COSMIC Single-Cell and Spatial Atlas: Lung, Blood, Nasal, and Imaging Mass Cytometry Data from Fatal COVID-19 in a Malawian Population

This dataset release accompanies the study "Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population" (Nyirenda, Hardy, Da Silva Filho et al., Nature Medicine, 2024; https://doi.org/10.1038/s41…).

The COSMIC (COVID-19 Single-cell Malawi Investigation Cohort) atlas comprises six annotated single-cell and imaging datasets from postmortem lung, blood, and nasal tissue collected from Malawian adults with fatal COVID-19, non-COVID-19 lower respiratory tract disease (LRTD), and non-LRTD controls. This is the first spatially resolved single-cell atlas of fatal COVID-19 from a sub-Saharan African population, a critically underrepresented group in the Human Cell Atlas.

Included datasets:

• COSMIC_Lung_Atlas.h5ad — 66,882 integrated lung cells (immune + stromal), scRNA-seq and snRNA-seq
• COSMIC_Lung_Immune_Atlas.h5ad — 29,217 lung immune cells, reclustered at higher resolution
• COSMIC_Lung_Stromal_Atlas.h5ad — 37,090 lung stromal cells, reclustered at higher resolution
• COSMIC_Nasal_Atlas.h5ad — 8,098 nasal cells from inferior turbinate sampling
• COSMIC_Blood_Atlas.h5ad — 13,350 peripheral blood mononuclear cells (PBMCs)
• COSMIC_IMC_Lung.h5ad — 76,369 cells from 118 regions of interest profiled by imaging mass cytometry (IMC) using a 39-antibody panel

Key findings: The Malawian COVID-19 cohort is characterized by a dominant IFN-γ response in lung-resident CD206⁺ alveolar macrophages — in contrast to the type I/III interferon responses predominating in Northern Hemisphere cohorts. Neutrophil-driven pathology was associated with vascular damage, while macrophage-driven pathology was linked to alveolar damage. Nasal cell transcriptomes paralleled lung responses more closely than blood.

Data access: All atlases are interactively browsable via CellxGene VIP at https://cellatlas-cxg.mvls.…

Raw data: EBI ArrayExpress accession E-MTAB-13544

Keywords: single-cell RNA-seq, spatial transcriptomics, imaging mass cytometry, COVID-19, SARS-CoV-2, lung, Africa, Malawi, macrophage, interferon, Human Cell Atlas, sub-Saharan Africa, postmortem, autopsy