SARS-CoV-2 lineage dynamics

This web resource shows the epidemiological dynamics of SARS-CoV-2 lineages in individual countries/regions based on viral genome sequence data shared via GISAID. This analysis suggests potential variants of interest (VOIs), as lineages that rise significantly in frequency over time. These lineages may have a selective advantage to spread in the host population, for example due to more efficient transmission, replication or immune evasion. Notably, lineages might also be falsely identified as VOIs in case of unrepresentative sampling, e.g. data biases towards certain areas, large clonal outbreaks or population bottlenecks. Information should therefore be interpreted in combination with epidemiological information and experimental evidence that amino acid changes observed in a certain lineage are likely to confer a selective advantage. The S-protein allele dynamics tab provides information on amino acid changes in the major surface protein that distinguish a lineage rising in prevalence from the parental one in individual countries.

SARS-CoV-2 lineage dynamics by region

Country/Region-wise lineage analyses are available for red-shaded countries/regions directly by clicking on the map area. Data derived from GISAID and JHU CSSE COVID-19 Data.

Prevalence of potential variants of interest for SARS-Cov-2 across countries

Relative frequencies for SARS-CoV-2 potential variants of interest (pVOIs) identified in individual countries and most abundant worldwide pVOIs correspond to lineages found to be significantly on the rise over time, which can indicate a selective advantage to spread in the host population (Method). Dark blue indicates a frequency of one, white a frequency of zero. pVOIs are sorted from top to bottom by decreasing prevalence over all countries/regions. For further information about the SARS-CoV-2 lineage names, which follow the Pangolin nomenclature, see the FAQ. Note that country/region-wise frequency coloring is for the previous month, to avoid inaccuracies due to low sample numbers for the current ones.

Antigenic Alteration Scores for current SARS-Cov-2 lineages per country/region

Global map that depicts the assigned antigenic score per country/region in the previous month. The score is representative of the circulating lineages in the previous month, their potential antigenicity and frequency in that country/region. A dark blue represents a country antigenic score of 0 while red depicts a country antigenic score of 10. Countries/regions with higher antigenic scores have higher frequency circulating lineages that scored higher for potential antigenicity based on the methodology outlined here (Method).