Single-cell transcriptomics revealed 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 (scRNA-seq) of 245 618 high-quality cells from 12 major tissues, combined with 123 bulk transcriptome datasets. This resource is integrated with cross-species data from Homo sapiens, Eptesicus fuscus, Sus scrofa, Mus musculus, and Panthera tigris. Our analysis reveals a myeloid-biased hematopoiesis in pangolin bone marrow, dominated by monocytes and T cells, which contrasts sharply with the lymphoid-skewed composition observed in H. sapiens and M. musculus. We also identify species-specific features, including thyroid-specific expression of FKBP5 in M. pentadactyla, and MIF-signaling-mediated cellular interactions in intestinal lymph. Furthermore, key viral receptors ( AXL, NRP1, DPP4, ACE2, SCARB1, and UVRAG) are broadly expressed in immune cells (e.g., B cells, T cells, and macrophages), fibroblasts, and endothelial cells across tissues, as confirmed by single-cell and bulk transcriptomic analyses. Cross-species comparisons reveal fundamental differences in splenic immune architecture, hematopoietic lineage distribution, and viral receptor expression. Together, these findings based on single-cell transcriptomic profiling establish a molecular and cellular framework for understanding pangolins as potential mixing vessels for viruses and provide a foundation for the targeted surveillance of emerging zoonotic pathogens.