The East Smithfield plague pits, which were used for mass burials in 1348 and 1349. Credit: Museum of London Archaeology (MOLA)
Key points:
- An analysis of more than 600 genome sequences from around the globe has shed more 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 the lineages.
- More than genetic data is needed to understand past, present and future pandemics.
Seeking to better understand more about the origins and movement of bubonic plague, researchers have completed a painstaking granular examination of hundreds of modern and ancient genome sequences, creating the largest analysis of its kind.
Published in Communications Biology, the research features an analysis of more than 600 genome sequences from around the globe, spanning the plague’s first emergence 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 quickly discovered that a species-wide clock model was unstable and did not lead to reproducible estimates. One reason is because Y. pestis evolves at a very slow pace—making it almost impossible to determine exactly where it originated. Humans and rodents have carried the pathogen around the globe through travel and trade, allowing it to spread faster than its genome evolved. Genomic sequences found in Russia, Spain, England, Italy and Turkey, despite being separated by years are all identical, for example, creating enormous challenges to determining the route of transmission.
Thus, the multi-institutional research team developed a new approach in which each Y. pestis population was assessed independently. This enabled them to identify and date five populations throughout history, including the most famous ancient pandemic lineages which they now estimate had emerged decades or even centuries before the pandemic was historically documented in Europe.
“We recommend this approach for future studies, as the full global diversity of Y. pestis can be utilized without down-sampling,” the team wrote in their paper.
Even with their success, the researchers say more information is needed to construct past pandemics—and future ones. In addition to genetic information, historical, ecological, environmental, social and cultural contexts are equally important.
“Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics,” the team concludes.