"Sexual" population structure and genetics of the malaria agent P. falciparum

Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity

Cryptosporidium is a leading cause of severe diarrhea and mortality in young children and infants in Africa and southern Asia. More than twenty Cryptosporidium species infect humans, of which C. parvum and C. hominis are the major agents causing moderate to severe diarrhea. Relatively few genetic markers are typically applied to genotype and/or diagnose Cryptosporidium. Most infections produce limited oocysts making it difficult to perform whole genome sequencing (WGS) directly from stool samples. Hence, there is an immediate need to apply WGS strategies to 1) develop high-resolution genetic markers to genotype these parasites more precisely, 2) to investigate endemic regions and detect the prevalence of different genotypes, and the role of mixed infections in generating genetic diversity, and 3) to investigate zoonotic transmission and evolution. To understand Cryptosporidium global population genetic structure, we applied Capture Enrichment Sequencing (CES-Seq) using 74,973 RNA-based 120 nucleotide baits that cover ~92% of the genome of C. parvum. CES-Seq is sensitive and successfully sequenced Cryptosporidium genomic DNA diluted up to 0.005% in human stool DNA. It also resolved mixed strain infections and captured new species of Cryptosporidium directly from clinical/field samples to promote genome-wide phylogenomic analyses and prospective GWAS studies.

Tracking antimalarial drug resistance using mosquito blood meals: a cross-sectional study

BACKGROUND

Strong surveillance systems with wide geographic coverage are needed to detect and respond to reports of antimalarial drug resistance on the African continent. We aimed to assess the utility and feasibility of using blood-fed mosquitos (xenomonitoring) to conduct rapid surveillance of molecular markers associated with resistance in human populations.

METHODS

We conducted three cross-sectional surveys in two rainy seasons and the interim dry season in southwest Burkina Faso between Oct 10, 2018, and Sept 17, 2019. We collected human blood samples and blood-fed mosquitos residing in household clusters across seven village sectors. Samples were assessed for Plasmodium falciparum with ultrasensitive quantitative PCR, genotyped for two markers of reduced drug susceptibility, pfmdr1 256A>T (Asn86Tyr) and pfcrt 227A>C (Lys76Thr), and sequenced for four markers of clonality. We assessed statistical equivalence using a 10% margin of equivalence.

FINDINGS

We identified 551 infections in 1483 human blood samples (mean multiplicity of infection [MOI] 1·94, SD 1·47) and 346 infections in 2151 mosquito blood meals (mean MOI 2·2, SD 1·67). The frequency of pfmdr1 Asn86Tyr was 4% in survey 1, 2% in survey 2, and 12% in survey 3 in human samples, and 3% in survey 1, 0% in survey 2, and 8% in survey 3 in mosquito blood meals, and inter-host frequencies were statistically equivalent in surveys 1 and 2 (p<0·0001) but not Survey 3 (p=0·062) within a tolerability of 0·10. The frequency of pfcrt Lys76Thr was 16% in survey 1, 55% in survey 2, and 11% in survey 3 in humans and 40% in survey 1, 72% in survey 2, and 13% in survey 3 in mosquitos, and inter-host frequencies were equivalent in survey 3 only (p=0·032) within a tolerability of 0·10. In simulations, multiple but not preferential feeding behaviour in mosquitos reduced the accuracy of frequency estimates between hosts, particularly for markers circulating at higher frequencies.

INTERPRETATION

Molecular markers in mosquito blood meals and in humans exhibited similar temporal trends but frequencies were not statistically equivalent in all scenarios. More work is needed to determine empirical and pragmatic thresholds of difference. Xenomonitoring might be an efficient tool to provide rapid information on emerging antimalarial resistance in regions with insufficient surveillance.

FUNDING

National Institute of Allergy and Infectious Diseases.

TRANSLATION

For the French translation of the abstract see Supplementary Materials section.

Genetic Diversity of Plasmodium vivax Field Isolates from the Thai–Myanmar Border during the Period of 2006–2016

