Prototype — a technical demonstrator, not a reference database.

Yersinia pestis branch 2.MED

branch — Parent taxon : Y.pestisNCBI taxid 632

Medievalis. Central Asian foci; historically associated with the second pandemic though the medieval genomes themselves fall basal to this branch.

Branch 2.MED carries biovar Medievalis, defined by glycerol fermentation together with the inability to reduce nitrate. Its present-day distribution is central Asian, in the rodent foci around the Caspian.

The name records a nineteenth-century hypothesis rather than a genomic result, and it is the source of a persistent confusion worth stating plainly: the genomes recovered from second pandemic burials do not fall within this branch. Ancient genomes from Black Death victims sit basal to the divergence that gave rise to 2.MED, so the biovar name should be read as a historical label attached by phenotype, not as evidence that this branch caused the medieval pandemic.

Plasmid content

Copy number is a per-genome measurement, never a species constant.

Replicon present partial absent not measured
chromosome 3 0 0 0
pMT1 2 1 0 0
pCD1 2 0 0 1
pPCP1 1 0 1 1

Defining markers

cgMLST is the reference typing method for the genus (BIGSdb-Pasteur). SNP branch nomenclature applies to Y. pestis alone, which is a monomorphic clone.

TypeCodeSource
other Biovar Medievalis: glycerol +, nitrate -Devignat 1951; branch assignment from Cui et al. 2013

Typing equivalences

Three cgMLST schemes coexist for the genus and have never been compared in the literature. They are shown side by side; this atlas does not arbitrate between them.

SystemCodeMatch
biovarMedievalisexact
cui20132.MEDexact
pandemicHistorically associated with the second pandemicapproximate

Genomes (3)

AccessionStrain CountryCollection year Assembly level
GCA_000006645.1 KIM Complete Genome
GCA_000169655.1 K1973002 Contig
GCA_000182705.1 KIM D27 Scaffold

API : /api/v1/taxa/2.MED