Genomic study sheds light on protective effects of malaria vaccine candidate

International team finds genetic variation in protein targeted by the world’s most advanced malaria vaccine candidate influences its ability to counteract the disease

An international team led by researchers from the Broad Institute of MIT and Harvard, the Harvard T.H. Chan School of Public Health, and Fred Hutchinson Cancer Research Center has used cutting edge genomic methods to uncover key biological insights that help explain the protective effects of the world’s most advanced malaria vaccine candidate, RTS,S/AS01 (RTS,S).

Applying highly sensitive sequencing technology to more patient samples than previously tested, the team was able to determine that genetic variation in the protein targeted by RTS,S influences the vaccine’s ability to ward off malaria in young children. The work, which was published online October 21st by the New England Journal of Medicine (NEJM), could inform future vaccine development.

“This is an example of the benefits of applying genomics to a real world problem of global health importance,” said Dyann Wirth, co-director of the Broad’s Infectious Disease Program and the Richard Pearson Strong Professor of Infectious Diseases and chair of the Department of Immunology and Infectious Diseases at the Harvard T.H. Chan School of Public Health. Wirth, along with Peter Gilbert of Fred Hutchinson Cancer Research Center, led the study. 

Malaria is a global health threat responsible for hundreds of millions of infections and more than half a million deaths annually in tropical and subtropical regions of the world. The disease is caused by intracellular protozoan parasites from the genus Plasmodium, which are transmitted to humans by mosquito vectors.

RTS,S is designed to target a fragment of a specific protein, circumsporozoite (CS), that sits on the surface of the Plasmodium falciparum parasite. The CS protein is capable of provoking an immune response that can prevent parasites from infecting the liver, where they typically mature and reproduce before dispersing and invading red blood cells, leading to symptomatic malaria. RTS,S aims to trigger that response as a way to protect against the disease. However, the CS protein is genetically diverse – perhaps due to its evolutionary role in the immune response – and RTS,S includes only one version (or “allele”) of the protein. The current study sought to test whether alleles of CS that matched the one targeted by RTS,S were linked with better vaccine protection. 

Through a collaboration with the vaccine division of the healthcare company GlaxoSmithKline, researchers from Harvard and the Broad obtained blood samples from over 5,000 of the approximately 15,000 infants and children who participated in the vaccine’s phase 3 trial across 11 study sites in Africa between 2009 and 2013. The researchers were sent samples when the first symptomatic cases appeared in those vaccinated, as well as samples from all participants at month 14 and month 20 following vaccination. By sequencing those samples, the team determined that, while RTS,S provided at least partial protection against all strains of the parasite, it was significantly more effective at preventing malaria in children with matched allele parasites than in preventing malaria with mismatched allele parasites. The same effect was not noted in infants. 

Previous studies during the RTS,S’s phase 2 trials had not detected an allele-specific effect for this vaccine candidate. However, the current study benefited from a larger sample size and technological advances that made it possible to read the genetic samples with much greater sensitivity that, for instance, allowed for the detection of rare alleles and multiple parasite infections. 

“This is the first study that was big enough and used a methodology that was sufficiently sensitive to detect this phenomenon. Now that we know that it exists, it contributes to our understanding of how RTS,S confers protection and informs future vaccine development efforts,” said Dan Neafsey, associate director of the Genomic Center for Infectious Diseases at the Broad and co-first author of the NEJM paper.

Combined with the new methodology for generating genetic data, the study used new statistical methods for analyzing the data. 

“This uniquely valuable data set posed some challenges to data analysis. The statistical team extended methods previously developed for HIV to provide interpretable answers about differential vaccine efficacy by malaria genetics,” said Gilbert, who is a member of the Vaccine and Infectious Disease Division and director of the statistical center for the HIV Vaccine Trials Network at the Fred Hutchinson Cancer Research Center.

This powerful approach can now be applied not only to malaria but also to other major infectious diseases that involve highly variable vaccine targets. It is already being applied in HIV vaccine trials, and Wirth’s team has made plans to apply it in future malaria vaccine trials. Furthermore, the work underscores how a full and comprehensive catalogue of the genetic diversity of key pathogens could inform the design of robust, effective vaccines.

“Now that we understand that at least in the case of this immune response, that there’s an allele-specific aspect to it – a particular parasite strain or type creates a certain immune response in the individual – this finding can color how we approach future vaccine discovery and development,” said Wirth.

RTS,S is the first malaria vaccine candidate to complete phase 3 trials. Originally designed by scientists at GlaxoSmithKline (GSK) in 1987, development of the vaccine is now being advanced by a public-private partnership between GSK and PATH Malaria Vaccine Initiative. 

The study was supported by the National Institute of Allergy and Infectious Diseases (NIAID), one of the National Institutes of Health, under contract No. HHSN272200900018C; the Bill & Melinda Gates Foundation; and the PATH Malaria Vaccine Initiative.

Others who worked on the study include researchers from the Broad Institute of MIT and Harvard; Fred Hutchinson Cancer Research Center; University of Washington; Harvard T.H. Chan School of Public Health; GlaxoSmithKline (Germany); Ifakara Health Institute (Tanzania); Kwame Nkrumah University of Science and Technology (Ghana); Albert Schweitzer Hospital (Gabon); University of Tübingen’s Institute of Tropical Medicine (Germany); Centro de Investigaçåo em Saúde de Manhiça (Mozambique); ISGlobal, Barcelona Centre for International Health Research, Universitat de Barcelona (Spain); Kintampo Health Research Centre (Ghana); KEMRI-Wellcome Trust Research Program (Kenya); PATH Malaria Vaccine Initiative; Medical Research Council Unit (Gambia); National Institute for Medical Research (Tanzania); London School of Hygiene and Tropical Medicine (UK); Institut de Recherche en Sciences de la Santé (Burkina Faso); U.S. Centers for Disease Control and Prevention; University of North Carolina, Chapel Hill; UNC Project (Malawi); KEMRI/CDC Research and Public Health Collaboration (Kenya); KEMRI-Walter Reed Project (Kenya); Swiss Tropical and Public Health Institute (Switzerland); University of Copenhagan (Denmark); and Simmons College School of Nursing and Health Sciences.

About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to

About the Harvard T.H. Chan School of Public Health
Harvard T.H. Chan School of Public Health brings together dedicated experts from many disciplines to educate new generations of global health leaders and produce powerful ideas that improve the lives and health of people everywhere. As a community of leading scientists, educators, and students, we work together to take innovative ideas from the laboratory to people’s lives—not only making scientific breakthroughs, but also working to change individual behaviors, public policies, and health care practices. Each year, more than 400 faculty members at Harvard Chan teach 1,000-plus full-time students from around the world and train thousands more through online and executive education courses. Founded in 1913 as the Harvard-MIT School of Health Officers, the School is recognized as America’s oldest professional training program in public health. For further information about the Harvard Chan, go to

About Fred Hutchinson Cancer Research Center
At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer with minimal side effects. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first and largest cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Private contributions are essential for enabling Fred Hutch scientists to explore novel research opportunities that lead to important medical breakthroughs. For more information visit or follow Fred Hutch on Facebook, Twitter or YouTube.

Paper cited:
Neafsey, D., Juraska, M. et al. Genetic diversity and protective efficacy of the RTS,S/AS01 malaria vaccine. New England Journal of Medicine. Online: October 21, 2015. DOI: 10.1056/NEJMoa1505819.