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Patients with pre\u2010existing autoimmune conditions can therefore be at increased risk of severe COVID\u201019 and\/or associated sequelae, yet SARS\u2010CoV\u20102 infection in this group has been little studied. Here, we performed single\u2010cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS\u2010CoV\u20102 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell\u2013cell communication that substantially shape the immune response under SARS\u2010CoV\u20102 infection. While enrichment of HLA\u2010DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type\u2010I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS\u2010CoV\u20102 in patients with pre\u2010existing autoimmunity, highlighting important considerations for disease treatment and follow\u2010up.<\/jats:p>","DOI":"10.1002\/eji.202350633","type":"journal-article","created":{"date-parts":[[2023,10,6]],"date-time":"2023-10-06T17:39:37Z","timestamp":1696613977000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Single\u2010cell multi\u2010omics analysis of COVID\u201019 patients with pre\u2010existing autoimmune diseases shows aberrant immune responses to infection"],"prefix":"10.1002","volume":"54","author":[{"given":"Anis","family":"Barmada","sequence":"first","affiliation":[{"name":"Wellcome Sanger Institute Wellcome Genome Campus  Cambridge United Kingdom"},{"name":"Department of Medical Genetics University of Cambridge  Cambridge United 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