Measles may have emerged when large cities rose, 1500 years earlier than thought

BERLIN—On 3 June 1912, a 2-year-old girl at the Charité University Hospital here died of pneumonia following a measles infection. The next day, doctors took out her lungs, fixed them in formalin, and added them to a collection of anatomical specimens started by Rudolf Virchow, the "father of pathology." There they languished for more than 100 years—until Sebastien Calvignac-Spencer, an evolutionary biologist at the Robert Koch Institute, came across them in the basement of Berlin's Museum of Medical History.

Calvignac-Spencer and his team took a sample from the lungs, isolated RNA from it, and subsequently pieced together what is the oldest known genome of the measles virus. Its sequence helped them shed light on a much earlier period in measles' history. In a study posted to the preprint server bioRxiv today, the team concludes that the virus may have entered the human population as early as the fourth century B.C.E., rather than in medieval times, as previous research had suggested.

The work is technically brilliant, says evolutionary biologist Mike Worobey of the University of Arizona: "Just being able to get the measles virus out of these old, wet specimens. That sets the stage for all sorts of exciting work." Monica Green, a historian of infectious diseases at Arizona State University, Tempe, calls the sequencing "very impressive" as well but says the study lacks enough data points to "provide decisive answers" about measles' emergence. The authors agree. They hope sequences from antiquity, preserved in naturally mummified or frozen bodies, may one day do so.

Measles, which killed an estimated 142,000 people in 2017, is one of the most infectious human diseases. But when, where, and how it became a human pathogen is still debated. The closest relative of the measles virus is one that causes rinderpest, a disease that affected cattle, deer, buffalo, and other even-toed ungulate species before it was eradicated in 2011. Most researchers believe both viruses had a common ancestor that infected cattle. "The challenge is that … measles has left so few clear traces in historical disease descriptions," Green says.

Because measles spreads so fast and infection confers lifelong immunity, scientists estimate it needs populations of 250,000 to a half-million people to avoid burning itself out. Historians believe that the largest cities reached that size around the fourth century B.C.E. But when researchers in Japan used available genomes of the measles and rinderpest viruses to build a phylogenetic tree, enabling them to date the branches, they concluded in 2010 that measles didn't emerge until the 11th or 12th century C.E.

The uncertainty stems in part from a surprising lack of historic sequences. Only three genomes from measles viruses occurring before 1990 are known; the oldest is one isolated in 1954 that was turned into the first measles vaccine. So Calvignac-Spencer turned to the Berlin museum, whose shelves are filled with thousands of tissues and organs floating in formalin-filled glass cases, like aquariums of human anatomy.

Formalin fixes tissue by cross-linking proteins and other large molecules, including RNA, which the measles genome is made of. To extract RNA from such samples, scientists use techniques pioneered about 10 years ago by cancer researchers interested in formalin-fixed biopsies. "We put them at 98° for 15 minutes and that breaks the cross-links," Calvignac-Spencer says. This also breaks up RNA, but modern methods allow scientists to sequence the fragments and piece them back together.

Calvignac-Spencer's team drew up a new phylogenetic tree using the 1912 genome as well as a new one from 1960, pieced together from a sample in another collection, and other available genomes. The resulting tree suggests the disease could have jumped to humans as early as 345 B.C.—right around the time human populations reached the critical size.

The earlier date for measles' emergence also reflects the models that the team used to analyze the viral sequences. When drawing up a family tree using differences in genomes, researchers must estimate the speed at which viral genomes diverge. In the past, their estimates were often too high, because some deleterious mutations tend to disappear over time. The new model accounts for this effect, called purifying selection. It pushes back the divergence of measles and rinderpest even without including the 1912 genome. But the genome strengthens the new timeline, Calvignac-Spencer says.

The researchers can't rule out that the measles virus first circulated in humans and then jumped to cattle, but that seems unlikely, says Albert Osterhaus of the University of Veterinary Medicine in Hanover, Germany. For one, ungulate herds probably reached the critical population size long before humans did. And the closest relative of the two viruses, which is even older, causes peste des petits ruminants, a sheep and goat disease that probably crossed to cattle more easily than to humans.

Similar studies have suggested that HIV and other pathogens also took off in the wake of major changes in the human population structure, Worobey says. "It seems like changes in human ecology really did coincide with the successful emergence of these viruses."

The ability to fish viral RNA out of very old samples has renewed interest in the Virchow collection, says Thomas Schnalke, head of the museum. "It came as a kind of revolution for us that researchers are coming and saying: ‘Your samples are interesting for us again.’" Calvignac-Spencer has already labeled additional specimens he'd like to study with orange stickers. "It's a treasure trove," he says. "A window to the past that we can open now."