Post AurXLFenOBdWldcOBM by dryak@mstdn.science
 (DIR) More posts by dryak@mstdn.science
 (DIR) Post #AurXL5rXnvtOOHVQfI by dryak@mstdn.science
       2023-08-28T11:49:08Z
       
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       This toot thread is a follow up of  last week's thread:https://mstdn.science/@dryak/110944791704289812…
       
 (DIR) Post #AurXL7abNtWpkJavXE by dryak@mstdn.science
       2023-08-28T11:51:31Z
       
       0 likes, 1 repeats
       
       For the period of August 8-14, we have clear detections in Schwyz on August 13, 14, and 15; clear detection in Luzern on August 12; less distinct detection in Chur on August 13. There is a suspicion of detection in Basel on August 10. No detection in Laupen after August 5 and 6. For a representation of the basin that drains into these wastewater treatment plants, please refer to the map of that sister project:https://www.covid19.admin.ch/en/epidemiologic/waste-water…
       
 (DIR) Post #AurXLFenOBdWldcOBM by dryak@mstdn.science
       2023-08-28T11:53:40Z
       
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       We have also looked at mutations specific for sub-clades, but :- DK/UK clade: we don't find convincing evidence, but the signature mutations of this clade do not give us a very specific local haplotype to look for.- US/IL clade: we don't find evidence for the presence of US/IL sub-clade in our dataset- JP clade: cannot be investigated through combinations of mutations on the same amplicon.…
       
 (DIR) Post #AurXLaNqKPYP38qeAq by dryak@mstdn.science
       2023-08-28T12:05:44Z
       
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       We have updated our signatures using covSpectrum ( @chaoranchen ). Combinations on Artic v5.3.2 amplicons used to detect BA.2.86 bellow:(copy-pasteable version in Alt-Text)…
       
 (DIR) Post #AurXLif9Xw9aj90aGW by dryak@mstdn.science
       2023-08-28T12:08:49Z
       
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       The analysis was performed using our SIB Software Resource #Vpipe - the #NGS #bioinformatics pipeline tool for virus #sequencing. Detection handled by the component COJAC.More details on our project and procedure available at https://cov-spectrum.org/stories/wastewater-in-switzerland and at https://github.com/cbg-ethz/cowwid …#opensource#snakemake
       
 (DIR) Post #AurXLrdMBz44YBEmDQ by dryak@mstdn.science
       2023-08-28T12:10:06Z
       
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       Official upload of the raw data to ENA’s SRA is still a couple of weeks away. In the meantime, we will update shortly our shared folder containing compressed raw reads: https://polybox.ethz.ch/index.php/s/NHFcTLX412pjgg9Update: this week's batch is now available on the polybox link.…#FAIR#OpenScience#reproducibility
       
 (DIR) Post #AurXLzlnwSZjmhFdUe by dryak@mstdn.science
       2023-08-28T12:11:20Z
       
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       This data has been obtained through the effort of the WISE consortium - Wastewater Infectious diseases Surveillance and Epidemiology - a collaboration between the ETH Zürich groups CBG and cEvo, the EAWAG, and the FGCZ ( @CatharineAquino ); supported by the @snsf_ch and the BAG/FOPHThank you for your attention!