Biology subjects

Fola, A. A.

Publications and source records attributed to Fola, A. A..

3 recordsLinked to original sources

bioRxiv2026

Malaria control and the unexpected spread of diagnostic-resistant Plasmodium falciparum in Peru

Plasmodium falciparum parasites with deletions of the histidine-rich protein 2 and 3 (hrp2 and hrp3) genes evade detection by common rapid diagnostic tests (RDTs) and pose a growing threat to malaria control. While these deletions have emerged in multiple regions globally, the evolutionary forces driving their spread remain unclear. Here, we analyze 1,215 P. falciparum samples collected between 2003 and 2018 in Loreto, Peru. This region experienced a major decline in malaria transmission following the Project for Malaria Control in Andean Border Areas (PAMAFRO) and now harbors a high proportion of hrp2/3 deleted parasites despite limited RDT use. Using molecular inversion probe (MIP) sequencing across > 2,000 genome-wide loci, we observed a marked reduction in genetic diversity, increased clonality, and fixation of parasites with deletions of both hrp2 and hrp3 genes (hrp2-/3-) over time. Identity-by-descent (IBD) analysis revealed rapid expansion of a single hrp2-/3- dominant lineage in the post-PAMAFRO period, consistent with clonal replacement after intense malaria control. Targeted sequencing of the hrp2/3 regions showed conserved deletion breakpoints across three different lineages, indicative of recombination of a common haplotype into distinct genetic backgrounds. To investigate the evolutionary forces driving the fixation of hrp2-/3- in Loreto, we simulated allele frequency trajectories under different selection coefficients. We found that fixation of hrp2-/3- due solely to genetic drift (selection coefficient s = 0) is unlikely; a selection coefficient of s [≥] 0.03 was required for fixation to occur consistently. However, our simulations also indicate that a genetic bottleneck caused by PAMAFRO increased the likelihood of fixation through drift by 4.5- to 17-fold depending on the population. These findings suggest that hrp2-/3- fixation was likely driven by a combination of demographic changes resulting from PAMAFRO and selective advantage unrelated to RDT use. Our results demonstrate how intensive malaria control efforts can reshape parasite populations and underscore the value of expanded genomic surveillance as countries move toward malaria elimination.

genetics↗

bioRxiv2025

COATswga: A Coverage Optimizing and Accurate Toolkit for fast primer design in selective whole genome amplification

BackgroundDespite the transformative nature of next-generation sequencing in genomics, efficiently capturing underrepresented microbial DNA from complex biological mixtures, such as pathogens from host samples, remains a persistent challenge. Unwanted genomes make whole-genome sequencing (WGS) inefficient and expensive without enrichment of the targeted genome. Selective whole genome amplification (sWGA) uses primers that selectively bind to the target genome to preferentially amplify and enrich an entire microbial genome. However, existing sWGA primer design is often complicated and time-consuming, with primers usually having biased amplification producing uneven genome coverage. Developing faster primer design methods that ensure uniform, reliable microbial genome recovery are critical to improving sWGA. MethodsWe developed COATswga, a Coverage Optimizing and Accurate Toolkit for designing sWGA primer sets. The pipeline consists of three key steps: (1) primer discovery, using k-mer counting to identify all candidate primers in the target genomes; (2) filtering, where primers are screened for amplification potential, thermodynamic stability, and specificity; and (3) set formation, which uses a novel interval-based tiling algorithm. COATswga is parallelized for efficiency and supports pre-existing primer set refinement and gap filling. The pipeline was evaluated by designing primer sets for Plasmodium falciparum (strain 3D7) and benchmarking their performance against sets generated using similar pipelines. ResultsCOATswga-designed primers demonstrated superior enrichment based on both qPCR and long-read sequencing. In P. falciparum-spiked human DNA samples at parasitemia levels of 400, 100, and 10 parasites/L, COATswga primers achieved higher amplification efficiency and specificity compared to alternatives. At 100 parasitemia, COATswga yielded [~]99% of reads mapping to the P. falciparum genome with 82.5% of the genome having 5x coverage. Even at 10 parasites/uL, COATswga primers enabled effective amplification of key drug resistance genes (pfcrt and pfmdr1). Additionally, integration with molecular inversion probe (MIP) genotyping showed that COATswga greatly improved sequencing depth and target recovery in low-density infections compared to established sWGA primers. ConclusionCOATswga provides a robust and flexible solution for designing sWGA primers to reliably recover targeted genomes from complex samples. The new P. falciparum primer set performs well in low-parasitemia samples allowing more extensive application of sWGA in falciparum malaria genomics.

bioinformatics↗

bioRxiv2019

Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Monitoring the genetic structure of malaria parasite populations has been proposed as a novel and sensitive approach to quantify the impact of malaria control and elimination efforts. Here we describe the first population genetic analysis of sympatric Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from serial cross-sectional studies pre-(2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially in these communities (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. P. falciparum diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow between provinces. P. vivax prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, the emergence of clonal transmission and significant multilocus linkage disequilibrium (mLD) due to increased focal inbreeding post-LLIN was a strong indicator of impact on the parasite population using these markers. After eight years of intensive malaria control in PNG and substantial prevalence decline the impact on parasite population diversity and structure detectable by microsatellite genotyping was limited.

microbiology↗