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Welcome to VOCAL

The goal of Vocal is to detect sc-2 emerging variants from collected bases of genomes, before their annotation by phylogenetic analysis. It does so by parsing sc2 genomes and detecting amino acids mutations in the spike proteins that can be associated with a phenotypic change. The phenotypic changes are annotated according to the knowledge accumulated on previous variants. Owing to the limited size of the genome, convergent evolution is expected to take place.

An overview of the VOCAL architecture

VOCAL workflow

VOCAL workflow

First, VOCAL can start from a raw complete genomic sequence of SC2, or region for the spike protein or directly query large collection of sequences from our covSonar API. Then, we use a List of known mutations of concerns (MOCs), region of interest (ROIs), and lineage defined mutation to annotate the spike regions.

Next, We integrate extra information such as the known variant of concerns (VOCs) or variant of interest (VOIs) from online sources, antibody escape score from bloom lab, and meta information (such as our metafile from the DESH system). We pass all this information together through the VOCAL alert system to generate an alert level for the given sample. Finally, after we get the alert result, we generate a report to help us to get an overview of the prediction result or important detail.

VOCAL with Positive Selection and VOCAL-AutoMode

We obtained SARS-CoV-2 mutation information for each lineage. Further, we identified sites (codons) within the SARS-CoV-2 spike gene that are subject to positive selection based on the estimated ratio of non-synonymous to synonymous substitutions (dN/dS).

We utilised positive selection information and extended the VOCAL scoring scheme to be able to integrate a classification strategy directly. We settled first on binary classification by grouping what should raise a red, a pink or an orange alert together and applying the Decision Tree classifier (VOCAL-AutoMode).

Contact

Did you find a bug?🐛 Suggestion/Feedback/Feature request?👨‍💻 please visit GitHub Issues

For business inquiries or professional support requests 🍺 please contact

Dr. Hölzer, Martin(HoelzerM@rki.de) or Dr. Richard, Hugues (RichardH@rki.de)

Citation

xxx🚔 coming soon 🔜xxx

Version

VOCAL 0.8