# Examining SC2 Spike 452 Mutations

Wuhan reference at the site is amino acid L, so we are looking for L452 to anything.

This initial look excludes Mu (B.1.621)

Also of note, this initial look **excludes any codon coding for Leucine (L).** Meaning synonymous L.
>L452 to anything
WILDTYPE_452 = ["TTA", "TTG", "CTT", "CTC", "CTA", "CTG"]

Initial software and exports are located in
> /data/shares/veg/SARS-CoV-2/452Mutations
> /data/shares/veg/SARS-CoV-2/452Mutations/get_variants.py

Including
> /data/shares/veg/SARS-CoV-2/452Mutations/export/

GISAID data is from roughly mid-August
> WD = "/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/exports/1627776000/S"
> Analyzed file "sequences_nuc.bealign.fas" within that directory

This script creates a "452_Muts.txt" file, which is a csv formated file, header is the GISAID ID, and the codon present at the 452 site in spike.
>/data/shares/veg/SARS-CoV-2/452Mutations/get_variants.py

> epi_isl_583700,NTG
epi_isl_632904,ATG
epi_isl_626279,CGG
epi_isl_661243,CGG
epi_isl_666889,CGG
epi_isl_413695,---
epi_isl_429311,CGG
epi_isl_670699,CTN

This was then exported for each clade (with 245 clades total) in:
> /data/shares/veg/SARS-CoV-2/452Mutations/export

For analysis, we prioritized VOIs/VOCs and use the following code

> /home/aglucaci/SARS-CoV-2_Clades
> /home/aglucaci/Snakefile_452Muts
> /home/aglucaci/run_Silverback_452Muts.sh

Analysis is completed in
> /home/aglucaci/SARS-CoV-2_Clades/results/452_Muts

for the following clades
>drwxr-xr-x 2 aglucaci veg 32K Aug 27 12:06 AY.1.452
drwxr-xr-x 2 aglucaci veg 32K Sep 16 09:24 AY.3.452
drwxr-xr-x 2 aglucaci veg 36K Sep 1 15:29 B.1.1.7.452
drwxr-xr-x 2 aglucaci veg 32K Aug 25 17:15 B.1.351.452
drwxr-xr-x 2 aglucaci veg 32K Aug 27 16:53 B.1.525.452
drwxr-xr-x 2 aglucaci veg 36K Sep 1 12:44 B.1.526.452
drwxr-xr-x 2 aglucaci veg 32K Aug 30 18:25 B.1.617.1.452
drwxr-xr-x 2 aglucaci veg 36K Sep 23 18:41 B.1.617.2.452
drwxr-xr-x 2 aglucaci veg 32K Sep 6 00:12 C.37.452
drwxr-xr-x 2 aglucaci veg 32K Aug 26 21:47 P.1.1.452
drwxr-xr-x 2 aglucaci veg 32K Aug 25 17:23 P.1.452

## Summary and annotation json files are located in

On silverback
> /home/aglucaci/SARS-CoV-2_Clades/SummaryAndAnnotation/452_Muts

## Useful links
* https://outbreak.info/situation-reports?muts=S%3AL452R