SARS-CoV-2 JN.1
COVID-19 is still with us and it's underlying virus, SARS-CoV-2, is still evolving. The latest variant of concern is JN.1. As of February 2, 2024, the CDC estimates that JN.1 is the viral source of about 93% of all US COVID cases. JN.1 evolved from BA.2.86. BA.2.86 has a large number changes in the spike protein when compared to the original Wuhan sequence. The mutations gave BA.2.86 improved ability to evade the human immune system. In order to compare JN.1 changes to to BA.2.86, on January 22 I downloaded metadata for 16,460,375 sequences from GISAID . I also downloaded the full collection of FASTA SARS-CoV-2 sequences. The analysis that follows is similar to this post . GISAID FASTA headers changed so I had to update some of code. I also wanted to add argument types to the Python code. I used R to extract the BA.2.86 and JN.1 sequences from the metadata file. filter_chunk <- function (pango_lineage) { function (df, pos) { df <- suppressMess...