In a second paper, the NIH-led group also found that parasites resistant to chloroquine, a former mainstay antimalaria drug, arose in several geographic locations and rapidly spread across continents. This finding upends the long-held notion of some scientists that chloroquine resistance developed independently in only two areas in the mid-20th century and slowly spread to other countries from those sites. The new information implies that resistance to chloroquine and other antimalaria drugs can arise and spread more pervasively than previously thought and argues for careful drug-use monitoring programs.
The new reports appear in back-to-back papers published in the July 18 issue of Nature.
Plasmodium falciparum, the parasite responsible for most deadly cases of malaria, thrives in the tropics and infects about 300 million people annually. One to 2 million people, mostly infants and children, die of the disease each year. The number of cases of malaria worldwide is increasing, mainly because of the evolution of drug-resistant parasites.
Debate regarding the genetic diversity and origin of the parasite has been ongoing since the late 1990s. It was then that a group of evolutionary biologists first proposed a "Malaria Eve" hypothesis to explain the origin of the parasite. By examining 10 genes of the malaria parasite, these scientists proposed that the bug is relatively young 3,000 to 5,000 years old and genetically similar from place to place, and as such, should not be too difficult to control.
To explore the question in more detail, Xin-zhuan Su, Ph.D., and Jianbing Mu, Ph.D., of the National Institute of Allergy and Infectious Diseases (NIAID); Wen-Hsiung Li, Ph.D., and Kateryna Makova, Ph.D., of the University of Chicago; and their colleagues at the NIH National Center for Biotechnology Information (NCBI) looked for genetic differences among geographically distinct parasites. The five P. falciparum parasites they chose each hailed from a different geographical region: Southeast Asia, Africa, South America, Central America and Papua New Guinea. The researchers compared the same 204 genes in chromosome 3 of each of these parasites to see if they could detect any nucleotide differences. This painstaking process revealed great diversity in the five genomes. Based on these differences, the scientists estimate the earliest common parasite ancestor must be 100,000 to 180,000 years old, a timeframe coincident with human population expansion out of Africa. "We speculate," says Dr. Su, "that when the human population grew, the malaria parasite grew with it."
In the second study, Dr. Su, John Wootton, Ph.D., of NCBI, and their colleagues set out to obtain a detailed picture of the origin and spread of chloroquine-resistant P. falciparum. Dr. Su's group looked for genetic diversity in 87 parasites isolated from patients worldwide. For each isolate, the researchers typed 342 DNA markers over the entire parasite genome, including the gene linked to chloroquine resistance, and thereby revealed a "genetic fingerprint." This is the first time DNA fingerprinting of the entire genome has been done for a complex parasite, notes Dr. Su. As such, the data is more reliable and powerful than previous research findings to answer evolutionary questions.
Dr. Wootton then used computations based on population genetic theory and computer simulations to expose the recent evolutionary history hidden in segments of the parasite genomes. "This showed very clearly that a large segment of a parasite chromosome had hitchhiked along with the key chloroquine resistance gene," says Dr. Wootton. "This is a hallmark, we think, of how chloroquine has exerted strong Darwinian selection and profoundly influenced recent P. falciparum evolution." This analysis revealed at least four independent chloroquine resistance founder events: one in Southeast Asia in the late 1950s, which later spread throughout most of Asia and Africa; at least two in South America; and one in Papua New Guinea.
"This study changes our thinking about chloroquine resistance," says Dr. Su. "First, it has happened more frequently than we thought. Second, we now know that the African parasite that developed resistance in the late 1970s did not arise independently but came from Southeast Asia." It took only 10 to 15 years for these resistant parasites to spread throughout Africa. "This means that when a drug- or vaccine-resistant parasite arises, it will not take long for this resistance to spread to other continents, reflecting human travel, particularly by air, and the high transmission rate via mosquitoes in Africa."
Their genome-wide picture also shows how genetic recombination shuffling of DNA from two parent parasites has occurred rapidly and generated enormous genetic diversity. "This could enable the parasite to evolve resistance to multiple drugs and vaccines in the future," says Dr. Su.
NIAID is a component of the National Institutes of Health (NIH). NIAID supports basic and applied research to prevent, diagnose, and treat infectious and immune-mediated illnesses, including HIV/AIDS and other sexually transmitted diseases, illness from potential agents of bioterrorism, tuberculosis, malaria, autoimmune disorders, asthma and allergies.
NCBI is a component of the NIH National Library of Medicine. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
Press releases, fact sheets and other NIAID-related materials are available on the NIAID Web site at http://www.niaid.nih.gov.
The National Institute of Allergy and Infectious Diseases is a component of the National Institutes of Health, U.S. Department of Health and Human Services.
J Wootton et al. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature 418:320-323 (2002).