key: cord-0937804-nvljxp1q authors: Sen, Poonam; Kaur, Harpreet title: In Silico transcriptional analysis of asymptomatic and severe COVID-19 patients reveals the susceptibility of severe patients to other comorbidities and non-viral pathological conditions date: 2022-04-18 journal: bioRxiv DOI: 10.1101/2022.04.16.488556 sha: 0a203b92bc2cb0ef38ea0399ecbc763063dacbf8 doc_id: 937804 cord_uid: nvljxp1q COVID-19 is a severe respiratory disease caused by SARS-CoV-2, a novel human coronavirus. The host response to SARS-CoV-2 infection is not clearly understood. Patients infected with SARS-CoV-2 exhibit heterogeneous intensity of symptoms, i.e., asymptomatic, mild, and severe. Moreover, effects on organs also vary from person to person. These heterogeneous responses pose pragmatic hurdles for implementing appropriate therapy and management of COVID-19 patients. Post-COVID complications pose another major challenge in managing the health of these patients. Thus, understanding the impact of disease severity at the molecular level is vital to delineate the precise host response and management. In the current study, we performed a comprehensive transcriptomics analysis of publicly available seven asymptomatic and eight severe COVID-19 patients. Exploratory data analysis using Principal Component Analysis (PCA) showed the distinct clusters of asymptomatic and severe patients. Subsequently, the differential gene expression analysis using DESeq2 identified 1,224 significantly upregulated genes (logFC>= 1.5, p-adjusted value <0.05) and 268 significantly downregulated genes (logFC<= -1.5, p-adjusted value <0.05) in severe samples in comparison to asymptomatic samples. Eventually, Gene Set Enrichment Analysis (GSEA) of upregulated genes revealed significant enrichment of terms, i.e., anti-viral and anti-inflammatory pathways, secondary infections, Iron homeostasis, anemia, cardiac-related, etc. Gene set enrichment analysis of downregulated genes indicates lipid metabolism, adaptive immune response, translation, recurrent respiratory infections, heme-biosynthetic pathways, etc. In summary, severe COVID-19 patients are more susceptible to other health issues/concerns, non-viral pathogenic infections, atherosclerosis, autoinflammatory diseases, anemia, male infertility, etc. And eventually, these findings provide insight into the precise therapeutic management of severe COVID-19 patients and efficient disease management. In the current study, we obtained publicly available data (GSE178967) from the NCBI GEO Table 1 and Supplementary Table S1 , respectively. The summary of clinical information 129 extracted from the GEO series matrix is provided in Supplementary Table S2 . The summary of workflow, including pre-processing and normalization, is depicted in Figure 154 1. In pre-processing, we removed rows with NA, taken the average of duplicates genes using 155 aggregate function in R, and filtered out the genes having zero or low expression. In the current study, we analyzed the transcriptomic profiles of asymptomatic and severe 219 COVID-19 patients to compare the transcriptional changes and understand the biological 220 implications of infection. A publicly available RNA sequencing read count dataset was 221 extracted, pre-processed, and normalized. We performed exploratory data analysis using PCA 222 to understand variations between groups and to identify outliers. Subsequently, we performed 223 differential gene expression analysis between these identified groups (Severe vs. After the pre-processing, we are able to remove genes without identifiers, zero expression, 229 and low variance in the data. Thus, the total number of genes reduced from 188,753 to 35,587 230 in the data. Subsequently, this dataset was used for exploratory and DGE analysis. Table 2 . with respective gene description. terms for both upregulated (see Table S6 -S21, Supplementary File 2) and downregulated 298 gene sets (see Table S22 Association with organs other than the respiratory system 334 We also observed enriched pathways related to various organs, such as kidney-related The primary concern with highly transmissible COVID-19 disease is the lack of increased aspartate aminotransferase (AST), and alanine aminotransferase (ALT), and 508 increased interleukin 6 (IL-6), and decreased thrombocytes, reduced blood sodium. 