publication . Preprint . Article . 2021

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

Mariana Galvão Ferrarini; Avantika Lal; Rita Rebollo; Andreas J. Gruber; Andrea Guarracino; Itziar Martinez Gonzalez; Taylor Floyd; Daniel Siqueira de Oliveira; Justin Shanklin; Ethan Beausoleil; ...
Open Access
  • Published: 01 Dec 2021
  • Publisher: Cold Spring Harbor Laboratory
Abstract
The novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we analyzed public host and viral RNA sequencing data to better understand how SARS-CoV-2 interacts with human respiratory cells. We identified genes, isoforms and transposable element families that are specifically altered in SARS-CoV-2-infected respiratory cells. Well-known immunoregulatory genes including CSF2, IL32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were upregulated. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and eukaryotic initiation factor 4 (eIF4b). We also identified a viral sequence variant with a statistically significant skew associated with age of infection, that may contribute to intracellular host–pathogen interactions. These findings can help identify host mechanisms that can be targeted by prophylactics and/or therapeutics to reduce the severity of COVID-19.
Ferrarini & Lal et al. developed a novel bioinformatic pipeline to explore how SARS-CoV-2 interacts with human respiratory cells using public available host gene expression and viral genome sequence data. Several human genes and proteins were predicted to play a role in the viral life cycle and the host response to SARS-CoV-2 infection.
Sustainable Development Goals (SDG) [Beta]
Subjects
Medical Subject Headings: fungi
free text keywords: [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Article, SARS-CoV-2, RNA, Computational biology and bioinformatics, Transcriptomics, Viral infection, Biology (General), QH301-705.5, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Medicine (miscellaneous), Genetics, Biology, RNA, Disease, Polymerase, biology.protein, Genome, Betacoronavirus, biology.organism_classification, Viral life cycle, DNA sequencing, Transposable element, Heterogeneous Nuclear Ribonucleoprotein A1, Gene, Transcriptome, RNA-Seq, EIF4B, ddc:570
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