Biology subjects

Neafsey, D. E.

Publications and source records attributed to Neafsey, D. E..

At least 19 recordsLinked to original sources

bioRxiv2026

Genotypic evidence of vector-mediated selection on Plasmodium falciparum in infected field-collected Anopheles mosquitoes

Malaria-causing Plasmodium parasites are transmitted between vertebrate hosts via diverse species of Anopheles mosquitoes. The P47 protein in Plasmodium falciparum has been shown to affect transmission in various anopheline species by mediating evasion of mosquito innate immunity in an allele-specific manner. The Pfs47 gene that encodes P47 exhibits high genetic divergence across continents, as well as high genetic diversity within many parasite populations, but the impact of polymorphisms on transmission success in different sympatric vectors has not been previously studied in a field context. Here we report parasite genotyping data from naturally infected, field-collected mosquitoes at sites harboring at least two prevalent sympatric vector species, targeting Pfs47 in addition to the CSP, AMA1, SERA2, and TRAP parasite antigens. Collections took place at Ndangueng, Cameroon and Benguia, Gabon between November 2019 and July 2021, yielding infected Anopheles gambiae at both sites in addition to Anopheles moucheti in Cameroon and Anopheles funestus in Gabon. We found no significant difference in the mean number of parasite strains in infected sympatric mosquito species from each site. However, Pfs47 exhibited a significant difference in the prevalence of an amino acid polymorphism (I248L) between An. moucheti and An. gambiae in Cameroon. Polymorphisms at two additional positions (N272Y/I and P369H) displayed significant linkage disequilibrium with I248L, and there were significant differences in the distribution of Pfs47 haplotypes between sympatric mosquito species at both sites. These findings demonstrate divergent selection on P. falciparum mediated by sympatric vector species, suggesting that parasite genotype significantly impacts local vectorial capacity by modulating species-specific vector competence.

evolutionary biology↗

bioRxiv2026

Lowly polymorphic pathogen proteins may not be under evolutionary constraint

A central challenge in infectious disease biology is anticipating whether pathogen proteins targeted by vaccines, drugs, or diagnostics can evolve in ways that reduce intervention efficacy. Evolutionary constraint is therefore relevant to selecting targets likely to remain effective after deployment. Yet low diversity in contemporary pathogen populations is often interpreted as evidence of evolutionary constraint, an inference that can be misleading. In this Personal View, we use Plasmodium falciparum malaria to illustrate how contemporary population diversity and longer-term cross-species divergence can inform assessments of evolutionary constraint. A severe population bottleneck reduced diversity across the P. falciparum genome, meaning that low diversity in a particular protein-coding gene does not necessarily indicate unusual constraint. We place gene-level diversity in its genome-wide context, compare it with divergence across related ape-infecting malaria parasites, and examine how both relate to experimental essentiality. We then examine diversity and divergence along vaccine, drug, and diagnostic targets, considering them in relation to known resistance-associated mutations and other routes of evolutionary escape. We introduce PEEP (Protein Evolution Explorer for Plasmodium), a public interactive resource for exploring diversity and divergence across P. falciparum protein-coding genes and along individual proteins. Although our analyses focus on P. falciparum malaria, the implications extend across pathogens: low diversity alone is insufficient evidence of evolutionary constraint, and assessments of intervention durability should consider constraint alongside potential routes of evolutionary escape.

evolutionary biology↗

bioRxiv2026

Additional blood meals increase mosquito infectivity by accelerating the transcriptional development of Plasmodium sporozoites

Sporozoites, the infectious stage of Plasmodium malaria parasites, must invade two different tissues in two very different hosts to ensure transmission: the mosquito salivary glands and the human liver. Whether infectivity to hepatocytes is affected by physiological components, such as the availability of nutrients within the Anopheles female, is not well understood. Here we show that Plasmodium falciparum sporozoite infectivity to hepatocytes is increased if mosquitoes take an additional blood meal while oocysts are developing. Infection rates of HC04.J7 hepatocytes at 24 h were 1.8-fold higher for P. falciparum salivary gland sporozoites isolated from Anopheles gambiae females fed twice (2BF) compared to those which only received the infectious blood meal (1BF). This increase in infectivity was observed at an early infection timepoint (day 11) and was accompanied by a marked shift in the transcriptional profiles of 2BF salivary gland sporozoites, identifying genes likely involved in infection and development in the mammalian host. Overall, our data reveal new factors potentially involved in sporozoite infectivity, and have broad implications for understanding transmission of malaria in endemic areas where multiple blood meals commonly shape available resources for adult female mosquitoes.