509 We have also found that COVID 19 disease severity might impact fertility in the patients. As COVID-19 disease has a multifactorial response on the body, we need more clinical 519 features for prognosis, which can help us manage the diverse impact of COVID-19 on health. To address future novel virus disease management, we must not limit ourselves to real-time 521 therapeutics. Instead, we must continuously build the concepts of generalized host response 522 and disease progression on diverse tissues and subject groups. Timeline: WHO's COVID-19 response, World Health Organization WHO Director-General's opening remarks at the media briefing on 569 COVID-19 -11 Coronaviridae Study Group of the 573 International Committee on Taxonomy of, The species Severe acute respiratory syndrome-574 related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Worldometer: COVID-19 CORONAVIRUS PANDEMIC COVID-19: Discovery, 579 diagnostics and drug development A pneumonia outbreak associated with a new coronavirus of probable 584 bat origin Structure of SARS-CoV-2 spike protein, Current 586 Opinion in Virology COVID-19 and Multiorgan 588 Response Coronavirus Infections-More Than Just the 590 Common Cold Human SARS CoV-2 spike protein mutations Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like 605 mutations and deletions Omicron and Delta 607 variant of SARS-CoV-2: A comparative computational study of spike protein Challenges and burden of the 610 Coronavirus 2019 (COVID-19) pandemic for child and adolescent mental health: a narrative 611 review to highlight clinical and research needs in the acute phase and the long return to 612 normality Therapeutics and COVID-19: living guideline, WHO-2019-nCoV-therapeutics-2022.2, 614 World Health Organization Old and re-purposed drugs for the treatment of COVID-19 Why Do Some People Develop Serious COVID-19 Disease After 618 While Others Only Exhibit Mild Symptoms? Mutations in SARS-CoV-2; Consequences in structure, function, and pathogenicity 622 of the virus COVID-19: Pathogenesis, potential therapeutics and 625 vaccination strategies COVID-19 in Immunocompromised Hosts: What We Know So Far Risk Factors Associated With Acute Respiratory 631 Distress Syndrome and Death in Patients With Coronavirus Disease 634 Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a 635 systematic review and meta-analysis Angiotensin-converting enzyme 2 638 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with 639 atrial fibrillation Aging in COVID-19: Vulnerability, immunity and intervention COVID-19: Epidemiology, virology, and prevention Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-647 The epidemiology and pathogenesis of coronavirus 649 disease (COVID-19) outbreak 651 SARS-CoV-2 Detection in Fecal Sample from a Patient with Typical Findings of COVID-19 652 Pneumonia on CT but Negative to Multiple SARS-CoV-2 RT-PCR Tests on Oropharyngeal 653 and Nasopharyngeal Swab Samples Shedding of 656 SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and 657 the environment-based spread of COVID-19 Clinical features of patients 661 infected with 2019 novel coronavirus in Cytokine storm and leukocyte changes in 663 mild versus severe SARS-CoV-2 infection: Review of 3939 COVID-19 patients in China and 664 emerging pathogenesis and therapy concepts Post-COVID syndrome and suicide risk ACE2 receptor polymorphism: Susceptibility to 669 SARS-CoV-2, hypertension, multi-organ failure, and COVID-19 disease outcome Features of anosmia in COVID-19 Time between Symptom Onset, Hospitalisation and Recovery or Death: 675 Statistical Analysis of Belgian COVID-19 Patients Psychiatric and neuropsychiatric presentations associated with severe 679 coronavirus infections: a systematic review and meta-analysis with comparison to the 680 COVID-19 pandemic 684 L.L. Florencio, Defining Post-COVID Symptoms An Integrative Classification Gemelli Against, Persistent Symptoms in 688 Patients After Acute COVID-19 Post-discharge persistent symptoms and health-related quality of life after 692 hospitalization for COVID-19 Emerging threats from zoonotic coronaviruses-from SARS and 694 MERS to 2019-nCoV CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven 699 SARS-CoV-2 productively 704 infects human gut enterocytes Tissue 706 distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in 707 understanding SARS pathogenesis Receptor recognition and cross-species infections of SARS coronavirus SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells 713 together with innate immune genes Focus on Receptors for Coronaviruses with Special 715 Reference to Angiotensin-Converting Enzyme 2 as a Potential Drug Target -A Perspective How