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Series GSE231415 Query DataSets for GSE231415
Status Public on Jul 30, 2024
Title Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population II
Organisms Homo sapiens; synthetic construct; Severe acute respiratory syndrome coronavirus 2
Experiment type Expression profiling by high throughput sequencing
Summary Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of Spike in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets. Furthermore, we found that subvariants and putative quasi-species with alterations characteristic of future VOCs and/or predicted to be functionally important arose frequently, but always extinguished. Systematic screening of functionally relevant domains in pathogens could thus provide a powerful tool for monitoring spread and mutational trajectories, particularly those with zoonotic potential.
 
Overall design RNAseq and barcode analysis for 1987 human nasopharyngeal swabs for SARS-CoV-2, with 24 negative swabs and 43 synthetic controls.
 
Contributor(s) Aynaud M, Caldwell L, Al-Zahrani KN, Barutcu S, Chan K, Obersterescu A, Ogunjimi AA, Jin M, Zakoor K, Patel S, Padilla R, Jen M, Veniegas P, Dewsi N, Yonathan F, Zhang L, Ayson-Fortunato A, Aquino A, Krzyzanowksi P, Simpson J, Bartlett J, Lungu I, Wouters BG, Rini JM, Gekas M, Poutanen S, Pelletier L, Mazzulli T, Wrana JL
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Submission date May 01, 2023
Last update date Jul 30, 2024
Contact name Jeff Wrana
Organization name Lunenfeld-Tanenbaum Research Institute
Street address 600 University Avenue
City Toronto
State/province Ontario
ZIP/Postal code M5G 1X5
Country Canada
 
Platforms (2)
GPL19424 Illumina NextSeq 500 (synthetic construct)
GPL28867 Illumina NextSeq 500 (Homo sapiens; Severe acute respiratory syndrome coronavirus 2)
Samples (2054)
GSM7275242 12132022_H2O-multi-V1-2_S536_R1C3_23G_S66
GSM7275243 12132022_H2O-RT-V1-2_S83_R1C3_23A_S17
GSM7275244 12132022_HEK-200ng-SM4-2p66pg-V1-2_S386_R1C3_23E_S50
This SubSeries is part of SuperSeries:
GSE231416 Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population
Relations
BioProject PRJNA964787

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE231415_run139_BC_pair_analysis_filenames.txt.gz 75.7 Kb (ftp)(http) TXT
GSE231415_run139_R1BC_count_table.txt.gz 13.2 Kb (ftp)(http) TXT
GSE231415_run139_R2BC_count_table.txt.gz 9.8 Kb (ftp)(http) TXT
GSE231415_run139_count_table.txt.gz 10.1 Kb (ftp)(http) TXT
GSE231415_run141p3_BC_pair_analysis_filenames.txt.gz 92.4 Kb (ftp)(http) TXT
GSE231415_run141p3_R1BC_count_table.txt.gz 14.7 Kb (ftp)(http) TXT
GSE231415_run141p3_R2BC_count_table.txt.gz 18.0 Kb (ftp)(http) TXT
GSE231415_run141p3_count_table.txt.gz 10.4 Kb (ftp)(http) TXT
GSE231415_run141p6_BC_pair_analysis_filenames.txt.gz 38.3 Kb (ftp)(http) TXT
GSE231415_run141p6_R1BC_count_table.txt.gz 7.7 Kb (ftp)(http) TXT
GSE231415_run141p6_R2BC_count_table.txt.gz 9.0 Kb (ftp)(http) TXT
GSE231415_run141p6_count_table.txt.gz 5.9 Kb (ftp)(http) TXT
GSE231415_run27_BC_pair_analysis_filenames.txt.gz 17.2 Kb (ftp)(http) TXT
GSE231415_run27_R1BC_count_table.txt.gz 4.6 Kb (ftp)(http) TXT
GSE231415_run27_R2BC_count_table.txt.gz 5.3 Kb (ftp)(http) TXT
GSE231415_run27_count_table.txt.gz 3.9 Kb (ftp)(http) TXT
GSE231415_run31_BC_pair_analysis_filenames.txt.gz 61.4 Kb (ftp)(http) TXT
GSE231415_run31_R1BC_count_table.txt.gz 14.1 Kb (ftp)(http) TXT
GSE231415_run31_R2BC_count_table.txt.gz 14.6 Kb (ftp)(http) TXT
GSE231415_run31_count_table.txt.gz 10.7 Kb (ftp)(http) TXT
GSE231415_run38_BC_pair_analysis_filenames.txt.gz 50.1 Kb (ftp)(http) TXT
GSE231415_run38_R1BC_count_table.txt.gz 13.4 Kb (ftp)(http) TXT
GSE231415_run38_R2BC_count_table.txt.gz 14.4 Kb (ftp)(http) TXT
GSE231415_run38_count_table.txt.gz 12.0 Kb (ftp)(http) TXT
GSE231415_run46_BC_pair_analysis_filenames.txt.gz 57.1 Kb (ftp)(http) TXT
GSE231415_run46_R1BC_count_table.txt.gz 14.2 Kb (ftp)(http) TXT
GSE231415_run46_R2BC_count_table.txt.gz 14.5 Kb (ftp)(http) TXT
GSE231415_run46_count_table.txt.gz 11.6 Kb (ftp)(http) TXT
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Processed data are available on Series record
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