Spatial heterogeneity of the immune compartment within the lungs of critical COVID-19 patients

Cross AR, Sansom S, Roberts I, Cerundolo L, Melero I, De Andrea C, Landecho MF, Klenerman P,Hester J, Issa F Acute respiratory distress syndrome (ARDS) is a defining feature of severe infection with theSARS-CoV-2 virus. Approaches to understand the immune response during COVID-19 are largelyconfined to characterisation of circulating leukocytes, however this approach excludes the mostrelevant cells that are active at the site of infection and injury. The aim of this study was to characterise the immune landscape across the lungs of COVID-19patients. Lung samples from three critical COVID-19 patients were assessed for histopathology,viral load, and distribution using qPCR, in situ hybridisation and immunohistochemistry.Leukocyte distribution was then assessed, and the transcript profile of selected areas examinedagainst the >1800 genes in the Cancer Transcriptome Atlas panel on the NanoString GeoMxDigital Spatial Profiling platform. Lung samples exhibited a spectrum of typical COVID-19 pathology with diffuse alveolar damageconsistent with hyaline membrane and type II pneumocyte hyperplasia, interstitialinflammation, organising pneumonia and thrombi. All tissues tested positive for SARS-CoV-2RNA using qPCR, whilst spatially resolved techniques revealed only few and sparsely distributedcells carrying the viral nucleocapsid protein. Multiplexed immunofluorescence for lymphocytes(CD3+) and macrophages (CD68+) was used to select areas of immune enrichment for spatialtranscriptomic profiling. These targeted analyses highlighted functional pathways involved inthe interferon gamma response, TCR activation and antigen presentation. Comparison acrossimmune-enriched areas identified a heterogeneity in lung infiltrates with spatial separation ofchemokine and complement production. Our data identify pathological immune pathways thatare amenable to therapeutic intervention in critical disease.