A promising malaria vaccine’s protectiveness depends on genetics of parasite

An experimental vaccine poised to win World Health Organization approval as the first to even partially protect children against malaria works better against one strain of the disease-causing parasite than others. The finding helps explain the vaccine’s limited protection and provides insights into how to improve it.

An international team led by researchers at the Broad Institute of MIT and Harvard, the Harvard T.H. Chan School of Public Health and Fred Hutchinson Cancer Research Center uncovered the influence of genetic variation on vaccine effectiveness after applying cutting-edge DNA sequencing technology to almost 5,000 patient blood samples. They analyzed the genetic data using a statistical method called sieve analysis honed at Fred Hutch for evaluating vaccines against another genetically variable pathogen, HIV.

The study was published today in The New England Journal of Medicine. Earlier studies, using smaller sample sizes and less advanced sequencing and statistical methods, had failed to find an association.

The finding “can color how we approach future vaccine discovery and development,” said Broad senior associate member Dr. Dyann Wirth, a top malaria researcher at Harvard who led the study along with Fred Hutch biostatistician Dr. Peter Gilbert. “This is an example of the benefits of applying genomics to a real world problem of global health importance.”

More immediately, public health officials could use the study to strategically determine where and when the vaccine might deliver the best results, researchers said.

More than half a million people die annually from malaria, mostly children under age 5 in sub-Saharan Africa, and millions more are sickened. The mosquito-borne disease is caused by parasitic organisms. Developing a malaria vaccine has been a challenge because of the parasite’s complex life cycle and its agility at mutating to evade the immune system.

About 15 years ago, world leaders called for a renewed effort to fight the deadly disease. Since then, widespread distribution of insecticide-treated bed nets and a new combination of medicines have reduced malaria deaths by more than 50 percent. But because of the threat that the parasite could develop resistance to medications or insecticides, global health experts consider a vaccine – even a partially effective one – to be a vital tool.

The World Health Organization is expected to decide before the end of the year whether to recommend the use of the vaccine, known as RTS,S or Mosquirix, in countries with high malaria rates.

Study results

The pharmaceutical company GlaxoSmithKline began developing RTS,S in 1987. It is the first malaria vaccine candidate to have made it as far as a phase 3 trial. Final trial results published in April showed about one-third fewer episodes of clinical and severe malaria in young children who received three vaccine doses and a booster, with protection waning over time.

Vaccines generally work by exposing the body to a harmless version of an infecting agent or a fragment of it, which primes the immune system to block the pathogen. The RTS,S vaccine carries a fragment of a protein that sits on the surface of the parasite; the protein is capable of provoking an immune response in humans that is capable of stopping the parasite from maturing and multiplying in the liver. But the protein is genetically diverse across different strains of malaria – probably from frequent mutations to avoid immune detection – and RTS,S includes just one form, or allele.

The study published in today’s NEJM tested whether RTS,S provided better protection against parasites with alleles that matched that of the vaccine.

Researchers from the Broad Institute of MIT and Harvard analyzed blood samples from almost 5,000 of about 15,000 infants and children who participated in the phase 3 clinical trial at 11 study sites in six countries in Africa between 2009 and 2013. The large sample size combined with sensitive sequencing techniques that detected even rare alleles and infections by multiple parasites enabled researchers to find an allele-specific response that smaller studies had missed.

Fred Hutch’s Gilbert jumped at the chance to analyze what he called “this uniquely valuable data set.” He assembled a team of Fred Hutch quantitative scientists to design a statistical analysis plan.

Sieve analysis allows scientists to go beyond saying simply whether an experimental vaccine provides protection to more precisely identify why or why not. In this case, researchers compared parasite strains found in trial participants who received the vaccine but came down with malaria anyway to those who received a placebo and contracted malaria. The placebo group was more varied. In the vaccinated group, some strains were able to slip through sieve-like “holes” in the vaccine while others were blocked.

“This is the first time a malaria vaccine has had good enough protection to do a sieve analysis, and there were enough samples and enough malaria [cases],” said Gilbert, a member of the Vaccine and Infectious Disease Division and director of the statistical center for the Hutch-based HIV Vaccine Trials Network. “And the Broad and Harvard went to the trouble to measure all these sequences. Those three things were incredibly useful.”

Analyzing the data involved developing new statistical methods to handle the complexities of how the malaria parasite evolves and is transmitted, verifying their correctness in simulations and employing parallel computing – carrying out many calculations simultaneously – to handle the huge computational burden, Gilbert said. Dr. Michal Juraska, a Fred Hutch biostatistician and co-first author of the NEJM paper, led the development of the reproducible statistical code and data analysis with help from Fred Hutch bioinformatics expert Ted Holzman.

Juraska’s analysis found that although RTS,S provided at least partial protection against all strains of the parasite, it was significantly more protective at preventing malaria when the parasite matched the allele in the vaccine. Protection against disease from infection by parasites with matched alleles was 50.3 percent one year after the vaccination series, compared with 33.4 percent against mismatched malaria. 

“Now that we know that [the difference] exists, it contributes to our understanding of why the vaccine is not effective in all cases and informs future vaccine development efforts,” said Dr. Dan Neafsey, associate director of the Genomic Center for Infectious Diseases at the Broad and co-first author of the study.

Practical applications

One application of sieve analysis, once it’s learned that a vaccine’s efficacy depends on the genetics of the pathogen, is for the vaccine manufacturer to add a different strain or strains to the vaccine to increase its protectiveness.

But this knowledge could also help public health officials use RTS,S more effectively as is by choosing where and when to use it. Place matters: Parasites vary genetically in different regions of Africa, with some regions better matching the allele used in the vaccine, said Dr. Trevor Bedford, a Fred Hutch evolutionary biologist who helped in the analysis. And because the vaccine’s effectiveness against both matched and mismatched alleles wanes over time, timing also matters in many places where malaria is seasonal, peaking during and just after the rainy season.

 “You might expect the vaccine to work better in regions where the circulating parasites are similar to what’s in the vaccine,” said David Benkeser, a biostatistics doctoral student at the University of Washington under Gilbert who contributed a novel statistical method for the analysis.  “And if you can give the vaccine ideally right before a high-intensity [malaria] season, you might expect it’s going to protect very well in that window.”

The study found that at six months after vaccination, protection was higher than at one year – 70.2 percent against matched malaria and 56.3 percent against mismatched. And immediately after the vaccination series, protection against infection from matched malaria was 95 percent.

“WHO is going to be thinking about where and how to deploy the vaccine versus spending money on other malaria preventative systems like bed nets and insecticides – things we know are effective. They have to think about how to maximize the dollar spent,” said Benkeser. “I’m really curious to see what the people that we hand these results off to are going to do with them.”

The NEJM study was supported by the National Institute of Allergy and Infectious Diseases, the Bill and Melinda Gates Foundation and the PATH Malaria Vaccine Initiative.