High levels of genetic variants of Plasmodium vivax have previously been reported in Thailand. Circumsporozoite surface protein (CSP), merozoite surface protein (MSP), and microsatellite markers were used to determine the genetic polymorphisms of P. vivax. This study aimed to investigate the molecular epidemiology of P. vivax populations at the Thai–Myanmar border by genotyping the PvCSP, PvMSP-3α, and PvMSP-3β genes. Four hundred and forty P. vivax clinical isolates were collected from the Mae Sot and Sai Yok districts from 2006–2007 and 2014–2016. Polymerase chain reaction with restriction fragment length polymorphism (RFLP) was used to investigate the genetic polymorphisms of the target genes. Based on PCR band size variations, 14 different PvCSP alleles were identified: eight for VK210 and six for VK247. The VK210 genotype was the dominant variant during both sample collection periods. Based on PCR genotyping, three distinct types (A, B, and C) for both PvMSP-3α and PvMSP-3β were observed. Following RFLP, 28 and 14 allelic variants of PvMSP-3α and 36 and 20 allelic variants of PvMSP-3β with varying frequencies were identified during the first and second periods, respectively. High genetic variants of PvMSP-3 and PvCSP were found in the study area. PvMSP-3β exhibited a higher level of genetic diversity and multiple-genotype infection versus PvMSP-3α.

On the evolution of variation in sexual reproduction through the prism of eukaryotic microbes

Almost all eukaryotes undergo sexual reproduction to generate diversity and select for fitness in their population pools. Interestingly, the systems by which sex is defined are highly diverse and can even differ between evolutionarily closely related species. While the most commonly known form of sex determination involves males and females in animals, eukaryotic microbes can have as many as thousands of different mating types for the same species. Furthermore, some species have found alternatives to sexual reproduction and prefer to grow clonally and yet undergo infrequent facultative sexual reproduction. These organisms are mainly invertebrates and microbes, but several examples are also present among vertebrates suggesting that alternative modes of sexual reproduction evolved multiple times throughout evolution. In this review, we summarize the sex-determination modes and variants of sexual reproduction found across the eukaryotic tree of life and suggest that eukaryotic microbes provide unique opportunities to study these processes in detail. We propose that understanding variations in modes of sexual reproduction can serve as a foundation to study the evolution of sex and why and how it evolved in the first place.

Environmental factors and spatiotemporal distribution characteristics of the global outbreaks of the highly pathogenic avian influenza H5N1

The spread of highly pathogenic avian influenza H5N1 has posed a major threat to global public health. Understanding the spatiotemporal outbreak characteristics and environmental factors of H5N1 outbreaks is of great significance for the establishment of effective prevention and control systems. The time and location of H5N1 outbreaks in poultry and wild birds officially confirmed by the World Organization for Animal Health from 2005 to 2019 were collected. Spatial autocorrelation analysis and multidistance spatial agglomeration analysis methods were used to analyze the global outbreak sites of H5N1. Combined with remote sensing data, the correlation between H5N1 outbreaks and environmental factors was analyzed using binary logistic regression methods. We analyzed the correlation between the H5N1 outbreak and environmental factors and finally made a risk prediction for the global H5N1 outbreaks. The results show that the peak of the H5N1 outbreaks occurs in winter and spring. H5N1 outbreaks exhibit aggregation, and a weak aggregation phenomenon is noted on the scale close to 5000 km. Water distance, road distance, railway distance, wind speed, leaf area index (LAI), and specific humidity were protective factors for the outbreak of H5N1, and the odds ratio (OR) were 0.985, 0.989, 0.995, 0.717, 0.832, and 0.935, respectively. Temperature was a risk factor with an OR of 1.073. The significance of these ORs was greater than 95%. The global risk prediction map was obtained. Given that the novel coronavirus (COVID-19) is spreading globally, the methods and results of this study can provide a reference for studying the spread of COVID-19.

Malaria protection due to sickle haemoglobin depends on parasite genotype

Host genetic factors can confer resistance against malaria¹, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member^2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations.

A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.

Host Range of Cyclospora Species: Zoonotic Implication

Cyclospora is an intracellular, gastrointestinal parasite found in birds and mammals worldwide. Limited accessibility of the protozoan for experimental use, scarcity, genome heterogeneity of the isolates and narrow panel of molecular markers hamper zoonotic investigations. One of the significant limitation in zoonotic studies is the lack of precise molecular tools that would be useful in linking animal vectors as a source of human infection. Strong and convincing evidence of zoonotic features will be achieved through proper typing of Cyclospora spp. taxonomic units (e.g. species or genotypes) in animal reservoirs. The most promising method that can be employ for zoonotic surveys is next-generation sequencing.

The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels of relatedness. Yet, how local epidemiology affects the properties of such mixed infections remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to the Pf3k data set, we find that the rate of mixed infection varies from 29% to 63% across countries and that 51% of mixed infections involve more than two strains. Furthermore, we estimate that 47% of symptomatic dual infections contain sibling strains likely to have been co-transmitted from a single mosquito, and find evidence of mixed infections propagated over successive infection cycles. Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD.

