Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate and to those admitted at the Intensive Care Unit (ICU) is yet to be presented. We set to characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals. Materials and methods: The bulk RNA sequencing data with identifier PRJNA639275 was download from Sequence Reads Archive (SRA). The individuals were divided into: (i) healthy, n=34, severe, n=16, ICU, n=8, moderate, n=8, and convalescent, n=2. Fastqc version 0.11.9 and Cutadapt version 3.7 was used to asses the reads quality and to perform adapter trimming respectively. STAR was using to align reads to the reference genome and GATK best practice was followed to call variants using rnavar pipeline, part of the nf-core pipelines. Results: Our analysis demonstrated that convalescent, moderate, severe and those admitted to the ICU are characterized by different sets of unique RNAseq variants. The data shows that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as in the healthy controls. We showed that the healthy and SARS-CoV-2 infected individuals display different sets of expressed varinats which is characteristic of the patient phenotype. Conclusion: The individuals with severe, moderate, those admitted at the ICU, and convalescent individuals display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance management and control of SARS-CoV-2 infection in our population. Key words: RNAseq, variants, SARS-CoV-2, severe, ICU, moderate

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and what constitutes immunological responses in different human body sites in infected individuals is yet to be presented. We set to determine the various immune cell fractions in gargle solution, bronchoalveolar lavage fluid, nasopharyngeal, and urine samples post-SARS-CoV-2 infection in humans. Materials and methods: We downloaded proteomics data 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), PXD022889, n=18 (nasopharyngeal). MaxQuant was used for the peptide spectral matching using humans, and SARS-CoV-2 was downloaded from the UniProt database (Access date 9th January 2022). The protein count matrix was extracted from the proteins group file and used as an input for the cibersort for the immune cells fraction determination. Results: 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. Conclusion: Different body sites are characterized by different immune cells fractions in SARS-CoV-2 infected individuals. The findings in this study can inform public health policies and health professionals on treatment strategies and drive SARS-CoV-2 diagnosis procedures.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate, and those admitted to the intensive care unit (ICU) is yet to be presented. We characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals. Materials and methods The bulk RNA sequencing data with identifier PRJNA639275 were downloaded from Sequence Reads Archive (SRA). The individuals were divided into: (1) healthy, n = 34, moderate, n = 8, convalescent, n = 2, severe, n = 16, and ICU, n = 8. Fastqc version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. STAR was used to align reads to the reference genome, and GATK best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines. Results Our analysis demonstrated that different sets of unique RNAseq variants characterize convalescent, moderate, severe, and those admitted to the ICU. The data show that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as the healthy controls. We showed that the healthy and SARS-CoV-2-infected individuals display different sets of expressed variants characteristic of the patient phenotype. Conclusion The individuals with severe, moderate, those admitted to the ICU, and convalescent display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance the management and control of SARS-CoV-2 infection in our population.