Global evolution of SARS-CoV-2 and dynamic monitoring & prediction of COVID-19

Global Distribution of SARS-CoV-2 Lineage

Country/territory-wise SARS-CoV-2 lineage distributions of 121,618 genomes from GISAID (up to December 2, 2020) based on 206 marker SNV sites. In total 217,305 genomes were retrieved from GISAID (as of December 2, 2020),121,618 non-redundant genomes were used in the analysis after quality control. Criteria for quality control and redundancy filtering: 1) Ns < 5%; 2) length > 29,000 after removing Ns; 3) non-redundant sequences under the threshold of 99.99% sequence identity.

Distribution map
Card world
Development and prediction of global COVID-19 pandemic

Estimation of the reproduction number (R) and prediction of the infected population of SARS-CoV-2 for each country by fitting a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model.

Lineage Classification Tool

A tool for assigning SARS-CoV-2 genomes into defined lineages based on the combinations of bases at 206 marker SNV sites .

Surveillance of global dynamics of COVID-19 pandemic

Summary of global dynamics of COVID-19 pandemic, including the cumulative confirmed cases, daily confirmed cases, active confirmed cases, deaths, and matality for each country.

Variations in SARS-CoV-2

Visualizing variant sites (20,487 in total, degenerate bases excluded) in 121,618 SARS-CoV-2 genomes (site 221-29674) from GISAID (up to December 2, 2020). Quality control: 1) Ns < 5%; 2) length > 29,000 after removing Ns; 3) non-redundant sequences under the threshold of 99.99% sequence identity.

Publications