does coronavirus 718 kill? Clinicians trace a ferocious rampage through the body, from brain to toes Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19 US 731 Department of Health and Human Services Author Correction: A global database of COVID-19 vaccinations PIN83 736 The COVID-19 Research Database: Building One of the Largest PRO Bono Real-World 737 DATA Repositories CORD-19: 741 The Covid-19 Open Research Dataset LitCovid: an open database of COVID-19 literature A Web-Based Platform on Coronavirus Disease-19 to Maintain 746 Predicted Diagnostic, Drug, and Vaccine Candidates LitCovid-AGAC: cellular and molecular level 749 annotation data set based on COVID-19 PIN117 Identification of Patients Infection Prior to the New COVID-19 Diagnostic Code -a Premier Database Analysis, Value 753 in Health PRS30 COVID-19 RAPID Antigen Test False Positives 755 and False Negatives Reported to the FDA Manufacturer and User Facility Device 756 Experience Database A Tool for Early Prediction of Severe Coronavirus Disease Multicenter Study Using the Risk Nomogram in Wuhan and Guangdong, China Biofabrication: An 762 interesting tool to create in vitro model for COVID-19 drug targets A tool to 765 democratize CFD simulations for SARS-CoV-2 infection risk analysis Data Resource Profile: COVerAGE-DB: a global 768 demographic database of COVID-19 cases and deaths OxCOVID19 Database, a 772 multimodal data repository for better understanding the global impact of COVID-19 Patients Triage Algorithm Using Patient-Generated Health Data from Nationwide Multicenter 776 Database COVID-ONE-780 hi: The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical 781 Parameters HIT-COVID global database tracking public health interventions to COVID-19 Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 807 (EAVE II) Database Virtual dermatopathology: A potential educational tool during 809 COVID-19 pandemic CT-based radiomics as a tool to recognize COVID-19 positive 812 patients Cancer therapy tool informs COVID-19 vaccines Machine learning and COVID-19: a tool for 817 healthcare setting choice by primary care physicians Machine learning based decipherment of Cell 820 Population Data: a promising hospital front-door screening tool for COVID-19 Baseline signatures associated with clinical, virologic, and immunologic outcomes in 823 patients with mild to moderate COVID-19 Peginterferon lambda for the 829 treatment of outpatients with COVID-19: a phase 2, placebo-controlled randomised trial 3 -Data Preprocessing Data Mining Data Pre-processing Secondary Analysis of Electronic Health Records A Review on Data Preprocessing 837 Techniques Toward Efficient and Reliable Knowledge Discovery From Building Operational 838 Data Data Preprocessing in Data Mining Towards Explaining the Effects of Data Preprocessing on Machine 842 IEEE 35th International Conference on Data Engineering (ICDE) Principal component analysis Evaluation of 847 Normalization and PCA on the Performance of Classifiers for Protein Crystallization Images Moderated estimation of fold change and dispersion for 850 RNA-seq data with DESeq2 Heavy-tailed prior distributions for sequence count data: 852 removing the noise and preserving large differences silico Analysis of Transcriptomic Profiling 854 and Affected Biological pathways in Multiple Sclerosis, bioRxiv Effect of low-expression gene filtering on detection of 857 differentially expressed genes in RNA-seq data Building Predictive Models in R Using the caret Package Data Mining: Concepts and Techniques Principal component analysis for special types of data Bonferroni Correction Encyclopedia of Systems Biology When to use the Bonferroni correction, Ophthalmic and Physiological 868 Optics Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale 871 Transcriptomics Data MultipleTesting.com: A tool for life science 873 researchers for multiple hypothesis testing correction Ansari-Pour, Why, When and How to Adjust Your P Values? Best (but oft-forgotten) practices: the multiple problems of multiplicity-877 whether and how to correct for many statistical tests Classification of early and late stage liver 880 hepatocellular carcinoma patients from their genomics and epigenomics profiles Identification of LncRNAs as 883 Therapeutic Targets in Chronic Lymphocytic Leukemia, Columbia Undergraduate Science 884 analysis and prediction of 886 cholangiocarcinoma from transcriptomic profile of patients Flexible Heatmaps for Functional Genomics and Sequence 889 Features HeatmapGenerator: