ArticleMolecular systems biology2022
Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants.
Article in Molecular systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- Rewriting the viral script: post-translational modifications orchestrating SARS-CoV-2 pathogenesis and immune evasion.Frontiers in microbiology · 2026Review
- Systems Virology at Scale.Current opinion in systems biology · 2025Article
- KAP1 in antiviral immunity: dual roles in viral silencing and immune regulation.Frontiers in cellular and infection microbiology · 2025Review
- EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics.Genome biology · 2024Article
- Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach.Briefings in bioinformatics · 2023Article
- Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.Genome biology · 2023Article
- Article
- IPs-GRUAtt: An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection.Molecular therapy. Nucleic acids · 2023Article
- Multi-Omics Studies in Historically Excluded Populations: The Road to Equity.Clinical pharmacology and therapeutics · 2023Review
- Review
- Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants.Molecular systems biology · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
SARS-CoV-2 infection hijacks signaling pathways and induces protein-protein interactions between human and viral proteins. Human genetic variation may impact SARS-CoV-2 infection and COVID-19 pathology; however, the genetic variation in these signaling networks remains uncharacterized. Here, we studied human missense single nucleotide variants (SNVs) altering phosphorylation sites modulated by SARS-CoV-2 infection, using machine learning to identify amino acid substitutions altering kinase-bound sequence motifs. We found 2,033 infrequent phosphorylation-associated SNVs (pSNVs) that are enriched in sequence motif alterations, potentially reflecting the evolution of signaling networks regulating host defenses. Proteins with pSNVs are involved in viral life cycle and host responses, including RNA splicing, interferon response (TRIM28), and glucose homeostasis (TBC1D4) with potential associations with COVID-19 comorbidities. pSNVs disrupt CDK and MAPK substrate motifs and replace these with motifs of Tank Binding Kinase 1 (TBK1) involved in innate immune responses, indicating consistent rewiring of signaling networks. Several pSNVs associate with severe COVID-19 and hospitalization (STARD13, ARFGEF2). Our analysis highlights potential genetic factors contributing to inter-individual variation of SARS-CoV-2 infection and COVID-19 and suggests leads for mechanistic and translational studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.