Analysis of spike amino-acid mutations in BA.2.86 (a new second-generation BA.2 variant)

Small analysis by Jesse Bloom of spike mutations in BA.2.86, a new second-generation BA.2 variant with large number of mutations.

Some background on the small number of sequences for this variant can be found:

• the Pango GitHub issue

• another Pango GitHub issue

• Shay Fleishon's Twitter post

• Ryan Hisner's Twitter post

• Marc Johnson's Twitter post

The sequences analyzed in this repo are the first four reported isolates:

• hCoV-19/Israel/ICH-741198454/2023|EPI_ISL_18096761|2023-07-31
• hCoV-19/Denmark/DCGC-647646/2023|EPI_ISL_18097315|2023-07-31
• hCoV-19/Denmark/DCGC-647676/2023|EPI_ISL_18097345|2023-07-24
• hCoV-19/USA/MI-UM-10052670540/2023|EPI_ISL_18110065|2023-08-03
• hCoV-19/England/GSTT-230817LSBC55/2023|EPI_ISL_18111770|2023-08-13

These sequences are downloaded in ./gisaid_seqs, which is not tracked (see acknowledgments of submitters here). Within that subdirectory, the file ./gisaid_seqs/nextclade_muts.csv has the mutations in those sequences called using NextClade.

The file pango-consensus-sequences_summary.json has the clade founder sequences from Cornelius Roemer.

The Jupyter notebook analyze_muts.ipynb analyzes the spike amino-acid mutations in these sequences.

They are listed in the following files:

• spike_aa_muts_relative_to_BA.2.csv
• spike_aa_muts_relative_to_XBB.1.5.csv
• spike_aa_muts_relative_to_Wuhan-Hu-1.csv