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.