{"doi":"10.3389/fpara.2023.1067966","title":"Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high transmission","abstract":"<jats:p>A major motivation for developing molecular methods for malaria surveillance is to measure the impact of control interventions on the population genetics of <jats:italic>Plasmodium falciparum</jats:italic> as a potential marker of progress towards elimination. Here we assess three established methods (i) single nucleotide polymorphism (SNP) barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) <jats:italic>var</jats:italic>coding (fingerprinting <jats:italic>var</jats:italic> gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in 82.3% (median 3; range 1-18) and 57.8% (median 2; range 1-12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose ~200 low-complexity infections biased to single and double clone infections for analysis. Each genotyping method presented a different pattern of change in diversity and population structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (i.e., SNPs &amp;lt; microsatellites &amp;lt; <jats:italic>var</jats:italic>). <jats:italic>Var</jats:italic>coding and microsatellite genotyping showed the overall failure of the IRS intervention to significantly change the population structure from pre-IRS characteristics (i.e., many diverse genomes of low genetic similarity). The 24-SNP barcode provided limited information for analysis, largely due to the biallelic nature of SNPs leading to a high proportion of double-allele calls and a view of more isolate relatedness compared to microsatellites and <jats:italic>var</jats:italic>coding. Relative performance, suitability, and cost-effectiveness of the methods relevant to sample size and local malaria elimination in high-transmission endemic areas are discussed.</jats:p>","journal":"Frontiers in Parasitology","year":2023,"id":639857,"datarank":0.6581180744221673,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.13825768900220828,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.13825768900220828,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":9,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":369430,"name":"Kathryn E. 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