An approach of scoring early host immune response from oro-nasopharyngeal swabs predicts covid-19 outcome providing possibility of early therapeutic intervention

Abstract Unpredictable fatal outcome of COVID-19 is attributed to dysregulated inflammation. The purpose of this study was to develop biomarkers for early detection of host immune impairment which may in turn identify high risk patients. We used RT-PCR to evaluate if impaired anti-inflammatory response (as defined by undetectable IL-10 in the presence of high expression of a representative interferon response gene) and/or impaired adaptive T cell response, assessed in leftover RNA samples extracted from oro-nasopharyngeal swab of COVID-19 patients at diagnosis, could serve as early prognostic marker/s. We demonstrate that a T cell response based ‘severity score’ comprising rational combination of Ct values of target genes can identify high risk noncomorbid potentially critical COVID-19 patients with a sensitivity of 91% (95% CI:58.7-99.8) and specificity of 92.6% (95% CI:75.7-99). Although inclusion of co-morbid patients reduced sensitivity to 77% (95% CI: 54.6-92.2), the specificity was still 94% (95% CI: 79.8-99.3). The work flow developed in the same pipeline of the COVID-19 diagnostic samples can also reduce expenditure and reporting time of the test for an earliest clinical decision ensuring possibility of early prophylactic treatment and rational management of patients.