Covid-19 Variants & Lineages
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 And possibly warn if the lineage has been withdrawn?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https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt Some of the lineages are reassigned or withdrawn.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