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@corneliusroemer corneliusroemer released this 16 Jun 16:51
· 534 commits to release since this release
2022-06-16--16-03-24--UTC
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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
Assets 2