microbiology↗

bioRxiv2025

The Portable Microhaplotype Object and Tools

Structured AbstractO_ST_ABSMotivationC_ST_ABSThe rapid increase in the generation of targeted sequencing data offers immense potential for research, medicine, and public health, however the lack of an established standard for these data has led to disparate solutions for data storage. A widely accepted standard is essential for data sharing, reuse, and the coordinated development of interoperable analysis tools. ResultsWe propose the Portable Microhaplotype Object (PMO), a standardized format for efficiently and losslessly storing phased targeted sequencing data (microhaplotypes). The PMO format is JSON-based, allowing efficient, relational storage of genetic data together with relevant metadata to minimize orphaned data. The format includes required fields and a curated set of optional fields leveraging established ontologies. To facilitate ease of use, we developed pmotools-python, an open-source package for creating, manipulating, and exporting PMO data into common formats. Additionally, we provide a simple web-based app to quickly create PMO files from tabular inputs, making the format accessible to a wide variety of users. Example datasets from Plasmodium, Anopheles, Escherichia coli, and Staphylococcus aureus demonstrate the broad applicability of the approach. PMO will streamline data sharing, foster interoperability, and accelerate the development of harmonized analysis tools. Availability and implementationThe Portable Microhaplotype Object (PMO) project, including the ontology specification, software tools, example datasets, and tutorials, is freely available athttps://plasmogenepi.github.io/PMO_Docs/. Key software components and datasets have archived releases with DOIs to ensure permanence, detailed in the Supplementary Text 1-5. Contactkathrynmmurie@gmail.com or nickjhathaway@gmail.com

bioinformatics↗

bioRxiv2025

Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus)

Timber rattlesnakes (Crotalus horridus) face escalating threats in the Northeastern Appalachians, including habitat fragmentation, human encroachment, and the fungal pathogen Ophidiomyces ophiodiicola. Using untargeted sequencing of DNA extracted from scale clips, we generated both host whole-genome and metagenomic data for 97 snakes from eight populations. Analysis of the snake genomes shows the populations surveyed exhibit relatively low levels of inbreeding and are genetically distinct, but that the degree of separation correlates only weakly with geographic distance. A genome-wide association analysis identified a locus associated with black-to-yellow color variation that contains an aldehyde dehydrogenase gene (ALDH4A1) related to genes involved in hair color differences in humans. Metagenomic analysis showed that O. ophiodiicola read counts were generally higher in snakes exhibiting clinical signs of Snake Fungal Disease, but some visually asymptomatic snakes had high pathogen loads. Together, these findings highlight the dual utility of untargeted sequencing for population genetics and pathogen surveillance, providing a foundation for future studies of adaptation, disease dynamics, and conservation in this declining species.

genomics↗

bioRxiv2025

Population genomics of Anopheles darlingi, the principal South American malaria vector mosquito

Malaria in South America remains a serious public health problem. Anopheles (Nyssorhynchus) darlingi is the most important malaria vector across tropical Latin America. Vector-targeted disease control efforts require a thorough understanding of mosquito demographic and evolutionary patterns. We present and analyze whole genomes of 1094 A. darlingi (median depth 18x) from six South American countries. We observe deep geographic population structure, high genetic diversity including thirteen putative segregating inversions, and no evidence for cryptic sympatric taxa despite high interpopulation divergence. Strong signals of selection are plausibly driven by insecticides, especially on cytochrome P450 genes, one of which we validated experimentally. Our results will facilitate effective mosquito surveillance and control, while highlighting ongoing challenges that a diverse vector poses for malaria elimination in the western hemisphere.

evolutionary biology↗

bioRxiv2025

Heterogeneous constraint and adaptation across the malaria parasite life cycle

Evolutionary forces vary across genomes, creating disparities in how traits evolve. In organisms with complex life cycles, it is unclear how intrinsic differences among discrete life stages impact evolution. We looked for life history-driven changes in patterns of adaptation in Plasmodium falciparum, a malaria-causing parasite with a multi-stage life cycle. Categorizing genes based on their expression in different life stages, we compared patterns of between- and within- species polymorphism across stages by estimating nonsynonymous to synonymous substitution rate ratios (dN/dS) and mean pairwise nucleotide diversity (NS/S). Considering these alongside estimates of Tajimas D, fixation probability, adaptive divergence proportion and rate, and FST, we looked for changes in the drift-selection balance in life stages subject to transmission bottlenecks and changes in ploidy. We observed signals of reduced selection efficacy in genes exclusively expressed in sporozoites, the parasite form transmitted from mosquitoes to humans and often targeted by vaccines and monoclonal antibodies. We discuss implications for how parasites evolve to resist therapeutics and consider functional, molecular, and population genetic factors that could contribute to these patterns.

