Person Who Had Measles 100 Years Ago Helps Scientists Trace Origins Of Virus

August 12, 2020

A diseased human lung, fixed in the preservative formalin for more than 100 years, has helped scientists trace the history of the measles virus back to its origins in the 6th century BCE.

Over the years, this lung has been kept in the basement of the Berlin Museum of Medical History along with hundreds of other lung specimens that were collected and preserved between the 1870s and 1930s. In search of a well-preserved respiratory pathogen, Sebastian Calvignac-Spencer, a virologist at the Robert Koch Institute, and his research team went down to the basement and looked at each jar. “It was a matter of serendipity,” says Calvignac-Spencer, and the team found one belonging to a 2-year-old measles patient who died of the disease in 1912 The lungs.

The team managed to take samples of the virus from 108-year-old lung tissue and used genetic material – the oldest measles genome ever sequenced – to learn more about the pathogen’s origins. In a new study published today (June 18) in the journal Science, they estimate that measles may have diverged from its closest known relative, a now-eradicated bovine virus, as early as 528 BCE.

The new estimate suggests that the virus may be “more than 1,000 years older than any previous estimate,” Calvignac-Spencer said.

A rare discovery.
According to a 2011 report in the journal Molecular Biology and Evolution (MBE), previous studies predicted that measles and the extinct bovine virus (known as “bovine plague”) split from their most recent common ancestor between the 11th and 12th centuries. However, the Persian physician Muhammad ibn Zakariya al-Razi wrote a clinical description of measles in the 10th century, so some things don’t add up.

Joel Wertheim, an author of the MBE report and an assistant professor of medicine at the University of California, San Diego, said, “The split between measles and rinderpest has clearly been underestimated.” He was not involved in the new scientific study. These underestimates stem from two key problems: the lack of old measles samples and false assumptions about how the virus mutates over time, which biases evolutionary models toward “ridiculously recent dates,” Wertheim said.

Wertheim and his collaborators developed a new model to explain these factors and push the date of origin back to the late ninth century, but “we don’t think we were right,” he said. Now, Calvignac-Spencer and his team have reached a more realistic estimate, in part by incorporating the newly discovered 1912 specimen into their analysis, Wertheim said.

The authors note that the oldest measles genome ever sequenced was in 1954, before the team found the 1912 sample. Scientists estimate the rate of evolutionary change, or the extent and rate of viral mutations, by comparing samples collected at different times and tracking differences in their genetic code. The more and older the samples we study, the clearer this rate of change becomes, Calvignac-Spencer said.

But the backbone of the measles virus is RNA, a type of genetic material that degrades rapidly compared to its more robust cousin, DNA.The 1912 sample escaped that fate because the lungs had been immobilized in formalin, a preservative that blocks chemical reactions that would otherwise degrade the RNA. Formalin also “sticks” preserved RNA to nearby molecules, making it difficult to extract, Calvignac-Spencer says.

To unstick the RNA, the team cut 0.007 ounces (200 milligrams) of tissue from the lungs and boiled the tiny samples so that the sticky molecules inside could be separated without destroying the RNA. The team then constructed “a nearly complete” genome from the rescued RNA, they wrote. To further flesh out their evolutionary model, the team searched the genetic sample collection at Germany’s National Reference Laboratory and found two measles samples collected in 1960 to add to their analysis.

Building a better model
The team built their evolutionary model from a 1912 sample, a 1960 sample, and 127 additional samples, most of which were collected in the 1990s or later. The second model compares about 50 measles sequences to the cattle rinderpest virus (PPRV), which was declared eradicated in 2011, and its closest relative, the small ruminant virus that infects goats and sheep, to determine when these pathogens split from their common ancestor.

In both models, Calvignac-Spencer said, the team took into account a phenomenon called “purifying selection,” which many previous studies have ignored. While some evolutionary pressures add beneficial mutations to the genome and keep them stable over time, so-called purifying selection removes harmful mutations from the genome before they accumulate. These complementary forces help set the pace of evolutionary change, so to estimate when measles first appears, you have to take purifying selection into account, Wertheim says.

“By taking purification selection into account, you can change [your estimate] by an order of magnitude,” he says. He adds that purifying selection in part causes certain segments of the genome to mutate easily and frequently, while other parts of the genome remain virtually unchanged.” You’ll have several mutations that hit the same spot over and over again, “but because you only have a limited sample, you may miss some of them, Calvignac-Spencer says. The team designed their model to capture these mutations that might otherwise be missed.

The “earliest possible date for the establishment of measles in the human population” occurred around the 6th century B.C., based on the timing of the divergence of cattle rinderpest and measles, but the exact date the virus first infected people remains unknown.

The authors note that around 2,000 to 2,500 years ago, humans began building settlements large enough to sustain a measles outbreak, providing the virus with the opportunity to establish itself. Measles tends to die down in communities of fewer than 250,000 people, they write, because residents quickly become immune to the disease or die, so “small human populations can only serve as dead-end hosts.”

Calviniak Spencer said he is interested in discovering ancient measles samples, if they exist, in order to further refine our understanding of the history of the pathogen. Wertheim said he predicts that more virologists will join the search for ancient samples lurking in museum basements and hospital archives.

“I was amazed when I saw that they were able to extract a virus from lung tissue that was more than 100 years old,” Wertheim said. I think more virologists will start using “older and more ancient viruses because people are becoming more ambitious and encouraged by these results,” he added.