COVID-19 Associated Pulmonary Aspergillosis Isolates are genomically diverse but are more similar to each other in their responses to infection-relevant stresses

Secondary infections caused by the pulmonary fungal pathogen <em>Aspergillus fumigatus</em> are a significant cause of mortality in patients with severe COVID-19. Even though epithelial cell damage and aberrant cytokine responses have been linked with susceptibility to coronavirus associated pulmonary aspergillosis (CAPA), little is known about the mechanisms underpinning co-pathogenicity. Here, we analysed the genomes of 11 <em>A. fumigatus</em> strains from patients with CAPA in four different clinical settings. CAPA isolates are genomically diverse but are phenotypically similar across infection-relevant stresses. Phenotypically, CAPA strains are more similar to the <em>A. fumigatus</em> A1160 reference strain except for interactions with human immune cells wherein macrophage responses were similar to those induced by the Af293 reference strain. In contrast to previous reports, CAPA strains did not cluster based on geographic origin. A larger number of isolates from CAPA patients should be studied to identify genetic drivers of co-pathogenicity in patients with COVID-19. <br> This dataset contains the genome assemblies and annotations used in the manuscript.