evolutionary biology↗

bioRxiv2025

Distinguishing new from persistent infections at the strain level using longitudinal genotyping data

MotivationLongitudinal pathogen genotyping data from individual hosts can uncover strain-specific infection dynamics and their relationships to disease and intervention, especially in the malaria field. An important use case involves distinguishing newly incident from pre-existing (persistent) strains, but implementation faces statistical challenges relating to individual samples containing multiple strains, strains sharing alleles, and markers dropping out stochastically during the genotyping process. Current approaches to distinguish new versus persistent strains therefore rely primarily on simple rules that consider only the time since alleles were last observed. ResultsWe developed DINEMITES (Distinguishing New Malaria Infections in Time Series), a set of statistical methods to estimate, from longitudinal genotyping data, the probability each sequenced allele represents a new infection harboring that allele, the total molecular force of infection (molFOI, the cumulative number of newly acquired strains over time) for each individual, and the total number of new infection events for each individual. DINEMITES can handle time points with missing sequencing data, incorporate treatment history and covariates affecting the rate of new or persistent infections, and can scale to studies with thousands of samples sequenced across multiple loci containing hundreds of possible alleles. In synthetic evaluations, the DINEMITES Bayesian model, which generally outperformed an alternative clustering-based model also developed in this work, accurately estimated key clinical parameters such as molFOI (bias 2.5, compared to -12.2 for a typical simple rule). When applied to three real longitudinal genotyping datasets, the model detected 33%, 112%, and 359% more average infections per participant than would have been detected by applying a typical simple rule to the equivalent datasets without sequencing. Availability and implementationDINEMITES is freely available as an R package, along with documentation, tutorials, and example data, at https://github.com/WillNickols/dinemites.

genomics↗

bioRxiv2024

Temporal patterns of haplotypic and allelic diversity reflect the changing selection landscape of the malaria parasite Plasmodium falciparum

Populations of the malaria parasite Plasmodium falciparum regularly confront orchestrated changes in frontline drug treatment that drastically alter the parasites selection landscape. When this has occurred, the parasite has successfully adapted to the new drugs through novel resistance mutations. These novel mutations, however, may emerge in a genetic background already shaped by prior drug selection. In some instances, selection imposed by distinct drugs has targeted the same loci in either synergistic or antagonistic ways, resulting in genomic signatures that can be hard to attribute to a specific agent. Here, we use two approaches for detecting sequential bouts of drug adaptation: haplotype-based selection testing and temporal changes in allele frequencies. Using a set of longitudinally acquired samples from French Guiana, we determine that since the introduction of the drug artemether-lumefantrine (AL) in 2007 there have been rapid hard selective sweeps at both known and novel loci. We additionally identify genomic regions where selection acted in opposing directions before and after widespread AL introduction. At four high-profile genes with demonstrated involvement in drug resistance (crt, mdr1, aat1, and gch1), we saw strong selection before and after drug regime change; however, selection favored different haplotypes in the two time periods. Similarly, the allele frequency analysis identified coding variants whose frequency trajectory changed sign under the new drug pressure. These selected alleles were enriched for genes implicated in artemisinin and/or partner drug resistance in other global populations. Overall, these results suggest that drug resistance in P. falciparum is governed by known alleles of large effect along with a polygenic architecture of more subtle variants, any of which can experience fitness reversals under distinct drug regimes.

genomics↗

bioRxiv2024

Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Along an Anthropogenic Gradient in Gabon

