Proteomic deconvolution reveals distinct immune cells in different body sites in SARS-Cov-2 positive individuals

<strong>Background: </strong>Severe acute respiratory syndrome <em>coronavirus 2</em><em><strong> (</strong></em>SARS-CoV-2) continues to be a significant public-health challenge globally. SARS-CoV-2 is a novel virus, and the precise nature of what constitutes the immunological responses in different human-body sites in infected individuals is still unclear. Proteomic datasets were used to characterize the various immune-cell fractions in gargle solution, bronchoalveolar lavage fluid, nasopharyngeal, and urine samples post-SARS-CoV-2 infection in humans. <strong>Materials and methods: </strong>The raw proteomic data used in this study were downloaded from (https://www.ebi.ac.uk/pride/ ) with the following identifiers: PXD019423, n=3 (gargle solution); PXD018970, n=15 (urine); PXD022085, n=5 (bronchoalveolar lavage fluid); and PXD022889, n=18 (nasopharyngeal). MaxQuant was used for the human peptide spectral matching, and SARS-CoV-2 proteome database was downloaded from the UniProt (Access date 9th January 2022). To ensure accuracy in our analysis, we processed these proteomic data in a single MaxQuant run to ensure sample cross normalization. The protein count matrix was extracted from the proteins group file and used as an input for the Cibersort for the immune cell fraction determination. <strong>Results: </strong>The body of individuals infected with the SARS-CoV-2 virus is characterized by different fractions of immune cells in bronchoalveolar lavage fluid (BALF), nasopharyngeal, urine, and gargle solution. BALF has more abundant memory B cells, CD8, activated mast cells, and resting macrophages than urine, nasopharyngeal, and gargle solution. Our analysis also demonstrates that each body site comprises different immune-cell fractions post-SARS-CoV-2 infection in humans. <strong>Conclusion: </strong>Different body sites are characterized by different immune cell fractions in SARS-CoV-2-infected individuals. The findings in this study could inform public health policies and health professionals on treatment strategies and drive SARS-CoV-2 diagnosis procedures. <strong>Keywords: Proteomic, SARS-CoV-2, Deconvolution, Immune-cell fraction</strong>