Longitudinal mucosal immune response to SARS-CoV-2 starting prior to infection

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PROJECT SUMMARY Morbidity and mortality in COVID-19 is the result of an exaggerated inflammatory response causing severe tissue and organ damage. However, the biological mechanism for why some individuals progress from initially stable to ultimately critical condition has not been fully elucidated. This work proposes that the immune response at the site of infection during the earliest stage of infection plays a deterministic role on subsequent pathology; namely that a delayed or suppressed type 1 interferon response in the respiratory mucosa within the first few days of infection permits rapid viral proliferation with minor symptoms, but eventually leads to the high viral loads and exaggerated inflammatory response seen later in disease. Further, the proposed project will test whether a delayed interferon response is the result of previously documented age-related dysfunction. It also seeks to determine whether direct SARS-CoV-2 mediated disruption of host splicing can also suppress interferon signaling in the early stage of infection. To do this, the study will leverage a unique set of longitudinal paired nasal swab and saliva samples from individuals who are initially negative for SARS-CoV-2 infection, but become infected while being prospectively sampled with high frequency (twice per day) as part of an IRB-approved (#20- 1026) COVID-19 household transmission study that the applicant co-designed and co-leads (since August 2020) at the California Institute of Technology. The transcriptome present in these samples will be analyzed to measure gene and isoform expression from which leukocyte recruitment and activation, including through interferon signaling can be inferred, through the elusive early stage of infection and the full course of the illness. Longitudinal differential expression and differential splicing paths in patients as young as age 6, and of advanced age will be assessed to identify whether age-related differences in immune response (in particular, interferon signaling) lead to more rapid increases in viral load, and subsequent symptom severity. In addition, from an RNA sequencing library enriched for nascent pre-mRNAs, splicing defects such as intron retention will be measured, to identify whether virus-mediated disruption of splicing also leads to a suppressed or delayed early interferon response permissive of rapid viral proliferation. COVID-19 is a public health threat, and in line with the mission of the NIAID, the results of this study can provide mechanistic insights into the pathophysiology of SARS-CoV-2 infection, to potentially identify novel or more efficient targets for the prevention or treatment of severe disease. In addition, the proposed project offers an excellent training opportunity for the applicant to gain knowledge and skills in immunology, virology/coronavirus biology, mechanisms of human RNA splicing, and generation analysis and interpretation of RNA sequencing data, with mentorship from Dr. Rustem Ismagilov, Dr. Akiko Iwasaki, and Dr. Mitch Guttman, who are experts in the aforementioned fields.