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Malaria Parasite DNA From Eradicated European Strain Sheds Light on Historic Disease Distribution

NEW YORK (GenomeWeb) – An international research team has sequenced previously eradicated European strains of the human malaria parasite that they recovered from old medical slides, filling in gaps for the historical distribution of the disease.

The results were published today in the Proceedings of the National Academy of Sciences.

Both of the sequenced human malaria parasites, Plasmodium vivax and Plasmodium falciparum, are among the most significant human pathogens. P. vivax is the most widely distributed human malaria parasite outside of Africa, while P. falciparum is responsible for more than 90 percent of malarial deaths and exists predominantly in sub-saharan Africa.

Researchers have been studying both species extensively to understand how they continue to evolve and spread, including a study published recently in Nature Genetics that uncovered how P. vivax has been evolving on the global scale.

Researchers believe that modern-day distribution of malaria is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia based on previous phylogenetic analyses of Plasmodium parasites, the researchers wrote in the paper. "A major outstanding question is the phylogenetic affinity of the malaria-causing parasites Plasmodium vivax and falciparum in historic southern Europe — where it was endemic until the mid-20th century, after which it was eradicated across the region," they wrote.

The team acquired a set of slides from the medical collection of Ildefonso Canicio, a Spanish malaria researcher from the early 1900s. The slides contained blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944. Due to the degraded natures of the samples, the researchers extracted DNA from the slides using a silica spin column-based protocol previously developed for ancient museum samples, prepared DNA libraries using a New England Biolabs sample prep kit, and sequenced them on Illumina platforms.

The team further selected for parasite DNA sequences by performing capture depletion to ensure that P. falciparum and P. vivax reads were the only ones present out of an initial abundance of human DNA. This procedure, enabled by the MYbait Human Whole Genome Capture Kit from oligo product firm MYcroarray, entailed depleting human content by performing whole-genome capture with human baits and shotgun sequencing what would normally be considered the waste product, followed by capture enrichment using whole-genome bait synthesized from P. falciparum genomic DNA.

They then reconstructed genomes for both species and performed a phylogenetic analysis.

The researchers found that the P. falciparum mtDNA sequence represented the full length of the mitochondrial genome, with 5,827 nucleotides, and they found three mutations present in the three slides that are also shared with present-day infected Indian individuals, which lines up well with historical accounts. In the phylogenetic analysis, the researchers found that the P. vivax mtDNA clustered close to the haplotype most commonly found today in the Americas.           

"Our results provide strong support for the hypothesis that the dominant present-day South American haplotypes were indeed carried from Europe by post-Columbian travelers and that these haplotypes are in fact the closest modern representatives of the ancestral Eurasian P. vivax stock," the researchers wrote. However, they did point out that because of the limited genetic data available from this source population it's not possible to ascertain if all American strains derive from the European continent. 

"We are currently searching for additional malaria slides among antique medical collections along Europe to obtain further information on the genetic diversity of the European Plasmodium strains," the researchers wrote. "With the methodology developed in the present research, we hope we could be able to retrieve also a substantial fraction of the nuclear genome of these parasites."