New method better tracks Black Death bacteria over time

The East Smithfield plague pits, which were used for mass burials in 1348 and 1349. Credit: Museum of London Archeology (MOLA)

Key points:

• An analysis of more than 600 genomic sequences from around the world has shed light on the deadly but elusive Black Death.
• A new approach in which each Y. pestis population is assessed independently has allowed researchers to better date lineages.
• It takes more than genetic data to understand past, present and future pandemics.

Seeking to better understand the origins and movements of bubonic plague, researchers performed a careful granular examination of hundreds of modern and ancient genomic sequences, creating the largest analysis of its kind.

Posted in Communications Biology, the research presents an analysis of more than 600 genomic sequences from around the world, covering the first emergence of plague in humans 5,000 years ago, the Plague of Justinian, the medieval Black Death and the current (or third ) pandemic, which began in the early 20th century.

First, the researchers examined the Y. pestis as a whole, but they soon discovered that a species-scale clock model was unstable and did not lead to reproducible estimates. One of the reasons is that Y. pestis evolves at a very slow rate, making it almost impossible to determine its exact origin. Humans and rodents carried the pathogen around the world through travel and trade, allowing it to spread faster than its genome evolved. The genomic sequences found in Russia, Spain, England, Italy and Turkey, although separated by years, are all identical, for example, which creates enormous challenges in determining the route of transmission.

Thus, the multi-institutional research team developed a new approach in which each Y. pestis population was independently assessed. This allowed them to identify and date five populations throughout history, including the most famous ancient pandemic lineages that they believe emerged decades, if not centuries, before the pandemic was historically documented in Europe.

“We recommend this approach for future studies because the full global diversity of Y. pestis can be used without downsampling,” the team writes in their paper.

Even with their success, the researchers say more information is needed to construct past and future pandemics. In addition to genetic information, historical, ecological, environmental, social and cultural contexts are equally important.

“Despite this methodological advance, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient to accurately reconstruct the timing and the spread of plague epidemics in the short term,” the team concludes.