Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE190680
Status 2022/2/23
Title Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. While viral infections elicit a conserved immune response, it is not known whether SARS-CoV-2 variants, which display reduced neutralizing activity by vaccine-elicited antibodies, prompt specific genomic immune responses. To test this, we generated and investigated the transcriptomes in PBMCs from hospitalized patients infected with either the Alpha variant (n=36) or with the Alpha variant that had acquired the E484K escape mutation (Alpha+E484K) (n=13). We identified a gene module preferentially activated in patients infected with the Alpha+E484K variant and in patients infected with the Alpha (n=9) and Gamma (n=3) variants that also carry by the E484K escape mutation. The E484K signature was enriched for genes preferentially expressed in monocytes and linked to severe viral infection. However, both cohorts had undergone similar treatments and no differences in disease severity were reported suggesting that this signature reflects a variant response and does not necessarily associate with disease outcome. Additionally, longitudinal transcriptome analyses revealed a more persistent retention of immune signatures in Alpha+E484K patients throughout the entire course of COVID-19 disease and convalescence. While the OAS1 Neanderthal mutation has been linked to a milder COVID-19 pathology, we did not identify significant immune transcriptomes differences in the 25 patients homozygous for this mutation. Our study offers insights into distinct molecular immune responses elicited by SARS-CoV-2 variants carrying the E484K escape mutation throughout the COVID-19 disease.
Samples
GSM ID Sample info Characteristics Description
GSM5728928 Alpha_S27_2nd gender:Female; age:75; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728885 Alpha_E484K_S40_2nd gender:Male; age:73; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728929 Alpha_S28_1st gender:Male; age:81; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728886 Alpha_E484K_S40_3rd gender:Male; age:73; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728887 Alpha_E484K_S41_1st gender:Male; age:84; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728930 Alpha_S28_2nd gender:Male; age:81; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728888 Alpha_E484K_S41_2nd gender:Male; age:84; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728931 Alpha_S29_1st gender:Female; age:78; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728889 Alpha_E484K_S41_3rd gender:Male; age:84; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728890 Alpha_E484K_S45_1st gender:Male; age:57; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728932 Alpha_S29_2nd gender:Female; age:78; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728891 Alpha_E484K_S45_2nd gender:Male; age:57; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728892 Alpha_E484K_S51_1st gender:Male; age:86; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728933 Alpha_S30_1st gender:Female; age:76; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728893 Alpha_E484K_S51_2nd gender:Male; age:86; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728934 Alpha_S30_2nd gender:Female; age:76; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728894 Alpha_E484K_S52_1st gender:Female; age:78; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728895 Alpha_E484K_S53_1st gender:Female; age:87; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728935 Alpha_S31_1st gender:Male; age:72; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728896 Alpha_E484K_S53_2nd gender:Female; age:87; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728897 Alpha_E484K_S53_3rd gender:Female; age:87; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728936 Alpha_S32_1st gender:Male; age:86; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728898 Alpha_E484K_S54_1st gender:Female; age:80; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728937 Alpha_S33_1st gender:Female; age:84; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728899 Alpha_E484K_S54_2nd gender:Female; age:80; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728938 Alpha_S33_2nd gender:Female; age:84; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728900 Alpha_E484K_S54_3rd gender:Female; age:80; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728939 Alpha_S34_1st gender:Female; age:81; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728901 Alpha_E484K_S57_1st gender:Female; age:61; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728902 Alpha_E484K_S58_1st gender:Male; age:45; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728940 Alpha_S34_2nd gender:Female; age:81; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728903 Alpha_E484K_S59_1st gender:Male; age:82; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728904 Alpha_E484K_S59_2nd gender:Male; age:82; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728941 Alpha_S35_1st gender:Female; age:67; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728914 Alpha_S10_2nd gender:Female; age:53; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728905 Alpha_E484K_S59_3rd gender:Male; age:82; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728915 Alpha_S11_1st gender:Female; age:65; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728906 Alpha_E484K_S60_1st gender:Male; age:74; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728916 Alpha_S11_2nd gender:Female; age:65; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728942 Alpha_S35_2nd gender:Female; age:67; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728917 Alpha_S11_3rd gender:Female; age:65; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728907 Alpha_E484K_S60_2nd gender:Male; age:74; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728943 