Detecting SARS Cov 2 Lineages And Mutational Load In Municipal Wastewater
Channel: R Consortium
Date: 2022-09-09

Nikolas Pechlivanis, a Ph.D. candidate at the Institute of Applied Biosciences, Centre for Research and Technology in Hellas, gave a short talk at the BioConductor Conference 2022. Pechlivanis gave his presentation on Detecting SARS Cov 2 Lineages And Mutational Load In Municipal Wastewater And A Use Case In The Metropolitan Area Of Thessaloniki, Greece.

Pechlivanis began his presentation by giving an overview on the project and explained the motivation to track the Covid SARS 2 virus using lineagespot. Lineagespot was developed for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). The tool accepts as input a VCF file, which contains all nucleotide (and the corresponding amino acid) mutations identified in a sample, along with a file containing all lineage-assignment mutations. Pechlivanis shared how the package works and gave an overview of the workflow, and quantification. Pechlivanis also discussed more about how the Lineagespot package was used to track in the area of Thessaloniki, Greece. The presentation concluded with Pechlivanis sharing future developments and gave acknowledgments to the other contributors of the project. 



Main Sections

0:00 Introduction
0:30 What is lineagspot? 
0:50 What is our motivation?
1:53 How does it work? Input-output
2:34 An overview of the workflow 
3:29 Quantifying lineage abundance
5:22 A use-case in the metropolitan area of Thessaloniki, Greece
6:19 lineagespot usage
6:45 Future development and acknowledgments

More Resources 

Bioconductor Conference Site: https://bioc2022.bioconductor.org/ 
BioC2022 Github: https://github.com/Bioconductor/BioC2022 

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