to curated viral reference databases and integrated with cell-type annotations derived from scRNA-seq analysis. This approach enables unbiased viral detection and cell-type–resolved mapping of viral signals without relying on predefined markers.
Results: Viral transcripts, including herpesviruses, hepatitis-related viruses, and endogenous retroviral elements, were detected across multiple CRC samples. Viral signals were enriched in specific immune cell populations, particularly B cells, myeloid cells, macrophages, NK cells, and T cells. Cell-type–level analyses revealed heterogeneous viral distributions and associations with immune-related transcriptional programs, suggesting potential interactions between viral presence and tumor-associated immune activity.
Conclusion: Our marker-independent single-cell framework enables scalable discovery and cell-type–resolved characterization of tumor-associated viral transcripts in CRC. The detection of diverse viral signals across immune compartments supports a role for viral components as potential modulators of the colorectal tumor microenvironment. This strategy provides a foundation for future studies investigating viral–host interactions and their implications for CRC biology and immune dynamics.