Genotyping genetically heterogeneous Cyclospora cayetanensis infections to complement epidemiological case linkage

Sexually reproducing pathogens such as Cyclospora cayetanensis often produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness of C. cayetanensis infections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to specimen pairs reflecting their most likely relationships. The approach was applied to data generated from a test cohort of 88 human fecal specimens containing C. cayetanensis, including 30 from patients whose infections were associated with epidemiologically defined outbreak clusters of cyclosporiasis. The ensemble assigned specimens to plausible clusters of genetically related infections despite their complex haplotype composition. These relationships were corroborated by a significant number of epidemiological linkages (P < 0.0001) suggesting the ensemble's utility for aiding epidemiological trace-back investigations of cyclosporiasis.

Mapping imported malaria in Bangladesh using parasite genetic and human mobility data

For countries aiming for malaria elimination, travel of infected individuals between endemic areas undermines local interventions. Quantifying parasite importation has therefore become a priority for national control programs. We analyzed epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data to measure the spatial spread of malaria parasites in southeast Bangladesh. We developed a genetic mixing index to estimate the likelihood of samples being local or imported from parasite genetic data and inferred the direction and intensity of parasite flow between locations using an epidemiological model integrating the travel survey and mobile phone calling data. Our approach indicates that, contrary to dogma, frequent mixing occurs in low transmission regions in the southwest, and elimination will require interventions in addition to reducing imported infections from forested regions. Unlike risk maps generated from clinical case counts alone, therefore, our approach distinguishes areas of frequent importation as well as high transmission.

Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission

Unlike in most pathogens, multiple-strain (polygenomic) infections of P. falciparum are frequently composed of genetic siblings. These genetic siblings are the result of sexual reproduction and can coinfect the same host when cotransmitted by the same mosquito. The degree with which coinfecting strains are related varies among infections and populations. Because sexual recombination occurs within the mosquito, the relatedness of cotransmitted strains could depend on transmission dynamics, but little is actually known of the factors that influence the relatedness of cotransmitted strains. Part of the uncertainty stems from an incomplete understanding of how within-host and within-vector dynamics affect cotransmission. Cotransmission is difficult to examine experimentally but can be explored using a computational model. We developed a malaria transmission model that simulates sexual reproduction in order to understand what determines the relatedness of cotransmitted strains. This study highlights how the relatedness of cotransmitted strains depends on both within-host and within-vector dynamics including the complexity of infection. We also used our transmission model to analyze the genetic relatedness of polygenomic infections following a series of multiple transmission events and examined the effects of superinfection. Understanding the factors that influence the relatedness of cotransmitted strains could lead to a better understanding of the population-genetic correlates of transmission and therefore be important for public health.

Genomic studies of P. falciparum reveal that multi-strain infections can include genetically related strains. P. falciparum must reproduce sexually in the mosquito vector. One consequence of sexual reproduction is that parasites cotransmitted by the same mosquito are related to one another. The degree of genetic relatedness of these parasites can be as great as that of full-siblings. However, our understanding of the cotransmission process is incomplete, and little is known of the role of cotransmission in influencing population genomic processes. To help bridge this gap, we developed a simulation model to determine which of the steps involved in transmission have the greatest impact on the relatedness of parasites cotransmitted by a mosquito vector. The primary goal of this study is to characterize the outcomes of cotransmission following single or multiple transmission events. Our model yields new insights into the cotransmission process, which we believe will be useful for understanding the results from more complicated population models and epidemiological conditions. Such an understanding is important for the use of population genomics to inform public health decisions as well as for understanding of parasite evolution.

Plasmodium vivax genetic diversity and heterozygosity in blood samples and resulting oocysts at the Thai-Myanmar border

Background

Polyclonal blood-stage infections of Plasmodium vivax are frequent even in low transmission settings, allowing meiotic recombination between heterologous parasites. Empirical data on meiotic products are however lacking. This study examined microsatellites in oocysts derived by membrane feeding of mosquitoes from blood-stage P. vivax infections at the Thai–Myanmar border.

Methods

Blood samples from patients presenting with vivax malaria were fed to Anopheles cracens by membrane feeding and individual oocysts from midguts were obtained by dissection after 7 days. DNA was extracted from oocysts and parental blood samples and tested by microsatellite analysis.

