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Updated: Apr 17, 2026
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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
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COVID-19 severity biomarkers identified by transcriptomics: a scoping review
Thais Teixeira Oliveira1, Viviane Priscila Barros de Medeiros1, Júlia Firme Freitas1
1Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil.
Infectious Diseases (London, England)
|April 15, 2026
Summary
This review highlights key immune genes and pathways altered by SARS-CoV-2 infection. Findings suggest potential biomarkers and therapeutic targets, but reproducibility challenges necessitate standardized research protocols for COVID-19 transcriptomics.
Area of Science:
- Molecular Biology
- Immunology
- Infectious Diseases
Background:
- Omics technologies, especially transcriptomics, were crucial for studying host and viral gene expression during the COVID-19 pandemic.
- Systematic reviews are vital for synthesizing findings from numerous COVID-19 research studies and identifying consistent patterns.
Purpose of the Study:
- To conduct a scoping review of human transcriptomic studies on SARS-CoV-2 infection.
- To identify and evaluate genes and pathways significantly affected by the virus between 2020 and January 2023.
Main Methods:
- Comprehensive literature search of PubMed and Scopus databases.
- Screening of studies based on predefined inclusion/exclusion criteria and journal ethics compliance (COPE/DOAJ).
- Two-step data extraction focusing on sample/patient characteristics, transcriptomic methods, and key findings.
Main Results:
- Consistent identification of immune-related genes and pathways across studies, despite methodological variations.
- Key findings include upregulated cytokines/chemokines (e.g., CXCL8, TNF-α, CCL2), interferon-stimulated genes (e.g., MX1, IFI27), and neutrophil markers (e.g., S100A8).
Conclusions:
- Recurrently identified genes show promise as prognostic biomarkers and therapeutic targets for COVID-19.
- Understanding immunopathological mechanisms is enhanced, aiding diagnostic tool and intervention development.
- Limited reproducibility highlights the need for standardized guidelines to improve the reliability of future transcriptomic research.
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