Species distributed across heterogeneous environments often evolve locally adapted populations, but understanding how these persist in the presence of homogenizing gene flow remains puzzling. In Gabon, Anopheles coluzzii, a major African malaria mosquito is found along an ecological gradient, including a sylvatic population, away of any human presence. This study identifies into the genomic signatures of local adaptation in populations from distinct environments including the urban area of Libreville, and two proximate sites 10km apart in the La Lope National Park (LLP), a village and its sylvatic neighborhood. Whole genome re-sequencing of 96 mosquitoes unveiled[~] 5.7millions high-quality single nucleotide polymorphisms. Coalescent-based demographic analyses suggest an[~] 8,000-year-old divergence between Libreville and La Lope populations, followed by a secondary contact ([~]4,000 ybp) resulting in asymmetric effective gene flow. The urban population displayed reduced effective size, evidence of inbreeding, and strong selection pressures for adaptation to urban settings, as suggested by the hard selective sweeps associated with genes involved in detoxification and insecticide resistance. In contrast, the two geographically proximate LLP populations showed larger effective sizes, and distinctive genomic differences in selective signals, notably soft-selective sweeps on the standing genetic variation. Although neutral loci and chromosomal inversions failed to discriminate between LLP populations, our findings support that microgeographic adaptation can swiftly emerge through selection on standing genetic variation despite high gene flow. This study contributes to the growing understanding of evolution of populations in heterogeneous environments amid ongoing gene flow and how major malaria mosquitoes adapt to human. SignificanceAnopheles coluzzii, a major African malaria vector, thrives from humid rainforests to dry savannahs and coastal areas. This ecological success is linked to its close association with domestic settings, with human playing significant roles in driving the recent urban evolution of this mosquito. Our research explores the assumption that these mosquitoes are strictly dependent on human habitats, by conducting whole-genome sequencing on An. coluzzii specimens from urban, rural, and sylvatic sites in Gabon. We found that urban mosquitoes show de novo genetic signatures of human-driven vector control, while rural and sylvatic mosquitoes exhibit distinctive genetic evidence of local adaptations derived from standing genetic variation. Understanding adaptation mechanisms of this mosquito is therefore crucial to predict evolution of vector control strategies.

evolutionary biology↗

bioRxiv2024

Systematic bias in malaria parasite relatedness estimation

Genetic studies of malaria parasites increasingly feature estimates of relatedness. However, various aspects of malaria parasite relatedness estimation are not fully understood. For example, estimates of relatedness based on whole-genome-sequence (WGS) data often exceed those based on more sparse data types. We explore systematic bias in relatedness estimation using theoretical, numerical and empirical approaches. Specifically, we use a non-ancestral model of pairwise relatedness to derive theoretical results; a simulation model of ancestry to independently verify and expand our theoretical results; and data on parasites sampled from Guyana to explore how theoretical and numerical results translate empirically. We show that allele frequencies encode, locus-by-locus, relatedness averaged over the set of sampled parasites used to compute them. These sample allele frequencies are typically plugged into the models used to estimate pairwise relatedness. Consequently, models of pairwise relatedness are misspecified and pairwise relatedness values are systematically underestimated. However, systematic underestimation can be viewed as population-relatedness calibration, i.e., a way of generating measures of relative relatedness. Systematic underestimation is unavoidable when relatedness is estimated assuming independence between genetic markers. It is mitigated when estimated using WGS data under a hidden Markov model (HMM), which exploits linkage between proximal markers. Estimates of absolute relatedness generated under a HMM using relatively sparse data should be treated with caution because the extent to which underestimation is mitigated is unknowable. That said, analyses dependent on absolute values and high relatedness thresholds are relatively robust. In summary, practitioners have two options: resolve to use relative relatedness estimated under independence or try to estimate absolute relatedness under a HMM. We propose various practical tools to help practitioners evaluate their situation on a case-by-case basis. Author summaryMalaria genomic epidemiology is increasingly recognised as a tool for public health. Relatedness, which captures likeness derived from common ancestry, is a useful concept for malaria parasites. Analyses of malaria parasite relatedness are important for generating results on spatiotemporal scales relevant to disease control. Since shared ancestry is unobservable, relatedness must be estimated under a statistical model. However, not all aspects of malaria parasite estimation are fully understood, including the effects of different data types. In this work, we characterise systematic biases in estimates of malaria parasite relatedness. Our analysis is three-fold: we mathematically interrogate a non-ancestral model of relatedness to derive theoretical results; simulate parasite ancestries from first principles to yield numerical results; and perform an empirical case study of parasites sampled from Guyana. We show that bias may be particularly pronounced when using sparse marker data from inbred parasite populations, which are often found in pre-elimination settings. We chart out a practical roadmap to enable practitioners to assess epidemiological settings on a case-by-case basis. Our findings are relevant to applications in malaria genomic epidemiology that use relatedness directly or indirectly, including molecular surveillance and the genetic-based classification of treatment failure.

