Published April 26, 2026 | Version v1
Dataset Open

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

Authors/Creators

  • 1. University of Glasgow, School of Infection and Immunity

Contributors

Producer:

  • 1. Unversity of Glasgow

Description

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/s41591-024-03354-3).

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.gla.ac.uk/COSMIC/

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

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Additional details

Identifiers

DOI
10.1038/s41591-024-03354-3

Funding

Bill & Melinda Gates Foundation
INV-018138
UK Research and Innovation
MR/V025856/1
Wellcome Trust
104111

References

  • Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population. Nyirenda J, Hardy OM, Silva Filho JD, Herder V, Attipa C, Ndovi C, Siwombo M, Namalima TR, Suwedi L, Ilia G, Nyasulu W, Ngulube T, Nyirenda D, Mvaya L, Phiri J, Chasweka D, Eneya C, Makwinja C, Phiri C, Ziwoya F, Tembo A, Makwangwala K, Khoswe S, Banda P, Morton B, Hilton O, Lawrence S, Dos Reis MF, Melo GC, de Lacerda MVG, Trindade Maranhão Costa F, Monteiro WM, Ferreira LCL, Johnson C, McGuinness D, Jambo K, Haley M, Kumwenda B, Palmarini M, Denno DM, Voskuijl W, Kamiza SB, Barnes KG, Couper K, Marti M, Otto TD, Moxon CA. Nat Med. 2024 Dec;30(12):3765-3777. doi: 10.1038/s41591-024-03354-3. Epub 2024 Nov 20. PMID: 39567718