high 891 performance RNAseq and microarray visualization software suite to examine differential 892 gene expression levels using an R and C++ hybrid computational pipeline Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Enrichr: a comprehensive gene set enrichment analysis web server 900 2016 update Gene 903 Set Knowledge Discovery with Enrichr Enrichr search engine, the Ma'ayan 908 Lab The GeneCards Suite: From Gene Data Mining 912 to Disease Genome Sequence Analyses The Human Gene Database RNAct: Protein-RNA interaction predictions for 919 model organisms with supporting experimental data Tissue-based map of the human proteome Towards a 930 knowledge-based Human Protein Atlas Treatment of COVID-19: old tricks for new 932 challenges Mechanisms and mediators of lung injury after acute kidney 934 injury Human kidney is a 937 target for novel severe acute respiratory syndrome coronavirus 2 infection The Novel 940 Coronavirus 2019 epidemic and kidneys Clinical characteristics of 113 deceased patients with coronavirus disease 2019: 944 retrospective study Disease characteristics and serological responses in 950 patients with differing severity of COVID-19 infection: A longitudinal cohort study in Dhaka Epidemiological and clinical characteristics of 99 cases of 954 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune 958 Response to Severe Acute Respiratory Syndrome Coronavirus Infection, mBio COVID-19 Infection: Concise 962 Review Based on the Immunological Perspective The Influence of Virus Infection on Microglia and 964 Accelerated Brain Aging Role of 966 myeloid-derived suppressor cells in viral respiratory infections; Hints for discovering 967 therapeutic targets for COVID-19 Functional 969 Activity of the Complement System in Hospitalized COVID-19 Patients: A Prospective 970 Cohort Study Rationale for targeting complement in COVID-19 Morphology of COVID-19-affected cells in 975 peripheral blood film Neutrophils in COVID-19 IFN signaling and neutrophil degranulation 981 transcriptional signatures are induced during SARS-CoV-2 infection Proteins associated with neutrophil degranulation are upregulated in 985 nasopharyngeal swabs from SARS-CoV-2 patients A neutrophil 990 activation signature predicts critical illness and mortality in COVID-19, medRxiv Lymphocyte Changes in Severe 992 COVID-19: Delayed Over-Activation of STING? Co-infections, secondary infections, and antimicrobial use 997 in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC 998 WHO CCP-UK study: a multicentre, prospective cohort study Secondary infection in COVID-19 critically ill patients: a retrospective 1002 single-center evaluation Role of the 1004 interferons in CD64 and CD169 expressions in whole blood: Relevance in the balance 1005 between viral-or bacterial-oriented immune responses Immune response activation and immunomodulation Sialoadhesin in recognition of self and non-self Interferon-inducible mechanism of dendritic cell-mediated HIV-1 dissemination 1013 is dependent on Siglec-1/CD169, PLoS pathogens Clinical research assessment by flow 1016 cytometry of biomarkers for infectious stratification in an Emergency Department Different bacterial and viral 1019 pathogens trigger distinct immune responses in a globally invasive ant Interrelatedness between dysbiosis in the gut microbiota due to 1022 immunodeficiency and disease penetrance of colitis Cardiovascular complications in COVID-1024 19 The role of the thymus in COVID-19 disease severity: 1026 implications for antibody treatment and immunization The Pivotal Role of Thymus in 1029 Atherosclerosis Mediated by Immune and Inflammatory Response -7) and its receptor Mas are expressed in the human testis: implications for 1033 male infertility Could COVID-19 have an impact on male fertility? Organ distribution of 1042 severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS 1043 patients: implications for pathogenesis and virus transmission pathways No evidence of severe acute respiratory syndrome-1047 coronavirus 2 in semen of males recovering from coronavirus disease Absence of 2019 novel coronavirus in semen and testes of COVID-19 1051 patientsdagger Assessment of SARS-CoV-2 in human semen-a cohort study Clinical Characteristics and Results of 1056 Semen Tests Among Men With Coronavirus Disease Male Fertility and the COVID-19 Pandemic: Systematic Review of the 1060 Literature Orchitis: a complication of 1062 severe acute respiratory syndrome (SARS) SARS-CoV-2, COVID-19 and the Ageing Immune System