Repository for suggesting new lineages that should be added to the current scheme
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Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by aineniamh over 3 years ago
Withdrawing lineages B.1.553 and B.1.608 addressing issues #82 and #81.
Published by chrisruis over 3 years ago
Published by aineniamh over 3 years ago
Published by chrisruis over 3 years ago
Published by aineniamh over 3 years ago
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
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
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by aineniamh over 3 years ago
Removal of low coverage B.1 sequences wrt issue #64.
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Published by chrisruis over 3 years ago
Added new lineage AU.1 with 353 sequence designations
Designation of sequence Australia/QLD1550/2021 updated from B.1.466.2 to AU.1
Published by aineniamh over 3 years ago
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 https://github.com/cov-lineages/pango-designation/commit/8a5d954ecf76b2d66c3b5d4f9c01c2985bd8f51b.
Published by aineniamh over 3 years ago
Addressing pangolearn issue #6, B.1.562.3 typo of B.1.526.3. 11 sequences changed.
Published by chrisruis over 3 years ago