Summer SARS-CoV-2 Variants
While in large measure, COVID-19 is being ignored by the public, the virus continues to mutate and may yet have some surprises for us. The Washington Post reports : Globally, over 1 million new covid-19 cases and more than 3,100 deaths were reported in the 28 days up to Aug. 3, according to the latest World Health Organization report — bringing the death toll to almost 7 million since the pandemic began. On August 7 2023, I downloaded 15, 849,028 metadata records from GISAID . This is up from 15,398,189 downloaded in April, but it seems that database growth has slowed. I searched the metadata for the top 5 emerging variants for the USA as listed by GISAID : XBB.1.16.6", XBB.1.5.59, EG.5.1, XBB.2.3.8, XBB.2.3. These are subvariants of the Omicron variants. I used the R code described in this post to plot the accumulation of sequences for the variants. system.time(df_variants_usa <- get_selected_variants_ch( "data/metadata.tsv" , select...