Population Structure Shapes Copy Number Variation in Malaria Parasites

Abstract

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.

Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia

“…Notably, we identified Duffy-binding protein (DBP) duplication events in 17 of 70 P. vivax isolates and multidrug-resistance protein 1 (MDR1) duplication events in 12 of 80 P. falciparum isolates. As in previous work in P. falciparum (33), no highconfidence CNV occurred in close proximity with the selective sweeps identified above.…”

“…Copy-number variants (CNVs) are important in the evolution of parasite populations (33). Using two complementary Results are presented by ranking on absolute normalized nS L score.…”

South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains

“…Our observation of higher likelihood of fixation of potentially deleterious mutations in P. falciparum strains from SEA compared to African strains is consistent with the previous observation of higher rate of potentially deleterious copy number variations in P. falciparum from SEA compared to Africa 21 . These observations suggest relaxed negative selection on P. falciparum from SEA compared to Africa and that SEA strains would have lower fitness than African strains.…”

“…The much larger population size of P. falciparum in Africa 21 , as also evidenced by the high rate of mixed strain infection ( Figure 6) should make it easier for resistance mutations to appear. Indeed, artemisinin resistance mutations in kelch13 gene were observed in samples from Africa, including the most common artemisinin resistance mutation C580Y 18 .…”

Antimalarial drug resistance: linking Plasmodium falciparum parasite biology to the clinic

“…In Southeast Asia, mefloquine or lumefantrine treatment both select for parasites with increased pfmdr1 copy number, a finding corroborated in vitro with genetically modified parasites 33,172 . This phenomenon, however, does not extend to Africa, where pfmdr1 copy-number variants are exceedingly rare 181 . A potential explanation is that the combination of lower drug pressure at the population level and more frequent mixed infections exacerbates the fitness cost resulting from pfmdr1 overexpression, and results in a predominance of single-copy pfmdr1 parasites.…”