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Nextstrain build for novel coronavirus (nCoV)
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README.md

This is a Nextstrain build for novel coronavirus (nCoV), visible at nextstrain.org/ncov.

Data

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 this description file.

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. Please add these as strains in data/sequences.fasta. Metadata for these viruses already exists in data/metadata.tsv. This data/sequences.fasta should just have strain name in the FASTA header, like so:

>Wuhan/WIV04/2019
attaaaggtttat...
>USA/IL1/2020
attaaaggtttat...
>Wuhan/WIV06/2019
ccttcccaggtaa...

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).

Current translations:

Language Translator(s) Latest version released
Mandarin Alvin X. Han, Fengjun Zhang 2020-01-25
Spanish Ch. Julian Villabona-Arenas 2020-01-25

Contributing

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 hello@nextstrain.org or on Twitter at @nextstrain.

Building

After provisioning the data/sequences.fasta file, the entire build can be regenerated by running

snakemake -p

with a local Nextstrain installation or by running

nextstrain build .

with a containerized Nextstrain installation.

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 >=6.2.0, released Jan 25, 2020.

Notes

There were apparently spurious SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts. A SNP at 18529 in BetaCoV/Wuhan/IVDC-HB-04/2020 appears directly adjacent to a long stretch of ambiguous bases and so has also been masked.

Site numbering and genome structure uses BetaCoV/Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 3 × 10^-4 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. The sample Wuhan/IPBCAMS-WH-05/2020 has been dropped from the analysis due to the appearance of clustered, spurious SNPs.

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