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Ana Duggan in the clean rooms of the McMaster Ancient DNA Centre (credit: JD Howell)

The genetics of Civil War era smallpox vaccination

McMaster Ancient DNA Centre researchers characterize the genetics of early smallpox vaccinations, extracting ancient DNA from the preserved scabs and lymph used to inoculate Civil War soldiers.

Jul 20, 2020

The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Authors: Ana T. Duggan, Jennifer Klunk, Ashleigh F. Porter, Anna N. Dhody, Robert Hicks, Geoffrey L. Smith, Margaret Humphreys, Andrea M. McCollum, Whitni B. Davidson, Kimberly Wilkins, Yu Li, Amanda Burke, Hanna Polasky, Lowell Flanders, Debi Poinar, Amogelang R. Raphenya, Tammy T. Y. Lau, Brian Alcock, Andrew G. McArthur, G. Brian Golding, Edward C. Holmes, & Hendrik N. Poinar

Genome Biology, July 2020. DOI:


Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.

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