H5N1 Update

By Ahmed Mostafa, Elsayed M. Abdelwhab, Thomas C. Mettenleiter, and Stephan Pleschka - mdpi.com/1999-4915/10/9/497/htm, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=92987475

H5N1, bird flu, continues to infect wild and domestic birds, cattle, cats, and humans. So far, luck has been with us and H5N1 hasn't become a serious threat to humans. That is unless you don't consider the price of eggs and the contribution that issue made to the current chaos and incompetence in Washington DC.

On Feb. 28, 2025, I downloaded 6,623 H5N1 HA sequences in FASTA format from GISAID in order to look at the current state of mutations in the virus data. The analysis below is similar to posts here and here.

I read the sequences into a dataframe with the FASTA header information becoming the columns of the dataframe. 

> df_2025_02_28 <- fasta2dataframe("data/gisaid_epiflu_sequence_HA_2025_02_28.fasta")

The fasta2dataframe function is described in this post. 

fasta2dataframe filters out all sequences with length below 1700. Next I wrote the filtered sequences to a new FASTA file.

> library(LocaTT)
> write.fasta(names = df_2025_02_28$seq.name, sequences = df_2025_02_28$seq.text, file = "data/gisaid_epiflu_sequence_HA_2025_02_28_len.fasta")

The sequences were aligned with MAFFT.

time mafft --6merpair --maxambiguous 0.05 --preservecase --thread -1 --addfragments data/gisaid_epiflu_sequence_HA_2025_02_28_len.fasta data/HA_reference.fasta > data/gisaid_epiflu_sequence_HA_2025_02_28_aln.fasta

I made some modification to simplify the Python program gisaid_H5N1_mutations.py.The updated program is available on GitHub. The first 10 rows of the output CSV file are show below.

reference_position	alignment_pos	ref_freq	alt_freq	ref_nucleotide	codon_pos	ref_aa	aa_name	ref_codon	alt_nucleotide	alt_aa	alt_aa_name	alt_codon	mutation	synonomous
4	37	0.8040201005025126	0.1564070351758794	G	4	E	Glu	GAG	A	K	Lys	AAG	E4K	non_syn
6	39	0.7986809045226131	0.1727386934673367	G	4	E	Glu	GAG	A	E	Glu	GAA	E4E	syn
18	51	0.6105527638190955	0.37170226130653267	A	16	L	Leu	CTA	T	L	Leu	CTT	L16L	syn
31	64	0.7842336683417085	0.198178392	G	31	V	Val	GTT	A	I	Ile	ATT	V31I	non_syn
93	126	0.6526381909547738	0.3473618090452261	A	91	Q	Gln	CAA	G	Q	Gln	CAG	Q91Q	syn
123	156	0.7956972361809045	0.20100502512562815	T	121	T	Thr	ACT	C	T	Thr	ACC	T121T	syn
154	187	0.8285175879396985	0.17132537688442212	A	154	T	Thr	ACA	G	A	Ala	GCA	T154A	non_syn
171	206	0.5855841708542714	0.39777010050251255	A	169	L	Leu	CTA	C	L	Leu	CTC	L169L	syn
174	210	0.5860552763819096	0.41363065326633164	C	172	C	Cys	TGC	T	C	Cys	TGT	C172C	syn
177	213	0.5910804020100503	0.40891959798994976	C	175	D	Asp	GAC	T	D	Asp	GAT	D175D	syn

Luckily, again no new reported mutations that seem likely to increase the ability of the virus to invade human cells.

The code can be found on GitHub.