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| 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 I |
| Organisms |
Homo sapiens; synthetic construct; Severe acute respiratory syndrome coronavirus 2 |
| Experiment type |
Other
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| 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.
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| Overall design |
RNAseq and sequence variant analysis for 63036 human nasopharyngeal swabs for SARS-CoV-2, with 1928 negative swabs and 2886 synthetic controls.
(part2) Additional RNAseq and sequence variant analysis for 3129 human nasopharyngeal swabs for SARS-CoV-2, with 283 negative swabs and 259 synthetic controls.
Please note that the 'sparseq_sample_data_GEOver_v3.txt' and 'sparseq_sample_data_GEOver_part2_v3.txt' files were replaced with the 'sparseq_sample_data_GEOver_v4.txt' and 'sparseq_sample_data_GEOver_part2_v4.txt', respectively, on Oct 10, 2024 (only to fix some typos in text fields, no change to the number of samples).
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| 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, Krzyzanowski P, Simpson J, Bartlett J, Lungu I, Wouters BG, Rini JM, Gekas M, Poutanen S, Pelletier L, Mazzulli T, Wrana JL |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 09, 2023 |
| Last update date |
Oct 10, 2024 |
| Contact name |
Jeff Wrana |
| Organization name |
Lunenfeld-Tanenbaum Research Institute
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| Street address |
600 University Avenue
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1X5 |
| Country |
Canada |
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| Platforms (6)
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| GPL17769 |
Illumina MiSeq (synthetic construct) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
| GPL26967 |
Illumina MiniSeq (synthetic construct) |
| GPL28867 |
Illumina NextSeq 500 (Homo sapiens; Severe acute respiratory syndrome coronavirus 2) |
| GPL30234 |
Illumina MiSeq (Homo sapiens; Severe acute respiratory syndrome coronavirus 2) |
| GPL33112 |
Illumina MiniSeq (Homo sapiens; Severe acute respiratory syndrome coronavirus 2) |
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| Samples (29)
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| GSM7036174 |
Negative human nasopharyngeal swab group 1 |
| GSM7036175 |
Negative human nasopharyngeal swab group 2 |
| GSM7036176 |
Negative human nasopharyngeal swab group 3 |
| GSM7036177 |
Negative human nasopharyngeal swab group 4 |
| GSM7036178 |
Negative human nasopharyngeal swab group 5 |
| GSM7036179 |
Negative human nasopharyngeal swab group 6 |
| GSM7037121 |
synthetic control group 1 |
| GSM7037122 |
synthetic control group 2 |
| GSM7037123 |
synthetic control group 3 |
| GSM7037124 |
synthetic control group 4 |
| GSM7037125 |
synthetic control group 5 |
| GSM7037126 |
synthetic control group 6 |
| GSM7039241 |
Positive human nasopharyngeal swab group 1 |
| GSM7039810 |
Positive human nasopharyngeal swab group 2 |
| GSM7043904 |
Positive human nasopharyngeal swab group 3 |
| GSM7043905 |
Positive human nasopharyngeal swab group 4 |
| GSM7043906 |
Positive human nasopharyngeal swab group 5 |
| GSM7043907 |
Positive human nasopharyngeal swab group 6 |
| GSM7044115 |
Positive human nasopharyngeal swab group 7 |
| GSM7044266 |
Positive human nasopharyngeal swab group 8 |
| GSM7044281 |
Positive human nasopharyngeal swab group 9 |
| GSM7044283 |
Positive human nasopharyngeal swab group 10 |
| GSM7044284 |
Positive human nasopharyngeal swab group 11 |
| GSM7257032 |
Negative human nasopharyngeal swab group 1 (part2) |
| GSM7257033 |
Negative human nasopharyngeal swab group 2 (part2) |
| GSM7257034 |
synthetic control group 1 (part2) |
| GSM7257035 |
synthetic control group 2 (part2) |
| GSM7257036 |
Positive human nasopharyngeal swab group 1 (part2) |
| GSM7257037 |
Positive human nasopharyngeal swab group 2 (part2) |
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| 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 |
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| Relations |
| BioProject |
PRJNA933169 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE224951_README_sample_annotations_GEOver_part2.txt |
968.3 Kb |
(ftp)(http) |
TXT |
| GSE224951_SRR_and_filenames_GEOver_README.txt.gz |
883.0 Kb |
(ftp)(http) |
TXT |
| GSE224951_SRR_and_filenames_GEOver_part2_README.txt |
240.1 Kb |
(ftp)(http) |
TXT |
| GSE224951_sparseq_control_data_GEOver.txt.gz |
137.7 Kb |
(ftp)(http) |
TXT |
| GSE224951_sparseq_control_data_GEOver_part2.txt.gz |
12.3 Kb |
(ftp)(http) |
TXT |
| GSE224951_sparseq_negative_data_GEOver.txt.gz |
97.2 Kb |
(ftp)(http) |
TXT |
| GSE224951_sparseq_negative_data_GEOver_part2.txt.gz |
14.3 Kb |
(ftp)(http) |
TXT |
| GSE224951_sparseq_sample_data_GEOver_part2_v4.txt.gz |
332.3 Kb |
(ftp)(http) |
TXT |
| GSE224951_sparseq_sample_data_GEOver_v4.txt.gz |
6.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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