marburg-virus-tree

Nextstrain build of the Orthomarburgvirus marburgense species taxon (taxonId: 3052505), members of this species are called marburgviruses. However, the species has two distinct lineages: ravn virus (RAVV) and marburg virus (MARV). Alignments use the official INSDC marburg virus reference sequence NC_001608.3.

Initial output can be viewed by pasting the results in the auspice folder into: https://auspice.us/.

Alternatively, you can run the build locally with:

micromamba create -f environment.yml
micromamba activate marburg-tree
snakemake fix_auspice_tree

About

This build uses nextstrain/ebola as a template.

It uses the paper: Gianguglielmo Zehender, Chiara Sorrentino, Carla Veo, Lisa Fiaschi, Sonia Gioffrè, Erika Ebranati, Elisabetta Tanzi, Massimo Ciccozzi, Alessia Lai, Massimo Galli, Distribution of Marburg virus in Africa: An evolutionary approach, Infection, Genetics and Evolution for clade names; link here. However, we choose not to show the B.1 clade as with additional samples the grouping is no longer very clear.

• I remove all sequences that have less than 10% coverage - this is sadly over 2/3rds of the data on NIH.

• The clock rate is set to 3.3 × 10−4 substitutions/site/year (as inferred by Zehender et al.) as there is limited collection date information. Without specifying a clock rate timetree sometimes infers negative clock rate and otherwise infers a clock rate in the magnitude of 7e-05 (8e-06 std) with a root in the 1300s or earlier. Specifying the clock ensures convergence and gives leads to accepted root time estimates in the 1800s.

• To give better time estimates the year of the ncbiReleaseDate is used as an upper time bound. This gives me reasonable time estimates. However, it should be possible to give a lower and upper bound to treetime to further refine this estimate - augur just does not currently accept the [lower_bound:upper_bound] treetime format.

• I use KX371887.3 Dianlovirus menglaense isolate Rousettus-wt/CHN/2015/Sharen-Bat9447-1, complete genome as an outgroup to root the tree and calculate a reconstructed root of the Marburg virus tree which is used refine branch lengths.