XBB.1.5 and More Chunking
This post is an addendum to a previous post . On January 9 2023, I downloaded a SAR-CoV-2 metadata file from GISAID. The file contained 14,499,984 observations of 24 variables. I was interested in the growth of the XBB.1.5 variant. XBB.1.5, also know as the Kraken subvarian t, has been in the news lately because it appears to have greater transmissibility than the other Omicron variants. Here's the plot of the top 5 emerging variants from GISAID: BQ.1.1.22, CH.1.1, XBB.1.5, BQ.1.1, BQ.1.23. XBB.1.5 isn't the major variant yet, but it is growing in the US. The plot above was created with the program get_selected_variants.R from GitHub . The code was described in the previous post . When I ran get_selected_variants.R, on Linux R version 4.1.2 it produced a warning. > system.time(df_variants_usa <- get_selected_variants( 'data/metadata.tsv' , selected_variants = selected_variants, title = 'Selected Variants USA 2023-01-09' , start_date = as.Date...