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German scientists have developed a molecular surveillance tool called CovRadar for the SARS-CoV-2 spike protein that can help epidemiologists and virologists to understand the pathogen better.
The findings, published in the preprint server bioRxiv, noted that the tool has an analysis pipeline and a web application.
According to the researchers, CovRadar is flexible and can handle large amounts of data, and users can customise it based on their needs.
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Both the pipeline and the app can be installed and run on local systems so that access-restricted sequences can be included, and all functionalities are offered at covradar.net.
How it works
The researchers claimed that CovRadar makes it possible to analyse and visualise more than 2,50,000 sequences.
It first extracts the regions of interest using local alignment and then develops a multiple sequence alignment, infers variants, consensus sequences, and phylogenetic trees. After this, it shows the results in an app to make reporting handy and flexible.
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The interactive report on the SARS-CoV-2 spike protein is an application written in Flask and Dash and is linked to a MySQL database.
The web app layout is similar to a PDF report with functionalities, including filtering, printing, and navigation in the side menu bars.
CovRadar can help with situations where zoonotic transmissions with host-specific mutations are possible.
The researchers analysed the positions in the current Danish mink data with high allele frequencies and compared the data with human data both before and after the mink outbreak by using CovRadar.
“CovRadar was designed to assist the molecular surveillance of the Corona spike protein used as a target for most vaccine candidates,” the authors of the study stated.
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