Elucidating persistent symptoms after Lyme borreliosis, tick-borne encephalitis and COVID-19

Patients with Lyme borreliosis (LB) often develop pain, fatigue, or neurocognitive symptoms that persist for months to years despite antibiotic therapy for Borrelia burgdorferi sensu lato infection, termed post-treatment LB symptoms / syndrome (PTLDS). These sequelae are quite heterogeneous, ranging from mild intermittent symptoms to debilitating syndromes that greatly impair the quality of life and require regular use of analgesics. The underlying causes are not well understood and there are no standardized biomarkers to identify patients at risk for such outcomes; they are indistinguishable by standard clinical and laboratory tests. As a result, treatment strategies are often ineffective, leaving patients and physicians in a quandary about how to restore health. Such symptoms may occur after any manifestation of LB and regardless of the infecting Borrelia species. Rather than persistent infection, our findings point to inappropriate immune responses which are shaped by host genetics as a possible cause of PTLDS. In particular, we found that patients with PTLDS have sustained elevated serum levels of IFNα and IL-23 which were associated with autoantibody responses and symptom severity, suggesting that they may play a pathogenic role. Moreover, in parallel studies we have identified single-nucleotide polymorphisms (SNPs) in host genes which were associated with excessive inflammation and more severe disease, providing a link between host genetics, inappropriate immunity, and PTLDS.  PTLDS represent a great clinical challenge. However, unremitting post-infectious symptoms are not unique to LB. Similar symptoms have also been observed after other bacterial or viral infections including tick-borne encephalitis (TBE), influenza, infectious mononucleosis, Q fever, and COVID-19. The fact that these sequelae occur following multiple unrelated infectious triggers irrespective of infecting pathogen speaks to a broader issue and suggests that a proportion of the population is genetically pre-wired for long-term post-infectious sequelae. In this proposal we are testing the HYPOTHESIS that persistent symptoms result from sustained IFNα-driven maladaptive immune responses that are shaped by genetic variation in host immune genes such as TLR1. Our specific aims are: Aim 1: Establish the role of IFNα in persistent symptoms after infectious disease by    a) determining the levels of IFNα in larger cohorts of patients with persistent symptoms following LB (Lyme neuroborreliosis or erythema migrans), TBE and COVID-19,                b) identifying cells and pathways that mediate IFNα responses using single cell RNAseq, and          c) ascertaining the role of gender and age (children vs adults) on the immune and clinical phenotype. Aim 2: Identify host genetic risk factors for PTLDS by    a) determining the frequency of >250,000 SNPs (mutations) using GWAS-based ImmunoArray in Lyme neuroborreliosis patients with PTLDS, and                                               b) correlating candidate SNPs with the number and severity (functional impairment) of persistent symptoms in patients. Aim 3: Ascertain the functional impact of candidate SNPs (e.g. TLR1) in    a) patients by assessing their effect on degree of local and systemic inflammation in CSF and serum,    b) ex vivo by testing cells from PTLDS patients with the candidate SNPs, and    c) in genetically-engineered CRISPR cell lines with or without SNP of interest.  In this proposal we are using cutting-edge genomic and transcriptomic approaches coupled with our well-defined patient cohorts and functional studies in cells and tissue, to identify specific host genes and delineate their functional consequence in dysregulated immunity in PTLDS as well as unremitting symptoms after TBE and COVID-19. With emergence of IL-23 and IFNα modulating therapies in other immune conditions, these findings provide new hope for more effective treatment for patients with unremitting post-infectious symptoms.