2022-07-27

Influenza Yamagata HA

Bug fix release (tag 2022-07-27T12:00:00Z)

Fix: The old tree used an incorrect genemap which caused Nextclade to crash. Now it works again.

Beware that Nextclade v2.0.0 until v2.3.0 have had a bug that means this dataset will crash.

You will have to upgrade to Nextclade v2.3.1 or use Nextclade v1 to use this dataset.

2022-07-26

SARS-CoV-2 and SARS-CoV-2-no-recomb

Bug fix release (tag 2022-07-26T12:00:00Z)

Fix: Ancestral reconstruction of mutations was wrong due to recombinants attaching directly to the root and causing the root mutations to be different from Wuhan.

This caused:

• displayed mutations in Auspice to be wrong for all tips since around the time recombinants were first included in the tree (since 2022-03-24T12:00:00Z)
• Some of the calculated reconstructed mutations on recombinants to be wrong, affecting nearest neighbor placement of some recombinants.

The fix will cause a few recombinants to become recombinants and improve QC values of some recombinants but should not have large effects overall.
The biggest perceived impact will be that mutations displayed by Auspice will now be correct.

2022-07-22

SARS-CoV-2 and SARS-CoV-2-no-recomb

New dataset version (tag 2022-07-22T12:00:00Z)

• Clades: BA.2.75 has been given the Nextstrain clade name 22D. Read more about the reasoning for the decision to give this lineage a name here nextstrain/ncov#984
• Data update: New pango lineages are included up to commit cov-lineages/pango-designation@65cb2e0...4213460)
• Fix: BA.2.38 no longer contains 6091T as defining mutation, should therefore catch many more Indian BA.2.38 (report by @silcn in nextstrain/nextclade#935)
• Fix: Genemap format now correct, compliant with GFF3, see #33 (report by @huddlej)
• virus_properties.json has been updated, including clade 22D

2022-07-12

2022-07-12

SARS-CoV-2

New dataset version (tag 2022-07-12T12:00:00Z)

• Fix: BA.2.75 lacked the characteristic S:R493Q reversion in the previous release, this is now fixed. This is the only change, otherwise this dataset is identical to 2022-07-11T12:00:00Z.

2022-07-11

2022-07-11

SARS-CoV-2

New dataset version (tag 2022-07-11T12:00:00Z)

• Pango lineages: In this release, Nextclade can assign Pango lineages up to BA.2.75
• Alignment params: Retry reverse complement flag is now set to true, so that reverse complement is tried if seed matching fails.
• Fixes: Some synthetic pango lineage sequences had wrong mutations, this is now fixed through a manually curated override file.

2022-06-29

MPXV B.1

New dataset version (tag 2022-06-29T12:00:00Z)

• Increased number of B.1 samples from ~100 to ~200 to improve phylogenetic placement of analyzed 2022 outbreak sequences

2022-06-14

3 Monkeypox (MPXV) datasets introduced

Three MPXV datasets are added with differing zoom levels containing:

• MPXV (All clades)
• hMPXV-1 (part of clade 3, source of 2017/2018/2022 outbreaks)
• hMPXV-1 B.1 (2022 outbreak lineage)

All 3 use the coordinate system of the recently designated NCBI Monkeypox reference sequence NC_063383 (MPXV-M5312_HM12_Rivers).

However, SNPs from two different ref sequences are added to the "all clades" and B.1 datasets to reduce the number of total mutations.

The B.1 dataset uses SNPs of ON563414.3 (MPXV_USA_2022_MA001) on top of a NC_063383 backbone.

The "all clades" build uses the SNPs of a reconstructed ancestral MPXV sequence that is the inferred most recent common ancestor of clades 1, 2 and 3, rooted with a Cowpox outgroup.

Only the MPXV (All clades) dataset can assign all clades 1, 2 and 3.
The hMPXV-1 dataset can be used if all viruses are from hMPXV-1.
The B.1 dataset is useful for 2022 outbreak sequences but will not be able to assign anything but B.1 lineages.