genetics↗

bioRxiv2024

Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana

Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016- 2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD [≥] 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD [≥] 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novel pfk13 mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation. Author SummaryMalaria is caused by eukaryotic Plasmodium parasites, which undergo sexual recombination within mosquitoes. In settings with low transmission, such as Guyana, these parasites often recombine with themselves, leading to the propagation of identical clones. We explored the population genomics of Plasmodium falciparum malaria parasites in Guyana over five years to characterize clonal transmission dynamics and understand whether they were influenced by local drug resistance mutations under strong selection, including pfk13 C580Y, which confers resistance to artemisinin, and pfcrt C350R, which confers resistance to piperaquine. Using whole genome sequencing on 1,463 samples, we identified 160 clones, in which all parasites share at least 90% of their genomes through recent common ancestry. We observed a decrease in frequency of the pfcrt C350R mutation, as well as the disappearance of pfk13 C580Y. Our findings contrast with the deterministic rise of drug resistance mutations observed in other geographic regions, sometimes associated with clonality. The simultaneous use of at least two different artemisinin combination therapies may have prevented the spread of an artemisinin-resistant clone in Guyana, suggesting a strategy for resistance management in other geographic regions.

genomics↗

bioRxiv2023

No Wolbachia protection against Plasmodium falciparum infection in the major malaria mosquito Anopheles moucheti

Since the discovery of natural malaria vector populations infected by the endosymbiont bacterium Wolbachia, a renewed interest has arisen for using this bacterium as an alternative for malaria control. Among naturally infected mosquitoes, Anopheles moucheti, a major malaria mosquito in Central Africa, exhibits one of the highest prevalences of Wolbachia infection. To better understand whether this maternally inherited bacterium could be used for malaria control, we investigated Wolbachia influence in An. moucheti populations naturally infected by the malaria parasite Plasmodium falciparum. To this end, we collected mosquitoes in a village from Cameroon, Central Africa, where this mosquito is the main malaria vector. We found that the prevalence of Wolbachia bacterium was almost fixed in the studied mosquito population, and was higher than previously recorded. We also quantified Wolbachia in whole mosquitoes and dissected abdomens, confirming that the bacterium is also elsewhere than in the abdomen, but at lower density. Finally, we analyzed the impact of Wolbachia presence and density on P. falciparum infection. Wolbachia density was slightly higher in mosquitoes infected with the malaria parasite than in uninfected mosquitoes. However, we observed no correlation between the P. falciparum and Wolbachia densities. In conclusion, our study indicates that naturally occurring Wolbachia infection does not affect P. falciparum development within An. moucheti mosquitoes.

microbiology↗

bioRxiv2022

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring low genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to multiple drug regimes. Using 166 newly sequenced whole genomes, we measure relatedness between parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore the role of recombination in spreading drug resistance mutations throughout the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in extremely small populations, as will occur in any region nearing malaria elimination.

evolutionary biology↗

bioRxiv2021

Integration of whole genome sequencing and transcriptomics reveals a complex picture of insecticide resistance in the major malaria vector Anopheles coluzzii

Insecticide resistance is a major threat to gains in malaria control, which have been stalling and potentially reversing since 2015. Studies into the causal mechanisms of insecticide resistance are painting an increasingly complicated picture, underlining the need to design and implement targeted studies on this phenotype. In this study, we compare three populations of the major malaria vector An. coluzzii: a susceptible and two resistant colonies with the same genetic background. The original colonised resistant population rapidly lost resistance over a 6-month period, a subset of this population was reselected with pyrethroids a third population of this colony that did not lose resistance was also available. The original resistant, susceptible and re-selected colonies were subject to RNAseq and whole genome sequencing, which identified a number of changes across the transcriptome and genome linked with resistance. Firstly, an increase in the expression of genes within the oxidative phosphorylation pathway were seen in both resistant populations compared to the susceptible control; this translated phenotypically through an increased respiratory rate, indicating that elevated metabolism is linked directly with resistance. Genome sequencing highlighted several blocks clearly associated with resistance, including the 2Rb inversion. Finally, changes in the microbiome profile were seen, indicating that the microbial composition may play a role in the resistance phenotype. Taken together, this study reveals a highly complicated phenotype in which multiple transcriptomic, genomic and microbiome changes combine to result in insecticide resistance.

genomics↗

bioRxiv2020

Population Genomics of Plasmodium vivax in Panama to Assess the Risk of Case Importation on Malaria Elimination

