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A false-colored electron micrograph of the malaria parasite (right) traveling through a cell.Image courtesy of Ute Frevert, false colored by Margaret Shear

Invisible to the naked eye, microbes live in a world where significance is measured more in the propensity to inflict and spread disease than in sheer physical size. A clear frontrunner in this context is the human malaria parasite, a pathogen that causes more than 1 million deaths each year in the developing world, though virtually none in developed countries like the United States. Now, an international team of scientists has created a modern genomic tool for probing the biology and evolution of the parasite that may help to rein in one of the world’s most devastating — and often neglected — infectious diseases.

A research group led by scientists from the Harvard School of Public Health and the Ó³»­´«Ã½, together with researchers in Senegal, has developed a genome-wide map that charts the genetic variability of the human malaria parasite, Plasmodium falciparum. Published in the December 10 advance online edition of Nature Genetics, the study reveals striking variability within the pathogen’s genome, including an initial catalog of nearly 47,000 specific genetic differences among parasites sampled worldwide. These differences lay the foundation for dissecting the functions of important parasite genes and for tracing the global spread of malaria. The work has already unearthed novel genetic regions that may underlie resistance to current drugs against the disease.

"Malaria remains a significant threat to global public health, driven in part by the genetic changes in the parasite that causes the disease," said senior author Dyann Wirth, a professor and chairman of the department of immunology and infectious diseases at the Harvard School of Public Health and the co-director of the Ó³»­´«Ã½â€™s Infectious Disease Initiative. "This study gives us one of the first looks at genetic variation across the entire malaria parasite genome — a critical step toward a comprehensive genetic tool for the malaria research community."

P. falciparum is the deadliest of the four parasites that cause malaria in humans. It kills one person every 30 seconds and most of its victims are children living in Africa, particularly in regions south of the Sahara. Adding to this awful toll, at least 500 million people are currently infected with P. falciparum and at least 2 billion are at risk, according to a recent study. Clearly a disease of poverty, malaria’s devastation is fueled in part by the abilities of the parasite to escape the body’s natural defenses and to overcome malaria drugs — abilities that can be strengthened through regular changes to its DNA. Despite decades of research, including the full genome sequencing of a P. falciparum isolate in 2002, the nature and extent of these genetic changes remain largely unknown.

To gain a broad picture of the parasite’s genetic variability — worldwide and genome-wide — the scientists analyzed more than 50 different P. falciparum samples from diverse geographic locations. This includes the complete genome sequencing of two well-studied samples as well as extensive DNA analyses of 16 additional isolates. The researchers compared the DNA sequences to each other and to the recently sequenced P. falciparum genome, uncovering extensive differences, including roughly 47,000 single letter changes called single nucleotide polymorphisms (SNPs). These SNPs represent more than double the anticipated level of diversity in the parasite’s DNA. Although preliminary work suggests there are many more SNPs to be found, this initial survey — similar to the recent HapMap project in humans — provides a key starting point for future systematic efforts to identify parasite genes that are essential to malaria. "The roles of most of the malaria parasite’s genes are still not known," said first author Sarah Volkman, a research scientist at the Harvard School of Public Health. "An important application of this new tool will be in pinpointing the genes that are vital to the development and spread of malaria."

The malaria research teamÓ³»­´«Ã½ and HSPH scientists who helped to build the new genetic map of P. falciparumFrom left to right, back row: Sarah Volkman, Pardis Sabeti, Roger Wiegand, Danny Milner, Amanda Lukens, Nira Mahesh, Cherie Ramirez.Front row: Rachel Daniels, Steve Schaffner, Dave DeCaprio, Dan Neafsey, David Rosen, Meg Andrews, Danny Park.Not pictured: Bruce Birren, Johanna Daily, Alan Derr, Manoj Duraisingh, James Galagan, Sante Gnerre, David Jaffe, Eric Lander, Evan Mauceli, Rob Onofrio, Liuda Siaugra, Nicole Stange-Thomann, Skye Waggoner, Dyann Wirth, Joanne Zainoun.Photo by Maria Nemchuk

Through its ability to highlight evolutionary differences among parasites, the map can be used to uncover genes that underlie malaria drug resistance — a major obstacle to adequate control of the disease. Using the tool to compare parasites exposed to different anti-malarial drugs, the scientists identified a novel region that is strongly implicated in resistance to the drug pyrimethamine, and also confirmed a region of the genome known to be involved in chloroquine drug resistance. "The same genetic principles used to study human evolution can provide important clues about malaria," said first author Pardis Sabeti, a postdoctoral fellow at the Ó³»­´«Ã½. "This tool has already yielded insights into the genetic changes that correlate with different drug treatments, pointing us to genes that may contribute to drug resistance."

The map can also define the genetic landscapes of different parasite populations. Applying it to parasites from various continents, the scientists discovered greater DNA variability among P. falciparum samples from Africa relative to those from Asia and the Americas. This knowledge guides the selection of genetic markers to track the transmission of distinct parasites, particularly ones that are virulent or drug resistant. It also lays the groundwork for connecting parasite genes with traits that vary geographically and bolster malaria’s foothold in many parts of the world.

The work is one of three large-scale studies of the P. falciparum genome that appear together in Nature Genetics, and it represents a collaborative effort among Boston area researchers and a scientific team led by Souleymane Mboup, a professor at the Cheikh Anta Diop University in Senegal where malaria is endemic. "We are grateful for the contributions of our colleagues in Senegal," said Wirth. "They are a crucial part of this collaboration."

Importantly, the efforts shared by this partnership continue. Several of the Ó³»­´«Ã½ and Harvard School of Public Health scientists who participated in the malaria study are in Senegal this week to conduct a genomics and bioinformatics workshop for scientists in West African nations. The workshop will help researchers in endemic areas learn about the new P. falciparum tool and apply it to their own studies of malaria.

The authors of the Nature Genetics paper include Ó³»­´«Ã½ scientists Bruce Birren, Dave DeCaprio, Alan Derr, James Galagan, Sante Gnerre, David Jaffe, Eric Lander, Evan Mauceli, Dan Neafsey, Robert Onofrio, Pardis Sabeti, Steve Schaffner, Liuda Siaugra, Nicole Stange-Thomann, Skye Waggoner, Roger Weigand and Joanne Zainoun; Harvard School of Public Health scientists Johanna Daily, Manoj Duraisingh, Amanda Lukens, Danny Milner, Sarah Volkman and Dyann Wirth; Harvard University scientist Daniel Hartl; and Cheikh Anta Diop University scientists Daouda Ndiaye, Omar Ndir and Ousmane Sarr.

Data from the study can be accessed through the public database or at the Ó³»­´«Ã½ .

Paper cited:

Volkman et al., (2006) ; Nature Genetics; DOI:10.1038/ng1930