One Mutation Makes Zika Virus Cause Severe Microcephaly

Transmission electron microscope image of Zika virus (red), isolated from a microcephaly case in Brazil. | NIAID

A single genetic change, acquired in 2013, likely gave the Zika virus the ability to cause severe fetal microcephaly, researchers report. The findings, published in Science on October 28, clarify how the virus evolved from a mostly benign illness into a pathogen of global concern.

"The most surprising result is that only one mutation would have such a dramatic effect on the viral neurovirulence in the brain to cause much more significant microcephaly," said Zhiheng Xu of the Chinese Academy of Sciences, a senior author on the study.

In the paper, first author Ling Yuan of the Chinese Academy of Sciences and a multidisciplinary team of researchers traced how Zika virus mutated over time, and then determined which modifications contributed to causing microcephaly by creating mutant viruses and testing them in mice.

Since 2016, ongoing Zika virus epidemics in the Americas have been declared a public health emergency by the World Health Organization, due to the link between infection during pregnancy and birth defects that was definitively established during the 2015 Brazilian outbreak. Before sweeping through the Americas, the virus was confined to a few countries in Africa and Southeast Asia for several decades, where it only sickened people occasionally and caused mild symptoms.

Scientists have only recently discovered details about how the pathogen damages developing neurons — even though a few cases of Zika virus-associated fetal microcephaly were described as early as 2013 after an explosive outbreak in French Polynesia. Why the virus transitioned to triggering severe neurological syndromes has remained a mystery.

"As a virologist, I believe every unexpected phenomenon has a reasonable genetic basis," said Chen-Feng Qin of Beijing Institute of Microbiology and Epidemiology, another senior author on the study.

Still, the researchers did not expect one single change to confer such dramatic results.

"We postulated that several more mutations are needed to have that kind of effect," said Xu.

By comparing contemporary Zika virus strains from the 2015 and 2016 South American epidemics with an ancestral Cambodian virus that was circulating in 2010, the researchers identified numerous changes in the pathogen's genome. Determining which mutations give the virus the ability to cause microcephaly, however, was no easy task.

"Other groups have predicated a panel of mutations that may have certain biological effects, but they failed to establish appropriate experimental systems to validate the hypothesis," said Qin.

Here, the researchers were able to construct and test seven different mutant viruses for the ability to cause microcephaly in mice.

"This study required a combination of experts and techniques. Dr. Qin's group is one of the few labs that can generate the mutated virus, while my lab is the best in generating Zika virus infection microcephaly models," said Xu.

Although all the viruses caused mild degrees of brain damage, one mutant in particular had strikingly more dramatic effects on brain size. The mutation that caused severe microcephaly — S139N, which replaced a single amino acid of a structural protein called prM within the pathogen's protective coat — also made the virus more lethal to human neuron precursor cells.

"Our study indicates that the old Asian strains cause much milder microcephaly. This would explain why a link between Zika virus and microcephaly was not observed earlier," said Xu.

Evolutionary analysis revealed when the change occurred, and further underscored its importance.

"Our findings perfectly match the epidemiological data," said Qin.

Qin said Wei-Feng Shi, a co-author from Taishan Medical School, "determined that the S139 mutation occurred on May 13, 2013, just before the sudden outbreak in French Polynesia, when fetus microcephaly cases were first described."

The scientists say that some other unknown viral proteins or genetic predispositions in those infected likely contribute to the complex clinical features of microcephaly. Research is ongoing to tease out how other mutations might cause birth defects and to monitor circulating Zika virus strains for any new changes.

"Our example shows that the virus is continuously evolving", said Qin. "The emergence of some other adaption mutations that may impact viral virulence deserves careful investigation."