Nextstrain build for novel coronavirus (nCoV)
|size (curr.)||2191 kB|
The nCoV genomes were generously shared via GISAID. 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. For a full list of attributions please see the metadata file.
Situation Report Translations
We welcome translations of the situation reports (narratives) into languages other than English (in particular to countries affected by the outbreak), and have been very impressed with the contributions provided so far. Please get in touch if you can help.
We suggest creating a branch for each language after the each release of the English version. Unfortunately this means that the changes are not visible through nextstrain.org until release, but we are working on improving this.
The situation reports are generated from Markdown files (such as this one for 2020-01-25).
|Language||Translator(s)||Latest version released|
|Mandarin||Alvin X. Han, Fengjun Zhang, Wei Ding||2020-01-30|
|Spanish||Ch. Julian Villabona-Arenas||2020-01-30|
|Portuguese||Glaucio Santos, Anderson Brito||2020-01-30|
|French||Etienne Simon-Lorière, Pierre Barrat-Charlaix||2020-01-30|
|German||Vielen Dank, Nicola Müller, Richard Neher||2020-01-30|
|Russian||Ivan Aksamentov, Vadim Puller||2020-01-30|
We welcome contributions from the community to make this effort as useful as possible to as many people as possible. If you spot errors or inaccuracies, please file an issue or make a pull request. Or get in touch over email at email@example.com or on Twitter at @nextstrain.
In order to run the Nextstrain build you must provision
nCoV genomes are not included as part of this repo as many of them are protected by the terms of GISAID sharing.
These genomes will need to be supplemented by the user.
To do so, register for an account at GISAID and then navigate to EpiCoV and click “Download”.
This should result in the file
Move this file to
ncov/data/gisaid_cov2020_sequences.fasta and then run
./scripts/normalize_gisaid_fasta.sh data/gisaid_cov2020_sequences.fasta data/sequences.fasta
This should be everything needed to have data for the build process described below as metadata for these viruses already exists in
After this, the entire build can be regenerated by running
with a local Nextstrain installation or by running
nextstrain build .
The resulting output JSON at
auspice/ncov.json can be visualized by running
auspice view --datasetDir auspice or
nextstrain view auspice/ depending on local vs containerized installation.
This requires Augur version >=6.3.0, released Feb 13, 2020.
Genomic epidemiology notes
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 0.8 × 10^-3 subs per site per year. There were SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts.