The repository cogcz was created to support the release of bi-weekly reports about the SARS-CoV-2 variants in the Czech Republic. The sections of the repository reflect contributions from individual COG-CZ members.
The establishment of the COG-CZ concortium was initiated by Michal Kolář, Jan Pačes, Vladimír Hampl, Martin Kolísko, and Karel Berka. The full list of contributors is stated in the report.
As the COG-CZ consortium aims to provide in-depth analyses of available viral whole-genome sequences, figures with specialized bioinformatical outputs can be found in the report.
The bioinformatical analyses cover phylogeny of SARS-CoV-2 isolates, differences in protein structures of SARS-CoV-2 lineages, geographical distribution of lineages, mutations spread inside the Czech Republic, the time course of the mutations and lineages. The report is not intended to bring new findings about virus biology.
The sequences are linked with metadata about sex, age, collection site, date of collection. So far, no interconnection between sequenced samples and vaccination status of the host has been possible to be evaluated.
The GISAID database were established as the primary source for the dataset of "Czech sequences", "Czech isolates", i.e. viral samples of persons taken inside the Czech Republic.
The sequences following the quality criteria summarized in the whitepaper are recommended to be uploaded to GISAID and considered for subsequent analyses.
The WGS sequencing effort has been made by public state and academic institutions led by the Institute of Molecular Biology, CAS, National Institute of Public Health, BIOCEV, Biology Centre, CAS, Palacký Univeristy in Olomouc.
Each consortium member can insert changes into the report directly by editting sections of this repository. Each editor shall establish his own branch. After merging, an updated pdf and html files will be automatically created. The report can be then downloaded in the GitHub Actions as the latest run.
The bi-weekly reporting started in the week 16, year 2021. The report is issued only in the Czech language.
