[R] Covid-19 Variants & Lineages

[Leonard Mada]

Dear R-Users,

1.) Is there a package which gives the full code of a Covid-19 
lineage/variant?

E.g. Omicron = B.1.1.529, while BA correspond to specific subtypes of 
Omicron:
BA.x:
BA.1 = B.1.1.529.1;
BA.1.1 = B.1.1.529.1.1;
BA.1.1.5 = B.1.1.529.1.1.5;

Is there any package to offer such trans-coding functionality? And 
possibly warn if the lineage has been withdrawn?

The full list is available on GitHub:
https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt
Some of the lineages are reassigned or withdrawn. It seems feasible to 
process this list.

2.) Covid Mutations
Is there a package to retrieve the full list of mutations of a specific 
lineage/variant?

E.g. each node in the "tree" B.1.1.529.1.1.5 accumulates 1 or more new 
mutations. It is probably very uncommon for a mutation to get mutated 
back; so the mutations accumulate.

The data on the NCBI page "Explore in SARS-CoV-2 Variants Overview" 
seems very difficult to download:
https://www.ncbi.nlm.nih.gov/activ
E.g.: (in the lower-left corner, but impossible to copy)
NSP1: S135R
NSP13: R392C
[...]


Maybe there is a package already offering such functionality. I am now 
looking over the documentation of the COVID19.Analytics package, but I 
may miss the relevant functions.


Sincerely,


Leonard