tetano
Editor, Senior Moderator
iScience
. 2020 Dec 16;24(1):101947.
doi: 10.1016/j.isci.2020.101947. eCollection 2021 Jan 22.
Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections
Simone A Thair[SUP] 1 [/SUP], Yudong D He[SUP] 1 [/SUP], Yehudit Hasin-Brumshtein[SUP] 1 [/SUP], Suraj Sakaram[SUP] 1 [/SUP], Rushika Pandya[SUP] 1 [/SUP], Jiaying Toh[SUP] 2 3 [/SUP], David Rawling[SUP] 1 [/SUP], Melissa Remmel[SUP] 1 [/SUP], Sabrina Coyle[SUP] 1 [/SUP], George N Dalekos[SUP] 4 [/SUP], Ioannis Koutsodimitropoulos[SUP] 5 [/SUP], Glykeria Vlachogianni[SUP] 6 [/SUP], Eleni Gkeka[SUP] 7 [/SUP], Eleni Karakike[SUP] 8 [/SUP], Georgia Damoraki[SUP] 8 [/SUP], Nikolaos Antonakos[SUP] 8 [/SUP], Purvesh Khatri[SUP] 2 3 [/SUP], Evangelos J Giamarellos-Bourboulis[SUP] 8 [/SUP], Timothy E Sweeney[SUP] 1 [/SUP]
Affiliations
Abstract
The pandemic 2019 novel coronavirus disease (COVID-19) shares certain clinical characteristics with other acute viral infections. We studied the whole-blood transcriptomic host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using RNAseq from 24 healthy controls and 62 prospectively enrolled patients with COVID-19. We then compared these data to non-COVID-19 viral infections, curated from 23 independent studies profiling 1,855 blood samples covering six viruses (influenza, respiratory syncytial virus (RSV), human rhinovirus (HRV), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), Ebola, dengue). We show gene expression changes in COVID-19 versus non-COVID-19 viral infections are highly correlated (r = 0.74, p < 0.001). However, we also found 416 genes specific to COVID-19. Inspection of top genes revealed dynamic immune evasion and counter host responses specific to COVID-19. Statistical deconvolution of cell proportions maps many cell type proportions concordantly shifting. Discordantly increased in COVID-19 were CD56[SUP]bright[/SUP] natural killer cells and M2 macrophages. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of the host response to SARS-CoV-2.
Keywords: Immunology: Bioinformatics; Molecular Biology; Transcriptomics.
. 2020 Dec 16;24(1):101947.
doi: 10.1016/j.isci.2020.101947. eCollection 2021 Jan 22.
Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections
Simone A Thair[SUP] 1 [/SUP], Yudong D He[SUP] 1 [/SUP], Yehudit Hasin-Brumshtein[SUP] 1 [/SUP], Suraj Sakaram[SUP] 1 [/SUP], Rushika Pandya[SUP] 1 [/SUP], Jiaying Toh[SUP] 2 3 [/SUP], David Rawling[SUP] 1 [/SUP], Melissa Remmel[SUP] 1 [/SUP], Sabrina Coyle[SUP] 1 [/SUP], George N Dalekos[SUP] 4 [/SUP], Ioannis Koutsodimitropoulos[SUP] 5 [/SUP], Glykeria Vlachogianni[SUP] 6 [/SUP], Eleni Gkeka[SUP] 7 [/SUP], Eleni Karakike[SUP] 8 [/SUP], Georgia Damoraki[SUP] 8 [/SUP], Nikolaos Antonakos[SUP] 8 [/SUP], Purvesh Khatri[SUP] 2 3 [/SUP], Evangelos J Giamarellos-Bourboulis[SUP] 8 [/SUP], Timothy E Sweeney[SUP] 1 [/SUP]
Affiliations
- PMID: 33437935
- PMCID: PMC7786129
- DOI: 10.1016/j.isci.2020.101947
Abstract
The pandemic 2019 novel coronavirus disease (COVID-19) shares certain clinical characteristics with other acute viral infections. We studied the whole-blood transcriptomic host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using RNAseq from 24 healthy controls and 62 prospectively enrolled patients with COVID-19. We then compared these data to non-COVID-19 viral infections, curated from 23 independent studies profiling 1,855 blood samples covering six viruses (influenza, respiratory syncytial virus (RSV), human rhinovirus (HRV), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), Ebola, dengue). We show gene expression changes in COVID-19 versus non-COVID-19 viral infections are highly correlated (r = 0.74, p < 0.001). However, we also found 416 genes specific to COVID-19. Inspection of top genes revealed dynamic immune evasion and counter host responses specific to COVID-19. Statistical deconvolution of cell proportions maps many cell type proportions concordantly shifting. Discordantly increased in COVID-19 were CD56[SUP]bright[/SUP] natural killer cells and M2 macrophages. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of the host response to SARS-CoV-2.
Keywords: Immunology: Bioinformatics; Molecular Biology; Transcriptomics.