Multi-omics approach to COVID-19: a domain-based literature review

Abstract

Background Omics data, driven by rapid advances in laboratory techniques, have been generated very quickly during the COVID-19 pandemic. Our aim is to use omics data to highlight the involvement of specific pathways, as well as that of cell types and organs, in the pathophysiology of COVID-19, and to highlight their links with clinical phenotypes of SARS-CoV-2 infection. Methods The analysis was based on the domain model, where for domain it is intended a conceptual repository, useful to summarize multiple biological pathways involved at different levels. The relevant domains considered in the analysis were: virus, pathways and phenotypes. An interdisciplinary expert working group was defined for each domain, to carry out an independent literature scoping review. Results The analysis revealed that dysregulated pathways of innate immune responses, (i.e., complement activation, inflammatory responses, neutrophil activation and degranulation, platelet degranulation) can affect COVID-19 progression and outcomes. These results are consistent with several clinical studies. Conclusions Multi-omics approach may help to further investigate unknown aspects of the disease. However, the disease mechanisms are too complex to be explained by a single molecular signature and it is necessary to consider an integrated approach to identify hallmarks of severity.

Kinetics of the B- and T-Cell Immune Responses After 6 Months From SARS-CoV-2 mRNA Vaccination in Patients With Rheumatoid Arthritis

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerges in 2019, causing the actual COronaVIrus Disease 2019 (COVID-19) pandemic. The clinical manifestations are wide from asymptomatic to mild infection of the upper respiratory tract until the severe respiratory failure that requires intensive care unit hospitalization (1)(2)(3)(4)(5)(6).…”

An integrated analysis and comparison of serum, saliva and sebum for COVID-19 metabolomics

“…To date, the vast majority of multi-omics studies of COVID-19 have focused on single biofluids, typically via proteomic and metabolomic analyses of blood 32 . Whilst blood-based pathway alterations are now well-described, especially dyslipidemia, amino acid dysregulation 33 , inflammatory responses, neutrophil activation and degranulation, and platelet degranulation 34 , other biofluids have not been investigated to the same degree. In this study sebum lipids showed patterns of strong correlation with serum metabolites in controls, but with major changes in COVID-19 positive participants, revealing disease-driven dysregulation in both biofluids.…”

Rare Variants in Inborn Errors of Immunity Genes Associated with Covid-19 Severity

“…In recent years, multi-omics studies have proven a powerful and successful strategy to provide a broader perspective in understanding disease development and biological phenomena. Several multi-omics analyses of Covid-19 have been proposed to integrate multiple "omes" data to unravel disease mechanisms at multiple omics levels (Overmyer et al 2021;Su et al 2020;Montaldo et al 2021;P. Wu, Chen, et al 2021;Stephenson et al 2021).…”

“…In recent years, multi-omics studies have proven a powerful and successful strategy to provide a broader perspective in understanding disease development and biological phenomena. Several multi-omics analyses of Covid-19 have been proposed to integrate multiple “omes” data to unravel disease mechanisms at multiple omics levels (Overmyer et al 2021; Su et al 2020; Montaldo et al 2021; P. Wu, Chen, et al 2021; Stephenson et al 2021). The integrative analyses of rare genome and other “omes” data (e.g., proteome, transcriptome, epigenome, metabolome, and microbiome) may inspire us to discover new risk factors for severe Covid-19 disease.…”