In-host evolution of SARS-CoV-2
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ABSTRACT:
PROVIDER: PRJEB47786 | ENA |
REPOSITORIES: ENA
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Project description:The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus’s effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways
2023-05-25 | E-MTAB-13028 | biostudies-arrayexpress
Project description:COVID-19 is a pandemic that shares only certain clinical characteristics with other acute viral infections. Here, we studied the whole-blood transcriptomic host response to SARS-CoV-2 and compared it with other viral infections to understand similarities and differences in host response. We profiled peripheral blood from 24 healthy controls and 62 prospectively enrolled patients with community-acquired lower respiratory tract infection by SARS-Cov-2 within the first 24 hours of hospital admission using RNA-seq. We also collected 23 independent studies that profiled 1,855 blood samples from patients with one of six viruses (influenza, RSV, HRV, Ebola, Dengue, and SARS). We identified differentially expressed genes that change in patients with COVID-19 or other viral infections. We show changes in gene expression in peripheral blood from patients with COVID-19 are highly correlated with changes in response to other viral infections (r=0.74, p<0.001). However, two genes, ACO1 and ATL3, show significantly different changes in expression. Pathway analysis of differentially expressed genes in patients with COVID-19 or other viral infections versus healthy controls also identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection, and cytokine production for over-expressed genes, as well as lymphocyte differentiation and T cell activation for under-expressed genes. When comparing transcriptome profiles of patients with COVID-19 directly with those with other viral infections, we found 114 and 302 genes were over- and under-expressed, respectively during COVID-19. Pathways analysis did not identify any significant pathways in these genes. Statistical deconvolution using immunoStates found that M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells, and total B cells showed changes consistently in the same direction across all viral infections including COVID-19. Those that increased in COVID-19 but decreased in non-COVID were CD56bright NK cells, M2 macrophages, and total NK cells. The concordant and discordant responses mapped out via such a comparison provides a window to explore the underlying biology of why COVID-19 is so different from other viral infections encountered so far. Together, results from pathway and immunoStates analyses help dissect major shifts in cellularity and activation of signaling pathways as part of host response to SARS-CoV-2
2020-12-10 | GSE152641 | GEO
Project description:SARS-CoV-2 is a beta coronavirus causing COVID-19 which first emerged in Wuhan, China and was later declared a pandemic by the World Health Organization. Since then the economical, health and human cost has been enormous for the world. However, little work has been done to understand the transcriptional changes brought about by the virus in human hosts. We have compared COVID-19 positive samples with negative samples from Indian patients to better understand the host response.. We find many genes related to immune response up-regulated in the COVID-19 patients. Many of these are the usual response genes against the viral infection but type I interferon appears to be a key immune response activated against SARS-CoV-2. A large number of the differentially expressed genes were down-regulated pointing towards translational arrest and down regulation of host mRNA during late infection. The down-regulated genes are well correlated with the clinical manifestations and symptoms due to SARS-CoV-2 infection such as the loss of smell and taste. We also find evidence of altered gene expression profiles associated with systemic complications such as neurological disturbances and high insulin requirement. Finally, we have identified many lncRNAs being down-regulated during COVID-19 infections. A few of these lncRNAs have functional role in viral infection. However, to understand the functional role of other lncRNAs, we looked at the function of their closest gene, since lncRNA are believed to have cis functionality. Our analysis suggests a role for lncRNA in down-regulation of metabolic and developmental processes during COVID-19 infection.
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