Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE152641
Status 2020/12/10
Title Transcriptomic Similarities and Differences in Host Response between SARS-CoV-2 and Other Viral Infection
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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
Samples
GSM ID Sample info Characteristics Description
GSM4622642 IMX_sample00016 disease:Healthy control; tissue:Whole blood; age:51; Sex:Female -
GSM4622643 IMX_sample00017 disease:Healthy control; tissue:Whole blood; age:35; Sex:Female -
GSM4622644 IMX_sample00018 disease:Healthy control; tissue:Whole blood; age:20; Sex:Male -
GSM4622645 IMX_sample00019 disease:COVID19; tissue:Whole blood; age:51; Sex:Female -
GSM4622646 IMX_sample00020 disease:COVID19; tissue:Whole blood; age:36; Sex:Female -
GSM4622647 IMX_sample00021 disease:COVID19; tissue:Whole blood; age:43; Sex:Male -
GSM4622648 IMX_sample00022 disease:COVID19; tissue:Whole blood; age:71; Sex:Female -
GSM4622695 IMX_sample00069 disease:COVID19; tissue:Whole blood; age:59; Sex:Female -
GSM4622649 IMX_sample00023 disease:COVID19; tissue:Whole blood; age:64; Sex:Male -
GSM4622696 IMX_sample00070 disease:COVID19; tissue:Whole blood; age:55; Sex:Female -
GSM4622650 IMX_sample00024 disease:COVID19; tissue:Whole blood; age:61; Sex:Female -
GSM4622651 IMX_sample00025 disease:COVID19; tissue:Whole blood; age:52; Sex:Male -
GSM4622697 IMX_sample00071 disease:COVID19; tissue:Whole blood; age:78; Sex:Female -
GSM4622652 IMX_sample00026 disease:COVID19; tissue:Whole blood; age:51; Sex:Male -
GSM4622698 IMX_sample00072 disease:COVID19; tissue:Whole blood; age:32; Sex:Female -
GSM4622653 IMX_sample00027 disease:COVID19; tissue:Whole blood; age:67; Sex:Male -
GSM4622699 IMX_sample00073 disease:COVID19; tissue:Whole blood; age:NA; Sex:Female -
GSM4622627 IMX_sample00001 disease:Healthy control; tissue:Whole blood; age:46; Sex:Male -
GSM4622628 IMX_sample00002 disease:Healthy control; tissue:Whole blood; age:61; Sex:Male -
GSM4622629 IMX_sample00003 disease:Healthy control; tissue:Whole blood; age:37; Sex:Male -
GSM4622654 IMX_sample00028 disease:COVID19; tissue:Whole blood; age:69; Sex:Male -
GSM4622630 IMX_sample00004 disease:Healthy control; tissue:Whole blood; age:48; Sex:Male -
GSM4622631 IMX_sample00005 disease:Healthy control; tissue:Whole blood; age:28; Sex:Male -
GSM4622632 IMX_sample00006 disease:Healthy control; tissue:Whole blood; age:45; Sex:Female -
GSM4622633 IMX_sample00007 disease:Healthy control; tissue:Whole blood; age:66; Sex:Male -
GSM4622634 IMX_sample00008 disease:Healthy control; tissue:Whole blood; age:31; Sex:Male -
GSM4622700 IMX_sample00074 disease:COVID19; tissue:Whole blood; age:62; Sex:Female -
GSM4622635 IMX_sample00009 disease:Healthy control; tissue:Whole blood; age:37; Sex:Male -
GSM4622655 IMX_sample00029 disease:COVID19; tissue:Whole blood; age:83; Sex:Male -
GSM4622701 IMX_sample00075 disease:COVID19; tissue:Whole blood; age:87; Sex:Female -
GSM4622636 IMX_sample00010 disease:Healthy control; tissue:Whole blood; age:38; Sex:Female -
GSM4622656 IMX_sample00030 disease:COVID19; tissue:Whole blood; age:62; Sex:Female -
GSM4622637 IMX_sample00011 disease:Healthy control; tissue:Whole blood; age:21; Sex:Female -
GSM4622638 IMX_sample00012 disease:Healthy control; tissue:Whole blood; age:31; Sex:Male -
GSM4622702 IMX_sample00076 disease:COVID19; tissue:Whole blood; age:76; Sex:Female -
GSM4622639 IMX_sample00013 disease:Healthy control; tissue:Whole blood; age:37; Sex:Female -
GSM4622640 IMX_sample00014 disease:Healthy control; tissue:Whole blood; age:61; Sex:Female -
GSM4622657 IMX_sample00031 disease:COVID19; tissue:Whole blood; age:68; Sex:Male -
GSM4622641 IMX_sample00015 disease:Healthy control; tissue:Whole blood; age:27; Sex:Male -
GSM4622703 IMX_sample00077 disease:COVID19; tissue:Whole blood; age:72; Sex:Male -
GSM4622658 IMX_sample00032 disease:COVID19; tissue:Whole blood; age:70; Sex:Male -
