Meta-analysis of orthogonal OMICs data from COVID-19 patients unveils prognostic markers and antiviral factors.

Coronavirus disease 2019 (COVID-19) pandemic has lasted more than a year since its first case in December 2019 and yet its social and economic burden continues to grow. While a tremendous amount of OMICs data has been generated from COVID-19 patient samples, the host antiviral response and markers of disease progression remain to be completely delineated. In this study, we have conducted a meta-analysis of published transcriptome and proteome profiles of the nasal swab and bronchioalveolar lavage fluid (BALF) samples of COVID-19 patients to identify high confidence upregulated host factors. This was followed by rank ordering, shortlisting, and validation of overexpression of a set of host factors in a nasal swab/BALF samples from a cohort of COVID-19 positive/negative, symptomatic/asymptomatic individuals. This led to the identification of host antiviral response in the upper respiratory tract and potential prognostic markers. Notably, SEPRIN B3 and Thioredoxin were identified as potential antiviral factors. In addition, several S100 family proteins were found to be upregulated in COVID-19 specific and disease severity dependent manner. Overall, this study provides novel insights into the host antiviral mechanisms and COVID-19 disease progression.