Immunological and Molecular Profiling of Pangolin Viruses at the Viral Interface

Pangolins have been identified as potential intermediate hosts for various viruses, including coronaviruses related to SARS-CoV-2 and MERS-CoV, yet the cellular mechanisms underlying their viral susceptibility remain poorly understood. Here, we establish the first comprehensive single-cell transcriptomic atlas for two pangolin species Manis pentadactyla and Manis javanica, generated through single-cell RNA sequencing of 246,813 high-quality cells from 12 major tissues, combined with bulk transcriptome profiling of 123 samples across multiple tissues. This resource is integrated with cross-species data from humans (Homo sapiens), the big brown bat (Eptesicus fuscus), domestic pigs (Sus scrofa), mice (Mus musculus), and tigers (Panthera tigris). Our analysis reveals a myeloid-biased hematopoiesis in pangolin bone marrow, dominated by monocyte and T cell, which contrasts sharply with the lymphoid-skewed composition observed in Homo sapiens and Mus musculus. We also identify species-specific features, including thyroid-specific expression of FKBP5 in Manis pentadactyla validated by qRT-PCR and western blot, suggestive of a role in immune-endocrine crosstalk, and MIF-signaling-mediated cellular interactions in intestinal lymphoid tissue. Furthermore, key viral entry factors (AXL, NRP1, DPP4, ACE2, SCARB1, UVRAG) are broadly expressed in immune cell (e.g., B cell, T cell, macrophage), fibroblast, and endothelial cell across tissues, as confirmed by both single-cell and bulk transcriptomic analyses. Cross-species comparisons uncover fundamental differences in splenic immune architecture, hematopoietic lineage distribution, and viral receptor expression. Together, these findings, reinforced by transcriptomic and molecular experimental validation, establish a molecular and cellular framework for understanding pangolins as potential mixing vessels for viruses and provide a foundation for targeted surveillance of emerging zoonotic pathogens.