A highly contagious herpes virus causes Marek's disease, a deadly illness that mainly infects chickens. While it does not make people sick, the virus causes tumors and paralysis in chickens and, if unchecked, can spread rapidly through entire flocks.

Beginning in the 1970s, widespread vaccination for the virus greatly reduced its impact on the poultry industry, but over the years, some strains of the virus have increased in virulence, causing more severe disease and evolving ways to break through and evade vaccine protection. A massive new study by researchers at Penn State and the U.S. Department of Agriculture (USDA), has now identified 10 regions in the virus's genome that likely played a role in the increases in virulence. The findings could inform the development of next-generation vaccines that are more effective at preventing future breakthroughs, according to the research team.

A paper describing the study published July 29 in the journal Science Advances.

Even with nearly universal vaccination, Marek's disease virus still circulates on poultry farms causing losses around the world, across the U.S. and here in Pennsylvania. We hope that our new study could help inform the design of next-generation vaccines that could potentially stop the virus from evading their protection."

Moriah L. Szpara, professor of biology and of biochemistry and molecular biology, Eberly College of Science, Penn State and leader of the research team

Co-author Andrew Read, Penn State's senior vice president for research, started studying the virus on Pennsylvania farms more than a decade ago to try to understand the complex relationship between vaccination, virus transmission and increases in virulence.

"This work shows the importance of sustained, collaborative research," Read said. "By following this virus over many years and combining expertise in virology, evolution, genomics and agriculture, we are now beginning to understand the biological mechanisms driving changes in virulence. That foundational knowledge is what ultimately will enable us to develop better tools to protect animal health and food production."

In the current study, the team took a genome-wide approach to try to find the genetic changes that could have led to increases in the virulence using a large collection of different strains of the virus, said Szpara, who is also a co-hire of Penn State's Huck Institutes of the Life Sciences. 

The team sequenced the entire genomes of 65 strains of the Marek's disease virus from a large collection maintained by the USDA. These strains were collected between 1962 and 2016, and each was classified using USDA-standardized tests into one of four disease categories. The categories, or pathotypes, are based on the severity of symptoms caused by a strain and its ability to break through the protection of vaccines, ranging from mild to highly virulent. While most Marek's disease virus strains can cause tumors in infected chickens, strains of high virulence can break through the earliest developed vaccines, and those of the highest virulence can break through second generation vaccines.

The research team first aligned the genome sequences of all 65 virus strains to find any differences. They found nearly 800 sites where a single letter in the DNA alphabet differed among virus strains and several sites where segments of DNA were inserted or deleted. They then built a family tree of the virus strains based on these similarities and differences to see how strains of different virulence were related to each other.

"We found that all of the highest virulence strains in our sample shared a common ancestor," said Alejandro Ortigas-Vasquez, graduate student in biology at Penn State and first author of the paper. "So, somewhere in this grouping of strains, a mutation or set of mutations must have occurred to allow them to break through vaccine protection. This narrows the search for DNA variants responsible for the most virulent strains."

The team then performed a genome-wide association study - or GWAS - to look for statistical correlations that show whether particular DNA variants are more likely to be found in strains that cause the most severe disease. These associations can potentially lead to identifying genes or other functional elements in the genome that are responsible for changes in virulence.

"We found 10 genomic variants that were statistically associated with virulence," Ortigas-Vasquez said. "Several of the sites we found had been seen in previous studies, but we also found new ones. The strongest of these associations was with a type of DNA variant called a tandem repeat where a segment of DNA gets duplicated. The next step will be to test the function of these variants."

Understanding the genetic changes in Marek's disease virus that led to differences in virulence could aid in the design of new more future-proof vaccines, the researchers said.

"The current vaccines delay symptoms rather than being completely preventative," Szpara said. "The third-generation vaccine is the most effective and can protect flocks against even the most virulent strains, but there are reports of so-called hypervirulent stains emerging that can evade even these vaccines."

In addition to Szpara, Read and Ortigas-Vasquez, the research team at Penn State included graduate student Utsav Pandey, senior research associate Andrew S. Bell, computational scientist Daniel W. Renner, research project manager Matthew J. Jones and Associate Professor of Biology David A. Kennedy, a co-hire of the Penn State Huck Institutes of the Life Sciences. The team also included Maciej F. Boni at Temple University and Hans H. Cheng and John R. Dunn of the USDA. 

This work was funded by the Ecology and Evolution of Infectious Diseases (EEID) program - a multi-agency effort supported by the U.S National Science Foundation (NSF), the National Institutes of Health (NIH) and the U.S. Department of Agriculture (USDA) - under award number R01GM105244; the NSF-NIH EEID program under award number R01GM140459; and the Pennsylvania Department of Health Commonwealth Universal Research Enhancement (CURE) Program. The Penn State Center for Infectious Disease Dynamics and Huck Institutes for the Life Sciences provided additional support.

Source:

Journal reference:

Ortigas-Vasquez, A., et al. (2026). Genome-wide analyses of an avian herpesvirus identify 10 loci associated with tumorigenicity and vaccine escape. Science Advances. DOI: 10.1126/sciadv.aee9024. https://www.science.org/doi/10.1126/sciadv.aee9024