Releases: cov-lineages/pango-designation
pango designations 1.2.1
- Several sequence names changed to match GISAID names
- Added lineage AV.1 from #73 containing 12 new sequence designations
pango designations v1.2
Release notes
Description
- Large scale designation release implementing an ambiguity threshold cut off of 5% of ambiguity within the coding region of SARS-CoV-2. This includes both N and non-N ambiguity.
- 1,382,550 sequences with ambiguity assessed, GISAID data as of 2021-05-07
Figure 1: Ambiguity content in sequences on GISAID, coloured by whether they have been designated a Pango lineage or not. Vertical dashed lines highlight the 1% and 5% ambiguity thresholds respectively.
Outcome
-
Designated sequences that passed amb threshold of 5%: 436,887
-
Number of sequences removed because of ambiguity calculation >5%: 18,246
Figure 2: Updated designation record to include only those sequences with a coding region ambiguity content less than 5%. Vertical dashed lines highlight the 1% and 5% ambiguity thresholds respectively. -
Note: designated sequences that didn't match a sequence in GISAID and so we'ren't checked for ambiguity: 18,665, many of these will be from COG-UK and are not yet on GISAID
-
Total sequences written to file: 455,552
Lineages that now have a less than 5 designated sequences
Total count = 4
Lineage previous_count new_count
C.10 4 4
C.6 4 3
AT.1 6 4
B.1.617 1 1
Lineage stats
- Lineages with altered designations: 912
- Total lineage count: 1288
pango designations 1.1.29
- Added recombinant lineage XA (parental lineages B.1.1.7 and B.1.177) from #63 containing 41 new sequence designations and 2 sequences with updated designations (Wales/ALDP-11CF93B/2021 and Wales/ALDP-125C4D7/2021, both formally designated B.1.1.7)
pango designations 1.1.28
- Added lineage B.1.351.3 from issue #65 . B.1.351.3 contains 99 new sequence designations and 1 sequence with an updated designation (Bangladesh/BCSIR-NILMRC-448/2021, previously designated B.1.351)
pango designations v1.1.27
Release notes
Removal of low coverage B.1 sequences wrt issue #64.
pango designations v1.1.26
- Added new lineage B.1.1.522 containing 45 new sequence designations
pango designations v1.1.25
- Added new lineage AU.2 with 24 new sequence designations
- Added new lineage AU.3 with 48 new sequence designations
pango designations v1.1.24
Added new lineage AU.1 with 353 sequence designations
Designation of sequence Australia/QLD1550/2021 updated from B.1.466.2 to AU.1
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.