This is a one-off Nextstrain build for SARS-like coronaviruses, visible at nextstrain.org/groups/blab/sars-like-cov.
Data
The Wuhan coronavirus genomes were generously shared by scientists at the Shanghai Public Health Clinical Center & School of Public Health, Fudan University (sample WH-Human_1) via this post on virological.org, and by scientists at the National Institute for Viral Disease Control and Prevention, China CDC (samples BetaCoV/Wuhan/IVDC-HB-01/2019, BetaCoV/Wuhan/IVDC-HB-05/2019, BetaCoV/Wuhan/IVDC-HB-04/2020) at the Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College (sample BetaCoV/Wuhan/IPBCAMS-WH-01/2019) and at the Wuhan Institute of Virology, Chinese Academy of Sciences (sample BetaCoV/Wuhan/WIV04/2019) via GISAID. We gratefully acknowledgement their contributions.
Background data for this build was sourced from Genbank via VIPR. Here, we downloaded all the SARS-like coronaviruses that were more than 5000 bases in length. These sequences are available in the repo at data/sequences.fasta.
Novel coronaviruses from Wuhan are not included as part of this repo as many of them are protected by the terms of GISAID sharing. Here, these 6 genomes will need to be supplemented by the user. Please add these as additional strains in data/sequences.fasta. Metadata for these 6 viruses already exists in data/metadata.tsv.
Building
After provisioning the data/sars-like-cov.fasta file, the entire build can be regenerated by cloning the repository and running
snakemake -p
with a local Nextstrain installation or by running
nextstrain build .
with a containerized Nextstrain installation.
The resulting output JSON at auspice/beta-cov.json can be visualized by running auspice view --datasetDir auspice or nextstrain view auspice/ depending on local vs containerized installation.
Notes
There were 5 SNPs present in the Wuhan samples in the first 11 bases of the alignment that are masked with N in the pipeline (via rule mask) as likely sequencing artifacts. Additionally, sample BetaCoV/Wuhan/IVDC-HB-05/2019 may have sequencing artifacts that make it appear more diverged than it actually is.