Fingerprinting transformed police investigations by making it possible to place a suspect at a crime scene with physical evidence. Similarly, genome sequencing has changed how disease detectives study outbreaks by allowing them to read a pathogen’s genes as a biological record of where it came from and how it spread.One way to think about sequencing is to imagine a virus or bacteria’s genome as a recipe book. Each gene is a recipe for making a protein. When scientists sequence a pathogen, they read the order of the genetic letters in those recipes.Over time, small changes appear in the recipes as the pathogen mutates. By comparing those changes in samples collected from different places and times, researchers can determine which infections are related and estimate when and where the pathogen entered a population.AdvertisementAdvertisementScientists have used sequencing in this way to track outbreaks of COVID-19, Ebola, mpox and foodborne illnesses. This information helps public health investigators connect cases that might otherwise seem unrelated.[embedded content]Still, genomic sequencing has limits. It can show that different pathogen strains are related, but it cannot fully explain why an outbreak began in one place, why it spread in a particular direction, or how human behavior shaped its course. Answering those questions requires combining genomic data with historical records, archaeological artifacts, trade records and epidemiological investigations.I am a chemist and the author of “Diseases Without Borders: Plagues, Pandemics, and Beyond,” a book for young adults on infectious disease and the ways it has shaped human history. In my research, I’ve found that while the genome can help researchers trace the evolutionary trail of a pathogen, other fields are needed to explain the environmental conditions that allowed this trail to become an outbreak.Ancient DNA tells only part of the storyAdvances in DNA sequencing and extraction over the past decade have made it possible to recover fragments of ancient DNA from bones and teeth. Researchers can use these genomes to study a metaphorical molecular fossil record of microbial evolution.AdvertisementAdvertisementThe Black Death, one of the deadliest pandemics in history, shows both the power and the limits of sequencing.The infectious disease behind the Black Death, plague, is caused by the bacterium Yersinia pestis. DNA recovered from the teeth of people buried more than 5,000 years ago in what is now Sweden revealed the existence of an ancestral form of Y. pestis that had not yet adapted to fleas.About 2,000 years later, the bacterium made an important evolutionary shift: It gained the ability to survive in fleas and pass back and forth between humans, rats and other mammals via flea bites. That change made the pathogen far more dangerous and helped pave the way for three great plague pandemics that followed: the Justinianic Plague from the sixth to eighth century; the Black Death and later waves from the 1300s into the 1700s; and the third pandemic from the 19th to mid-20th centuries.But how and why did plague emerge and move through human societies with such devastating results? Genetic results alone are not enough to answer these questions.When gravestones become genetic evidenceGeneticists needed archaeologists, paleoclimatologists and historians to complete the picture of the plague pandemics. The genome revealed the lineage. Other disciplines supplied the historical and environmental context.AdvertisementAdvertisementTwo 14th-century graveyards in what is now Kyrgyzstan provide a striking example of how historical evidence can guide genetic investigations into the origins of a pandemic.Historian Philip Slavin noticed archival records pointing to an unusual number of gravestones from 1338 and 1339. Some of those tombstones explicitly referred to a pestilence as the cause of death.That clue led to the next stage of the investigation, where archaeologist Maria Spyrou and her team extracted and sequenced ancient DNA from the skeletal remains of seven people buried in the graves and found genetic traces of Yersinia pestis in three of the skeletons. These strains were close precursors of the strain linked to the Black Death and ancestors of several modern Y. pestis lineages.The top map shows the locations of the gravesites in modern-day Kyrgyzstan, with regions of Y. pestis outbreaks shaded in blue. The map on the bottom left shows tombstones, burial dates and evidence of Y. pestis infection in a part of Kara-Djigach cemetery. The map on the bottom right shows annual numbers of tombstones fro …
