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", selected_variants = selected_variants, title = "Selected Variants USA 2023-08-08", start_date = as.Date("2022-09-01")))

This command produces a plot of the counts of sequences uploaded to the database.

Although the total counts for these variants is lower than those show here, it looks like EG.5.1 nicknamed the Eris variant, is becoming dominant.  

You can find the code to produce the plot here.