GSM4622704 IMX_sample00078 disease:COVID19; tissue:Whole blood; age:90; Sex:Male -
GSM4622659 IMX_sample00033 disease:COVID19; tissue:Whole blood; age:69; Sex:Female -
GSM4622705 IMX_sample00079 disease:COVID19; tissue:Whole blood; age:67; Sex:Male -
GSM4622660 IMX_sample00034 disease:COVID19; tissue:Whole blood; age:62; Sex:Male -
GSM4622706 IMX_sample00080 disease:COVID19; tissue:Whole blood; age:71; Sex:Male -
GSM4622661 IMX_sample00035 disease:COVID19; tissue:Whole blood; age:52; Sex:Male -
GSM4622707 IMX_sample00081 disease:Healthy control; tissue:Whole blood; age:30; Sex:Male -
GSM4622662 IMX_sample00036 disease:COVID19; tissue:Whole blood; age:50; Sex:Male -
GSM4622663 IMX_sample00037 disease:COVID19; tissue:Whole blood; age:65; Sex:Female -
GSM4622708 IMX_sample00082 disease:Healthy control; tissue:Whole blood; age:29; Sex:Male -
GSM4622709 IMX_sample00083 disease:Healthy control; tissue:Whole blood; age:32; Sex:Male -
GSM4622664 IMX_sample00038 disease:COVID19; tissue:Whole blood; age:61; Sex:Male -
GSM4622710 IMX_sample00084 disease:Healthy control; tissue:Whole blood; age:29; Sex:Male -
GSM4622665 IMX_sample00039 disease:COVID19; tissue:Whole blood; age:48; Sex:Female -
GSM4622666 IMX_sample00040 disease:COVID19; tissue:Whole blood; age:55; Sex:Male -
GSM4622711 IMX_sample00085 disease:Healthy control; tissue:Whole blood; age:22; Sex:Male -
GSM4622667 IMX_sample00041 disease:COVID19; tissue:Whole blood; age:52; Sex:Male -
GSM4622712 IMX_sample00086 disease:Healthy control; tissue:Whole blood; age:37; Sex:Male -
GSM4622668 IMX_sample00042 disease:COVID19; tissue:Whole blood; age:56; Sex:Male -
GSM4622669 IMX_sample00043 disease:COVID19; tissue:Whole blood; age:79; Sex:Male -
GSM4622670 IMX_sample00044 disease:COVID19; tissue:Whole blood; age:78; Sex:Male -
GSM4622671 IMX_sample00045 disease:COVID19; tissue:Whole blood; age:59; Sex:Female -
GSM4622672 IMX_sample00046 disease:COVID19; tissue:Whole blood; age:35; Sex:Female -
GSM4622673 IMX_sample00047 disease:COVID19; tissue:Whole blood; age:40; Sex:Male -
GSM4622674 IMX_sample00048 disease:COVID19; tissue:Whole blood; age:78; Sex:Male -
GSM4622675 IMX_sample00049 disease:COVID19; tissue:Whole blood; age:52; Sex:Male -
GSM4622676 IMX_sample00050 disease:COVID19; tissue:Whole blood; age:54; Sex:Male -
GSM4622677 IMX_sample00051 disease:COVID19; tissue:Whole blood; age:74; Sex:Male -
GSM4622678 IMX_sample00052 disease:COVID19; tissue:Whole blood; age:73; Sex:Male -
GSM4622679 IMX_sample00053 disease:COVID19; tissue:Whole blood; age:50; Sex:Female -
GSM4622680 IMX_sample00054 disease:COVID19; tissue:Whole blood; age:64; Sex:Male -
GSM4622681 IMX_sample00055 disease:COVID19; tissue:Whole blood; age:31; Sex:Female -
GSM4622682 IMX_sample00056 disease:COVID19; tissue:Whole blood; age:53; Sex:Male -
GSM4622683 IMX_sample00057 disease:COVID19; tissue:Whole blood; age:88; Sex:Male -
GSM4622684 IMX_sample00058 disease:COVID19; tissue:Whole blood; age:43; Sex:Male -
GSM4622685 IMX_sample00059 disease:COVID19; tissue:Whole blood; age:40; Sex:Male -
GSM4622686 IMX_sample00060 disease:COVID19; tissue:Whole blood; age:66; Sex:Male -
GSM4622687 IMX_sample00061 disease:COVID19; tissue:Whole blood; age:84; Sex:Male -
GSM4622688 IMX_sample00062 disease:COVID19; tissue:Whole blood; age:60; Sex:Female -
GSM4622689 IMX_sample00063 disease:COVID19; tissue:Whole blood; age:63; Sex:Male -
GSM4622690 IMX_sample00064 disease:COVID19; tissue:Whole blood; age:69; Sex:Female -
GSM4622691 IMX_sample00065 disease:COVID19; tissue:Whole blood; age:46; Sex:Male -
GSM4622692 IMX_sample00066 disease:COVID19; tissue:Whole blood; age:68; Sex:Male -
GSM4622693 IMX_sample00067 disease:COVID19; tissue:Whole blood; age:68; Sex:Male -
GSM4622694 IMX_sample00068 disease:COVID19; tissue:Whole blood; age:49; Sex:Male -
Platform GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
Literature 33437935  
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xCell Plot
* p<0.05 ** p<0.01