Yersinia pestis branch 1.ANT
African Antiqua branch. Carries the Great Lakes foci (Ituri in DRC, West Nile in Uganda, Usambara in Tanzania), introduced from Eurasia c. 1700-1900.
Branch 1.ANT is the African Antiqua branch. It carries the plague foci of the Great Lakes region — Ituri in the Democratic Republic of the Congo, West Nile in Uganda, Usambara in Tanzania — which together account for a substantial share of the world's reported human plague cases.
Genomic work places the introduction of this branch into East Africa at some point between roughly 1700 and 1900, from a Eurasian source, rather than in antiquity as the name Antiqua might suggest. The biovar label is a phenotypic classification from 1951 and does not encode age.
The branch illustrates a structural bias of the public record: the Great Lakes foci are among the most epidemiologically active in the world and among the least represented in sequence archives. The sampling map on this site shows that asymmetry directly, and it should be read as a statement about deposition practice rather than about where plague occurs.
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 | 0 | 0 | 1 |
pCD1 |
2 | 0 | 0 | 1 |
pPCP1 |
2 | 1 | 0 | 0 |
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.
| Type | Code | Source |
|---|---|---|
| other | Biovar Antiqua: glycerol +, nitrate + | Devignat 1951, Bull World Health Organ (biovar definition); 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.
| System | Code | Match |
|---|---|---|
| biovar | Antiqua | exact |
| cui2013 | 1.ANT | exact |
Genomes (3)
| Accession | Strain | Country | Collection year | Assembly level |
|---|---|---|---|---|
GCA_000013825.1 |
Antiqua | — | — | Complete Genome |
GCA_000169615.1 |
UG05-0454 | — | — | Contig |
GCA_000835005.1 |
Nairobi | Kenya | 1985 | Chromosome |
API : /api/v1/taxa/1.ANT