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.
【저자키워드】 SARS-CoV-2, viral infection, transcriptomics, Computational biology and bioinformatics, RNA, 【초록키워드】 COVID-19, coronavirus, Therapeutics, IL-6, SARS-COV-2 infection, variant, Infection, host response, severe acute respiratory syndrome Coronavirus, Betacoronavirus, Protein, Viral, severity of COVID-19, SARS-CoV-2 genome, Wuhan, age, Viral RNA, respiratory, mechanism, host gene expression, Interaction, ribonucleoprotein, life cycle, initiation factor, transposable element, acute respiratory syndrome, acute respiratory syndrome coronavirus, viral genome sequence, worldwide pandemic, novel Betacoronavirus, sequence, help, human respiratory cells, human genes, heterogeneous, sequencing data, viral life cycle, host–pathogen interactions, CSF2, hnRNPA1, nuclear, human gene, eIF4b, IL32, isoforms, SERPINA3, isoform, Host, Genes, respiratory cells, Wuhan, China, predicted, analyzed, identify, caused, conserved, contribute, interact, upregulated, reduce, statistically significant, differentially expressed, eukaryotic, human respiratory cell, the SARS-CoV-2 genome, 【제목키워드】 Viral, SARS-CoV-2 pathogenesis, predict, Factor, Host, analysis,