Yersinia pestis branch 1.ORI

Branch 1.ORI carries biovar Orientalis and is the branch of the third pandemic. It left Yunnan in the nineteenth century, reached Hong Kong in 1894 — where Alexandre Yersin isolated the organism during that outbreak — and from there was carried by steamship to port cities on every inhabited continent.

It is consequently the most geographically widespread branch of the species, and the source of the foci established in Madagascar, in the Americas (where it persists in rodent populations of the western United States and of South America) and in much of Africa and Asia. Its biovar is defined by the inability to ferment glycerol together with the ability to reduce nitrate.

Because 1.ORI spread within the era of maritime records, its phylogeography can be checked against documented shipping routes — a rare case where a bacterial phylogeny and an archive of human movement can be compared directly.