pango designations v1.1.23

Release notes

Update to designations of lineage B.1.575 and B.1.575.1.

USA and Aruba lineage with spike mutations "S:P681H","S:S494P" and "S:T716I".

From all SARS-CoV-2 genomes on GISAID as of 2021-04-25, any sequences with at least 8 of the SNPs below were aligned with a selection of B.1 genomes to place them within B.1 diversity. These sequences include previously designated B.1.575 sequences and a couple of sequences that had previously been designated as B.1.1.335.

snps = [
"S:D614G",
"S:P681H",
"S:S494P",
"S:T716I",
"N:T205I",
"orf1ab:T3750I",
"orf1ab:T3255I",
"orf1ab:T265I",
"M:182T",
"orf3a:Q57H"
]

Total designations of B.1.575 and sublineage B.1.575.1:

B.1.575 1,571
B.1.575.1 168

Designation changed to B.1.575:

2 B.1.1.335 sequences

See changes in commit 8a5d954.

pango designations v1.1.22

Release notes

Addressing pangolearn issue #6, B.1.562.3 typo of B.1.526.3. 11 sequences changed.

pango designations v1.1.21

• Added lineage P.1.2 from #56
• Added lineage B.1.622 from #58

v1.1.20

• Added lineage C.37 from #52
• Added lineage B.1.621 from #57

pango designations v1.1.19

Release notes

Update to B.1.617 to now designate specific sublineages representing three clusters. Full description found at #49 .

Final counts for updated designations:

B.1       40
B.1.617   1
B.1.617.1 468
B.1.617.2 112
B.1.617.3 23

B.1.617.sublineages.csv

v1.1.17

• Added 4 sublineages within B.1.438 - B.1.438.1 (Canada), B.1.438.2 (Mayotte/Reunion), B.1.438.3 (USA) and B.1.438.4 (USA)
• Added B.1.438 into lineage_notes.txt

pango designations v1.1.18

Release notes

Update to designation of B.1.617, described fully in issue #49.

Designated 605 sequences to B.1.617 and 34 sequences previously assigned B.1.617 (never designted) now designated B.1.

v1.1.16

• Added lineage B.1.619
• Added lineage B.1.620

v1.1.15

• Added lineage AT.1

v1.1.14

• Updated B.1.526 lineages
• Added lineage B.1.526.3