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possibly warn if the lineage has been withdrawn?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Some of the lineages are reassigned or withdrawn.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
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