Gene annotations follow the annotation used by NC_063383 and is of the form OPG001 (for OrthoPox Gene 001).
Since the alignment reference is always in NC_063383 coordinates, nucleotide and protein mutation position should usually be identical in alignments done with all three datasets.

Quality control parameters are subject to change, especially since "known" frame shifts and stop codons have not been annotated. For example, clade 1 sequences will always show around 7 frame shifts, yet these do not indicate quality problems.

New dataset version (tag 2022-06-14T12:00:00Z)

SARS-CoV-2

• Pango lineages: New lineages added up till pango-designation release v1.9 and beyond are now included, including among others BA.5.1-BA.5.3, BA.2.35-BA.2.48 and XV-XY

2022-04-28

New dataset version (tag 2022-04-28T12:00:00Z)

SARS-CoV-2 (with and without recombinants)

• Pango lineages: New lineages added up till pango-designation release v1.8 are now included, including among others BA.3.1, BA.2.14-BA.2.34 and XT-XU (in the default build, excluded from special "without recombinants" dataset).
• Clades: New Nextstrain clades included. BA.4 is 22A (Omicron), BA.5 is 22B (Omicron) and BA.2.12.1 is 22C (Omicron).

2022-04-08

New dataset version (tag 2022-04-08T12:00:00Z)

SARS-CoV-2 (with and without recombinants)

• Pango lineages: New lineages added up till pango-designation release v1.4 are now included, including among others BA.4-5, BA.2.9-BA.2.13 and XM-XS (in the default build, excluded from special "without recombinants" dataset). For now, BA.4-5 are included in Nextstrain clade 21L, together with BA.2 which is the most similar Omicron.
• Reference tree: The first 100 and last 200 sites (with respect to Wuhan reference) are now masked in the reference tree to reduce noise due to sites like 21 that were artifactually polymorphic.

2022-03-31

New dataset version (tag 2022-03-31T12:00:00Z)

SARS-CoV-2 (with and without recombinants)

• Pango lineages: New lineages added up till pango-designation release v1.2.137 are now included, including among others BA.1.18-19, BA.2.4-BA.2.8 and XG-XK (in the default build, excluded from special "without recombinants" dataset).
• Dataset: The sampling of sequences has changed slightly. Previously, every Nextstrain clade got around 30 random sequences belonging to this clade causing quite a bit of movement between releases. This is no longer the case. The tree is thus slightly smaller. The change is most noticeable for small Nextstrain clades like 20F.

2022-03-24

New dataset version (tag 2022-03-24T12:00:00Z)

SARS-CoV-2

• Recombinants: Recombinant Pango lineages are now included in the reference tree. Each recombinant is attached to the root node so as not to spawn false internal nodes in the tree that would attract bad sequences. As long as recombinants do not qualify for a Nextstrain clade, they will receive the place holder clade name recombinant. Pango lineages are provided if present. Beware that new unnamed recombinants with similar donors but slightly different breakpoint will attach to existing recombinants in the reference tree and thus get a wrong Pango lineage. A number of reversions and labeled mutations is a sign that you may have a similar but different recombinant.
• Pango lineages: In this release, Nextclade can assign Pango lineages up to pango-designation release v1.2.133, featuring Omicron recombinants like XD, XE and XF.
• QC: qc.json was updated with the most common stop codons and frameshifts that appear to be real and not artefacts (in ORFs 3a, 6, 7a, 7b,8, 9b)
• QC: virus_properties.json was updated and now contains more mutations that are common in 21K which should help identifying recombinants

SARS-CoV-2 without recombinants

• New dataset: Now that recombinants are included in the default SARS-CoV-2 tree, it is no longer easy to identify breakpoints and donors of new recombinants if they attach to existing recombinants on the tree. To facilitate the analysis of new potential recombinants, we have added a new dataset named "SARS-CoV-2 without recombinants" that does not include recombinants and can thus be used for recombinant analysis as before the inclusion of recombinants. This dataset should only be used for recombinant analysis, it will receive less attention than the main (default) SARS-CoV-2 dataset.
• Pango lineages: In this release, Nextclade can assign Pango lineages up to pango-designation release v1.2.133, except recombinants (lineages starting with X).