blab/sars-like-cov

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

sars-like-cov's Issues

there are several question about the data and logic this project

First, thank you for your providing of the metadate and code.
Afther build the environment of the nextstrain, I run this code succesfully, and there several question want to ask for help.

1. the computing of divergence with 'mutation_length' and 'branch_length', what' s the relation between them? and I am confused about how to get the mutation_length and branch_length?
2. why there are so many name :"NODE_00000XX" in the output josn even thoungh they have the div? and thus , the num of node in the end is much less than the data in metadata?

broken link in footer

The link in the description is to /sars-like-cov?clade=Wuhan which (i'm guessing) works locally but doesn't work on nextstrain.org. It should include the groups prefix, like so: /groups/blab/sars-like-cov?clade=Wuhan

Additionally, I think the filter names have changed from a previous build so I believe the desired link is /groups/blab/sars-like-cov?f_virus_type=Wuhan_coronavirus

A few collection dates for the SARS epidemic

Hi I found two websites with some collection dates for the SARS epidemic
http://covdb.popgenetics.net/v2/index/searchlist https://era.ed.ac.uk/bitstream/handle/1842/5859/Raghwani2012.pdf?sequence=3&isAllowed=y

GZ02 2003-02-11 GD01 2003-04-13 TW1 2003-03-30 SZ3 2003-05-15 SZ16 2003-05-15 CUHK-AG01 2003-03-15 GZ0401 2003-12-22 HC/SZ/79/03 2003-12-29 HC/GZ/81/03 2003-12-31 HC/GZ/32/03 2003-12-12 HC/SZ/61/03 2003-12-20 civet020 2004-01-02 PC4-227 2004-01-05 CFB/SZ/94/03 2003-12-29 PC4-13 2004-01-10 PC4-136 2004-01-05 GZ0402 2004-01-05 civet010 2004-01-02 B039 2004-01-05 civet007 2004-01-02 A022 2004-01-05 CUHK-W1 2003-03-15 GZ50 2003-02-20 CUHK-Su10 2003-03-05 Tor2 2003-04-13 Sin2679 2003-03-15 BJ01 2003-03-07 CUHK-AG02 2003-03-23 HKU-39849-recSARS-CoV-HKU 2003-04-16 Frankfurt-1 2003-03-15 Sin3725V 2003-04-15 Sin3765V 2003-04-15 ZJ0301-from-China 2003-04-21 BJ02 2003-04-21 Sin845 2003-04-07 BJ03 2003-06-03 WHU 2003-05-03 ZJ01 2003-05-12 GD69 2003-08-03 GZ-B 2003-03-15 GZ-A 2003-02-22 LC2 2003-03-15 HC/SZ/DM1/03 2003-10-22

You can see there the timetree I obtained after removing a few outlier sequences http://babarlelephant.free-hoster.net/dist/index.html?sarscov1.json

TreeTime?

The official ncov build for global human samples constructs a time-resolved tree. Can we do that here too? (their snakefile)

Add strains from Eliot et al.

We should update this build to include the following GenBank accessions from Eliot et al.:

• MZ937000 (BANAL-52)
• MZ937001 (BANAL-103)
• MZ937002 (BANAL-116)
• MZ937003 (BANAL-236)
• MZ937004 (BANAL-247)

These data don't appear to be publicly posted on GenBank yet, however.

Add strains from Starr et al.

I don't know if this is the most appropriate place to document this request (or maybe the betacoronavirus build is better?), but Starr et al. describes the evolution of Sarbecoviruses including the ACE2 binding capability of a virus found in Africa. This virus, BtKY72, is one of two viruses in Tyler's tree that originate from Europe or Africa. BtkY72 appears in the beta-cov build mentioned above but it doesn't appear in this build. The other most closely related strain, BM48-31/BGR/2008, is from Europe and does not appear in either this build or the beta-cov build.

Maybe a better solution is to encourage/help Tyler host his own community build for his existing tree, but alternately, we could add the following strains to this build:

• BtKY72 from Kenya
• BM48-31/BGR/2008 from Europe

Just curious

What does RaTG13 in BetaCoV/bat/Yunnan/RaTG13/2013 stands for? I think Ra stands for Rhinolophus affinis, but what is TG13 then?