COVID-19 progression towards ARDS: a genome wide study reveals host factors underlying critical COVID-19

Abstract

Coronavirus disease 2019 (COVID-19) is a viral infection produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus epidemic, which was declared a global pandemic in March 2020. The World Health Organization has recorded around 43.3 billion cases and 59.4 million casualties to date, posing a severe threat to global health. Severe COVID-19 indicates viral pneumonia caused by the SARS-CoV-2 infections, which can induce fatal consequences, including acute respiratory distress syndrome (ARDS). The purpose of this research is to better understand the COVID-19 and ARDS pathways, as well as to find targeted single nucleotide polymorphism. To accomplish this, we retrieved over 100 patients' samples from the Sequence Read Archive, National Center for Biotechnology Information. These sequences were processed through the Galaxy server next generation sequencing pipeline for variant analysis and then visualized in the Integrative Genomics Viewer, and performed statistical analysis using t-tests and Bonferroni correction, where six major genes were identified as DNAH7, CLUAP1, PPA2, PAPSS1, TLR4, and IFITM3. Furthermore, a complete understanding of the genomes of COVID-19-related ARDS will aid in the early identification and treatment of target proteins. Finally, the discovery of novel therapeutics based on discovered proteins can assist to slow the progression of ARDS and lower fatality rates.

Keywords: COVID-19; JAK-STAT pathway; acute respiratory distress syndrome.

Fig. 1.

Immunopathology of cells. IFN, interferon; IL-10, interleukin 10; TGF-β, transforming growth factor β.

Fig. 2.

COVID-19–ARDS pathway. COVID-19, coronavirus disease 2019; ARDS, acute respiratory distress syndrome; IL, interleukin; TNF-α, tumor necrosis factor α; IFN, interferon; IP-10, interferon-gamma-inducible protein 10; MIP-1, macrophage inflammatory protein 1.

Fig. 3.

Exploring and monitoring coronavirus disease 2019 (COVID-19) variants with Galaxy.

Fig. 4.

Galaxy server pipeline for single nucleotide polymorphism (SNP) variant analysis.

Fig. 5.

Per base quality score graph.

Fig. 6.

Per sequence GC content analysis.

Fig. 7.

Per base sequence quality before and after trimmomatic.

Fig. 8.

DNAH7 genes having one mutation.