Alpha_S38_1st gender:Male; age:83; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728908 Alpha_E484K_S62_1st gender:Female; age:31; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728944 Alpha_S38_2nd gender:Male; age:83; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728918 Alpha_S19_1st gender:Male; age:54; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728909 Alpha_E484K_S62_2nd gender:Female; age:31; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728919 Alpha_S19_2nd gender:Male; age:54; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728910 Alpha_E484K_S62_3rd gender:Female; age:31; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728920 Alpha_S20_1st gender:Female; age:93; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728945 Alpha_S38_3rd gender:Male; age:83; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728921 Alpha_S20_2nd gender:Female; age:93; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728911 Alpha_S08_1st gender:Male; age:67; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728922 Alpha_S21_1st gender:Male; age:60; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728946 Alpha_S42_1st gender:Female; age:69; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728923 Alpha_S21_2nd gender:Male; age:60; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728924 Alpha_S22_2nd gender:Male; age:39; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728925 Alpha_S23_2nd gender:Female; age:60; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728881 Alpha_E484K_S39_1st gender:Male; age:33; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728926 Alpha_S26_1st gender:Male; age:79; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728882 Alpha_E484K_S39_2nd gender:Male; age:33; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728927 Alpha_S27_1st gender:Female; age:75; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728912 Alpha_S08_2nd gender:Male; age:67; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728913 Alpha_S10_1st gender:Female; age:53; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728947 Alpha_S42_2nd gender:Female; age:69; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728883 Alpha_E484K_S39_3rd gender:Male; age:33; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728948 Alpha_S43_1st gender:Male; age:89; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728884 Alpha_E484K_S40_1st gender:Male; age:73; diseas state:COVID-19_Alpha_E484K varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728949 Alpha_S44_1st gender:Male; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728950 Alpha_S44_2nd gender:Male; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728951 Alpha_S44_3rd gender:Male; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728952 Alpha_S46_1st gender:Male; age:61; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728953 Alpha_S46_2nd gender:Male; age:61; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728954 Alpha_S46_3rd gender:Male; age:61; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728955 Alpha_S48_1st gender:Female; age:89; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728974 Alpha_S71_1st gender:Male; age:72; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728956 Alpha_S48_2nd gender:Female; age:89; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728975 Alpha_S71_2nd gender:Male; age:72; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728957 Alpha_S49_1st gender:Female; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728976 Alpha_S72_1st gender:Male; age:30; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728977 Alpha_S72_2nd gender:Male; age:30; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728978 Gamma_S64_1st gender:Male; age:61; diseas state:COVID-19_Gamma varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728979 Gamma_S65_1st gender:Female; diseas state:COVID-19_Gamma varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728980 Gamma_S67_1st gender:Male; age:57; diseas state:COVID-19_Gamma varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728958 Alpha_S49_2nd gender:Female; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728959 Alpha_S50_1st gender:Male; age:75; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728960 Alpha_S50_2nd gender:Male; age:75; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728961 Alpha_S55_1st gender:Female; age:77; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728962 Alpha_S56_2nd gender:Male; age:49; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728963 Alpha_S56_3rd gender:Male; age:49; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728964 Alpha_S61_2nd gender:Female; age:48; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728965 Alpha_S63_1st gender:Female; age:31; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728966 Alpha_S63_2nd gender:Female; age:31; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728967 Alpha_S66_1st gender:Female; age:72; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728968 Alpha_S66_2nd gender:Female; age:72; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728969 Alpha_S68_1st gender:Female; age:93; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728970 Alpha_S69_1st gender:Male; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728971 Alpha_S69_2nd gender:Male; age:80; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728972 Alpha_S70_1st gender:Male; age:92; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
GSM5728973 Alpha_S70_2nd gender:Male; age:92; diseas state:COVID-19_Alpha varient; geographical location:Ischgl, Austria; cell type:PBMC -
Platform GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
Literature 35181735  35784346  
Download Download xCell Data  Download Expression Analysis Data  
xCell Plot
* p<0.05 ** p<0.01