babarlelephant/sars-like-cov

This is a one-off Nextstrain build for SARS-like coronaviruses

This is a one-off Nextstrain build for SARS-like coronaviruses, visible at nextstrain.org/groups/blab/sars-like-cov.

Data

The SARS-CoV-2 coronavirus genomes were generously shared by scientists at the Shanghai Public Health Clinical Center & School of Public Health, Fudan University (WH-Human_1), at the National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China (Wuhan/IVDC-HB-01/2019, Wuhan/IVDC-HB-05/2019, IVDC-HB-04/2020) at the Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China (Wuhan/IPBCAMS-WH-01/2019), and at the Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China (Wuhan/WIV04/2019). Related SARS-like bat virus bat/Yunnan/RaTG13/2013 was shared by scientists at the Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China (Zhu et al) and related SARS-like pangolin viruses were shared by scientists at the State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China and at the State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, University of Hong Kong, Hong Kong (Lam, Cao et al). 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.

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.

The following viruses are not included as part of this repo as they are protected by the terms of GISAID sharing. Here, these genomes will need to be supplemented by the user. Please add these as additional strains in data/sequences.fasta. Metadata for these viruses already exists in data/metadata.tsv.

• bat/Yunnan/RaTG13/2013
• bat/Yunnan/RmYN01/2019
• bat/Yunnan/RmYN02/2019
• pangolin/Guangdong/1/2020
• pangolin/Guangdong/P2S/2019
• pangolin/Guangxi/P5E/2017
• pangolin/Guangxi/P4L/2017
• pangolin/Guangxi/P5L/2017
• pangolin/Guangxi/P1E/2017

Building

After updating 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/sars-like-cov.json can be visualized by running auspice view --datasetDir auspice or nextstrain view auspice/ depending on local vs containerized installation.