Malaria incidence in Panama has plateaued in recent years in spite of elimination efforts, with almost all cases caused by Plasmodium vivax. Notwithstanding, overall malaria prevalence remains low (fewer than 1 case per 1000 persons). We used selective whole genome amplification to sequence 96 P. vivax samples from Panama collected between 2007 and 2019 to study the population structure and transmission dynamics of the parasite. Imported cases resulting from increased levels of human migration could threaten malaria elimination prospects, and four of the samples evaluated came from individuals with travel history. We explored patterns of recent common ancestry among the samples and observed that a single highly genetically related lineage was dominant among the samples (47 out of 59 samples with good sequencing coverage), spanning the entire period of the collection (2007-2019) and all regions of the country. We also found a second, smaller clonal lineage of four parasites collected between 2017 and 2019. To explore the regional context of Panamanian P. vivax we conducted principal components analysis and constructed a neighbor-joining tree using these samples and samples collected worldwide from a previous study. Three of the four samples with travel history clustered with samples collected from their suspected country of origin (consistent with importation), while one appears to have been a result of local transmission. The small number of genetically unique Panamanian P. vivax samples clustered with samples collected from Colombia, suggesting they represent the genetically similar ancestral P. vivax population in Panama or were recently imported from Colombia. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination. Additionally, while we confirmed that P. vivax is imported to Panama from diverse geographic locations, the lack of impact from imported cases on the overall parasite population genomic profile suggests that onward transmission from such cases is limited and that imported cases may not presently pose a major barrier to elimination. Author SummaryPanama has greatly reduced P. vivax incidence, however, this progress has plateaued. Understanding parasite transmission patterns and identifying imported cases is critical to help Panama and other countries succeed in their elimination efforts. Genomic epidemiology and population genomics can help provide information needed to inform malaria control policy. In this study, we collected 100 Panamanian P. vivax samples from two collection periods (2007-2009 and 2017-2019), of which 59 yielded usable sequencing data. 4 samples had patient travel history data associated with them. We found that the majority of samples belong to a single highly related lineage, termed CL1. This lineage has persisted since at least 2007. We also highlight how genomic epidemiology can be used to spotlight parasites that may be imported as a result of human migration, as well as corroborate or refute the country of origin as suggested by patient travel history. We observe no evidence of outcrossing between these potentially imported parasites and the local Panamanian parasite population, suggesting that imported parasites are not driving ongoing malaria transmission in Panama. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination.

microbiology↗

bioRxiv2020

A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmitting Anopheles gambiae complex

The Anopheles gambiae complex consists of multiple morphologically indistinguishable mosquito species including the most important vectors of the malaria parasite Plasmodium falciparum in sub-Saharan Africa. Several lineages have only recently been described as distinct, including the cryptic taxon GOUNDRY in central Burkina Faso. The ecological, immunological, and reproductive differences among these taxa will critically impact population responses to disease control strategies and environmental changes. Here we examine whole-genome sequencing data from a longitudinal study of putative A. coluzzii in western Burkina Faso. Surprisingly, many samples are genetically divergent from A. coluzzii and all other Anopheles species and represent a new taxon, here designated Anopheles TENGRELA (AT). Population genetic analysis suggests that GOUNDRY sensu stricto represents an admixed population descended from both A. coluzzii and AT. AT harbors low nucleotide diversity except for the 2La inversion polymorphism which is maintained by overdominance. It shows numerous fixed differences with A. coluzzii concentrated in several regions reflecting selective sweeps, but the two taxa are identical at standard diagnostic loci used for taxon identification and thus AT may often go unnoticed. We present an amplicon-based genotyping assay for identifying AT which could be usefully applied to numerous existing samples. Misidentified cryptic taxa could seriously confound ongoing studies of Anopheles ecology and evolution in western Africa, including phenotypic and genotypic surveys of insecticide resistance. Reproductive barriers between cryptic species may also complicate novel vector control efforts, for example gene drives, and hinder predictions about evolutionary dynamics of Anopheles and Plasmodium.

evolutionary biology↗

bioRxiv2020

Identity-by-descent relatedness estimates with uncertainty characterise departure from isolation-by-distance between Plasmodium falciparum populations on the Colombian-Pacific coast

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for to date. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. The fraction of highly-related sample pairs (whose classification accounts for uncertainty) was greater within cities versus between. However, based on both the fraction of highly-related sample pairs and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with three separate transmission events involving parasites from five different clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this and alternative hypotheses. For the first time in malaria epidemiology, we account for uncertainty around estimated relatedness (an important consideration for future studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use a threshold-free approach to compare parasite populations, and identify clonal components in a statistically principled manner. The approaches we employ could be adapted to other recombining organisms with mixed mating systems, thus have broad relevance.

genetics↗