Tree Building Updates (09/06/2024)

What’s New?

As of September 6, 2024 CZ GEN EPI has been updated to implement the latest Nextstrain code for Mpox and SARS-CoV-2 tree builds.

Mpox Tree Builds

The latest updates include the latest definitions for Mpox lineages and clades. Therefore, tree builds will now follow Nextstrain’s coloring scheme for clades and lineages. Note the following:

• Sequence alignments and tree reconstruction method follow the strategy implemented through Nextstrain, including:
  • • masking of low complexity and repetitive regions, including the first 1350 and last 6422 base pairs of the MPXV genome and multiple repetitive regions of variable length
    • phylogenetic reconstruction using IQTREE-2.
    • clade assignment via clade definitions found here.
• Divergence and mutations are relative to the reference sequence MPXV-M5312_HM12_Rivers (GenBank accession ID NC_063383.1).
• The subsampling differs from Nexstrain’s implementation and follows a similar approach used for SARS-CoV-2 tree builds (click here for details).
• Targeted tree builds for mpox do not include randomly-selected samples over time. Targeted trees only include contextual samples that are closely related to user-selected focal samples at a 2 to 1 ratio. This allows users to build trees focused on specific samples or samples from specific clades. 

SARS-CoV-2 Tree Builds

CZ GEN EPI tree builds now include the latest definitions for SARS-CoV-2 lineages. Therefore, tree builds will now follow Nextstrain’s coloring scheme for clades and Pango lineages (click here for clade and lineage details).