Daniel Missailidis ¹ Esmaeil Ebrahimie ^2,3 Manijeh Mohammadi-Dehcheshmeh ² Claire Allan ¹ Oana Sanislav ¹ Paul Robert Fisher ¹ Stephanie Gras ^4,5,6 Sarah Jane Annesley ^1*

• ¹ Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
• ² Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Australia
• ³ School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, South Australia, Australia
• ⁴ Infection & Immunity program, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
• ⁵ Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Australia
• ⁶ Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, Australia

Long COVID is a debilitating condition that lasts for more than three months post-infection by SARS-CoV-2. On average, one in ten individuals infected with SARS-CoV-2 develops Long COVID worldwide. A knowledge gap exists in our understanding of the mechanisms, genetic risk factors, and biomarkers that could be associated with Long COVID. In this pilot study we used RNA-Seq to quantify the transcriptomes of peripheral blood mononuclear cells isolated from COVID-recovered individuals, seven with and seven without Long COVID symptoms (age-and sex-matched individuals), on average 6 months after infection. Seventy genes were identified as significantly dysregulated up-or down-regulated in Long COVID samples, and the vast majority were downregulated. The most significantly dysregulated upor downregulated genes fell into two main categories, either associated with cell survival or with inflammation. This included genes such as ICOS (FDR p = 0.024) and S1PR1 (FDR p = 0.019) that were both upregulp-regulated, indicating that a pro-inflammatory state is sustained in Long COVID PBMCs compared with Post-COVID recovered PBMCs. Functional enrichment analysis identified that immune-related functions were expectedly predominant among the dysregulated up-or down-regulated genes. The most frequently downregulated genes in significantly altered functional categories were two leukocyte immunoglobulin-like receptors LILRB1 (FDR p = 0.005) and LILRB2 (FDR p = 0.027). Downregulation of these inhibitory receptors similarly indicates a sustained proinflammatory state in Long COVID PBMCs. PCA analysis demonstrated that LILRB1 and LILRB2 expression discriminated all of the Long COVID samples from Post-COVID recovered samples. LILRB1 and LILRB2 should be validated as prospective biomarkers of Long COVID in larger cohorts, over time and against clinically overlapping conditions.