COVID-19 severity biomarkers identified by transcriptomics: a scoping review.

Omics technologies, particularly transcriptomics, were widely used during the COVID-19 pandemic to investigate host and viral gene expression. Given the substantial number of studies published during this period, systematic reviews are essential for synthesising findings and identifying consistent patterns. This scoping review aimed to identify and evaluate transcriptomic studies of SARS-CoV-2 infection in humans published between 2020 and January 2023, with a focus on genes and pathways affected by the virus. A comprehensive literature search was conducted using PubMed and Scopus, employing predefined keywords. Studies were screened using established inclusion and exclusion criteria, and only articles published in journals affiliated with the Committee on Publication Ethics (COPE) or Directory of Open Access Journals (DOAJ) were included. Data extraction followed a two-step process, collecting detailed information on sample and patient characteristics, transcriptomic methods, and main findings. Despite methodological differences and varying time points of sample collection, several immune-related genes and pathways were recurrently reported. These included cytokines and chemokines (e.g. CXCL8, TNF-α, CCL2, CXCL10, and IL-1B), interferon-stimulated genes (e.g. MX1, IFI27, IRF7, and ISG15), and neutrophil degranulation markers (e.g. S100A8 and S100A9). The recurrent identification of these genes underscores their potential as prognostic biomarkers and therapeutic targets, thereby contributing to a deeper understanding of immunopathological mechanisms and supporting the development of improved diagnostic tools and early intervention strategies. However, limited reproducibility across studies poses challenges for robust meta-analyses, underscoring the urgent need for standardised guidelines and protocols to improve consistency and reliability in future research.