2022-01-05

2022-01-05

SARS-CoV-2

New dataset version (tag 2022-01-05T19:54:31Z)

• Reference tree: Added more Omicron sequences, from all of BA.1/BA.2/BA.3
• Reference tree: General data update with new pango lineages
• Sample sequences: Added BA.2 and BA.3 to sample sequences

2021-12-16

Influenza

New dataset version (tag 2021-12-16T20:15:53Z)

• Clades: New WHO clades names are used
• Reference tree: Data source is now GISAID which means better global coverage

SARS-CoV-2

New dataset version (tag 2021-12-16T20:57:35Z)

• Clades: 21M (Omicron) added as Omicron catch all equivalent to pango B.1.1.529
• Clades: 21L elevated to 21L (Omicron) in line with WHO practice
• QC: Fixed known frameshift ORF7b:3 (was erroneously ORF7a:3)

2021-12-09

SARS-CoV-2

New dataset version (tag 2021-12-09T18:09:18Z)

• Clades: Omicron is split into 21K (Omicron) (pango BA.1) and 21L (pango BA.2). The minor clade 21L is at this point not called Omicron by WHO so it does not get the Omicron label for now.
• Reference tree: Data has been updated to early December
• Pango lineages designated until early December have been sampled in

2021-12-03--00-14-37--UTC

General

• Added explicit cache-control headers

SARS-CoV-2

• Sample sequences: Added two 21K (Omicron) sequences

2021-11-27

2021-11-27

SARS-CoV-2

New dataset version (tag 2021-11-27T11:53:22Z)

Changes

• Clades: 21K is renamed 21K (Omicron) in line with WHO elevation to VOC status

2021-11-26

2021-11-26

SARS-CoV-2

New dataset version (tag 2021-11-26T14:02:45Z)

Changes

• Data source: GISAID data is now used to generate the reference tree. This switch is necessary, because the new clade 21K (B.1.1.529) is only present in GISAID data, thus far.

Updates

• New clade: 21K (B.1.1.529) has been added to the reference tree
• Reference tree: Data has been updated to sequences submitted to GISAID by 2021-11-24
• Reference tree: Pango lineages designated until 2021-11-24 have been sampled into the tree

2021-11-16

SARS-CoV-2

New dataset version (tag 2021-11-16T16:38:05Z)

Changes

• Reference tree: Recombinant pango lineages (= those starting with X) have been excluded in order to reduce clade misassignment noise, in particular for short sequences like just S. Only one recombinant has been designated so far (XA) and it broke up the branch leading up to Alpha exerting bad influence that warranted removal.
• QC rules: The lists of known, (likely) biological and thus acceptable frame shifts and stop codons have been extended. The ~20 most common frame shifts and ~40 most common stop codons on genes ORF3a/6/7a/7b/8 are now declared known. Common frame shifts and stops on ORF1a/b and S are not declared known since these are most likely sequencing artefacts and not biological.

Updates

• Reference tree: Data has been updated to sequences submitted to Genbank by mid November
• Reference tree: Pango lineages designated until 2021-11-04 have been sampled into the tree
• Sample sequences