Genetic Diversity and Lack of Artemisinin Selection Signature on the Plasmodium falciparum ATP6 in the Greater Mekong Subregion

Abstract

The recent detection of clinical Artemisinin (ART) resistance manifested as delayed parasite clearance in the Cambodia-Thailand border area raises a serious concern. The mechanism of ART resistance is not clear; but the P. falciparum sarco/endoplasmic reticulum Ca2+-ATPase (PfSERCA or PfATP6) has been speculated to be the target of ARTs and thus a potential marker for ART resistance. Here we amplified and sequenced pfatp6 gene (∼3.6 Kb) in 213 samples collected after 2005 from the Greater Mekong Subregion, where ART drugs have been used extensively in the past. A total of 24 single nucleotide polymorphisms (SNPs), including 8 newly found in this study and 13 nonsynonymous, were identified. However, these mutations were either uncommon or also present in other geographical regions with limited ART use. None of the mutations were suggestive of directional selection by ARTs. We further analyzed pfatp6 from a worldwide collection of 862 P. falciparum isolates in 19 populations from Asia, Africa, South America and Oceania, which include samples from regions prior to and after deployments ART drugs. A total of 71 SNPs were identified, resulting in 106 nucleotide haplotypes. Similarly, many of the mutations were continent-specific and present at frequencies below 5%. The most predominant and perhaps the ancestral haplotype occurred in 441 samples and was present in 16 populations from Asia, Africa, and Oceania. The 3D7 haplotype found in 54 samples was the second most common haplotype and present in nine populations from all four continents. Assessment of the selection strength on pfatp6 in the 19 parasite populations found that pfatp6 in most of these populations was under purifying selection with an average dN/dS ratio of 0.333. Molecular evolution analyses did not detect significant departures from neutrality in pfatp6 for most populations, challenging the suitability of this gene as a marker for monitoring ART resistance.

Artemisinin Resistance-Associated Polymorphisms at the K13-Propeller Locus are Absent in Plasmodium falciparum Isolates from Haiti

“…We originally targeted the pfatpase6 gene, because it carried an SNP (S769N) that was associated with lowered sensitivity to artemether in an earlier investigation in French Guiana 20 ; however, we did not detect the S769N mutation in our preliminary sample (data not shown). With more recent studies unable to confirm the association of the S769N mutation with artemisinin resistance in other populations 21,22 and the recent identification of the K13-propeller as a strong candidate for artemisinin resistance, we decided to refocus our investigation on K13-propeller polymorphisms. To contribute to the growing knowledge about the global genetic diversity of the K13-propeller and establish a baseline for future surveillance of potential artemisinin resistance in Haiti, we sequenced an 810-base pair region of the K13-propeller from P. falciparum samples collected in Haiti between 2010 and 2013.…”

Examining Plasmodium falciparum and P. vivax clearance subsequent to antimalarial drug treatment in the Myanmar-China border area based on quantitative real-time polymerase chain reaction

“…However, no significant correlation was observed between these mutations and parasite clearance time. While our small sample size may have hidden other possible mutations or underestimated the frequency of the observed mutations, it is also possible that pfatp 6 does not play a key role in ACT resistance as shown in recent studies [ 29 , 73 , 74 ].…”

Experimental Models Point Mutations In Plasmodium falciparum pfatpase6 Gene Exposed to Recuring Artemisinin In Vitro

“…The in pfatpase6 gene in all populations, so that the pfatpase6 gene is still appropriate as a marker for monitoring artemisinin resistance against Plasmodium falciparum [25]. falciparum from Southeast Asia.…”