Nextstrain build for novel coronavirus SARS-CoV-2

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Latest Nextstrain COVID-19 situation report in English and in other languages. Follow @nextstrain for continual updates to data and analysis.

This phylogeny shows evolutionary relationships of hCoV-19 (or SARS-CoV-2) viruses from the ongoing novel coronavirus COVID-19 pandemic. This phylogeny shows an initial emergence in Wuhan, China, in Nov-Dec 2019 followed by sustained human-to-human transmission leading to sampled infections. Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of specific transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred transmission patterns are only a hypothesis.

There are thousands of complete genomes available now and this number increases by hundreds of every day. This visualization can only handle ~3000 genomes in a single view for performance and legibility reasons. Because of this we have to subsample available genome data for these analysis views. Our primary global analysis subsamples to 120 genomes per admin division per month. This will result in a more equitable global sequence distribution, but it hides samples available from regions that are doing lots of sequencing. To mitigate against this, we've set up separate analyses to focus on particular regions. They are available on the "Dataset" dropdown on the left or by clicking on the following links: Africa, Asia, Europe, North America, Oceania and South America.

Site numbering and genome structure uses Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 8 × 10-4 subs per site per year. Full details on bioinformatic processing can be found here.

Phylogenetic context of nCoV in SARS-related betacoronaviruses can be seen here.

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based. A full listing of all originating and submitting laboratories is available below. An attribution table is available by clicking on "Download Data" at the bottom of the page and then clicking on "Strain Metadata" in the resulting dialog box.