Results

A focused study of eight microsatellite markers was undertaken for nine blood stage infections from 2013, for which derived oocysts were studied in six cases. One or more alleles were successfully amplified for 131 oocysts, revealing high levels of allelic diversity in both blood and oocyst stages. Based on standard criteria for defining minor alleles, there was evidence of clear deviation from random mating (inbreeding) with relatively few heterozygous oocysts compared to variance across the entire oocyst population (F_IT = 0.89). The main explanation appeared to be natural compartmentalisation at mosquito (F_SC = 0.27) and human stages (F_CT = 0.68). One single human case produced a total of 431 successfully amplified loci (across 70 oocysts) that were homozygous and identical to parental alleles at all markers, indicating clonal infection and transmission. Heterozygous oocyst alleles were found at 15/176 (8.5%) successfully amplified loci in the other five cases. There was apparently reduced oocyst heterozygosity in individual oocysts compared to diversity within individual mosquitoes (F_IS = 0.55), but this may simply reflect the difficulty of detecting minor alleles in oocysts, given the high rate of amplification failure. Inclusion of minor allele peaks (irrespective of height) when matching peaks were found in related blood or oocyst samples, added 11 minor alleles for 9 oocysts, increasing the number of heterozygous loci to 26/176 (14.8%; p = 0.096).

Conclusion

There was an apparently low level of heterozygous oocysts but this can be explained by a combination of factors: relatively low complexity of parental infection, natural compartmentalisation in humans and mosquitoes, and the methodological challenge of detecting minor alleles.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-017-2002-x) contains supplementary material, which is available to authorized users.

Mapping sulphadoxine-pyrimethamine-resistant Plasmodium falciparum malaria in infected humans and in parasite populations in Africa

Intermittent preventive treatment (IPT) with sulphadoxine-pyrimethamine in vulnerable populations reduces malaria morbidity in Africa, but resistance mutations in the parasite dhps gene (combined with dhfr mutations) threaten its efficacy. We update a systematic review to map the prevalence of K540E and A581G mutations in 294 surveys of infected humans across Africa from 2004-present. Interpreting these data is complicated by multiclonal infections in humans, especially in high transmission areas. We extend statistical methods to estimate the frequency, i.e. the proportion of resistant clones in the parasite population at each location, and so standardise for varying transmission levels. Both K540E and A581G mutations increased in prevalence and frequency in 60% of areas after 2008, highlighting the need for ongoing surveillance. Resistance measures within countries were similar within 300 km, suggesting an appropriate spatial scale for surveillance. Spread of the mutations tended to accelerate once their prevalence exceeded 10% (prior to fixation). Frequencies of resistance in parasite populations are the same or lower than prevalence in humans, so more areas would be classified as likely to benefit from IPT if similar frequency thresholds were applied. We propose that the use of resistance frequencies as well as prevalence measures for policy decisions should be evaluated.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.

Impact of exposure to mosquito transmission-blocking antibodies on Plasmodium falciparum population genetic structure

Progress in malaria control has led to a significant reduction of the malaria burden. Interventions that interrupt transmission are now needed to achieve the elimination goal. Transmission-blocking vaccines (TBV) that aim to prevent mosquito infections represent promising tools and several vaccine candidates targeting different stages of the parasite's lifecycle are currently under development. A mosquito-midgut antigen, the anopheline alanyl aminopeptidase (AnAPN1) is one of the lead TBV candidates; antibodies against AnAPN1 prevent ookinete invasion. In this study, we explored the transmission dynamics of Plasmodium falciparum in mosquitoes fed with anti-AnAPN1 monoclonal antibodies (mAbs) vs. untreated controls, and investigated whether the parasite genetic content affects or is affected by antibody treatment. Exposure to anti-AnAPN1 mAbs was efficient at blocking parasite transmission and the effect was dose-dependent. Genetic analysis revealed a significant sib-mating within P. falciparum infra-populations infecting one host, as measured by the strong correlation between Wright's F_IS and multiplicity of infection. Treatments also resulted in significant decrease in F_IS as a by-product of drop in infra-population genetic diversity and concomitant increase of apparent panmictic genotyping proportions. Genetic differentiation analyses indicated that mosquitoes fed on a same donor randomly sampled blood-circulating gametocytes. We did not detect trace of selection, as the genetic differentiation between different donors did not decrease with increasing mAb concentration and was not significant between treatments for each gametocyte donor. Thus, there is apparently no specific genotype associated with the loss of diversity under mAb treatment. Finally, the anti-AnAPN1 mAbs were effective at reducing mosquito infection and a vaccine aiming at eliciting anti-AnAPN1 mAbs has a strong potential to decrease the burden of malaria in transmission-blocking interventions without any apparent selective pressure on the parasite population.

Population Genetics of Plasmodium vivax in Four Rural Communities in Central Vietnam

Background

The burden of malaria in Vietnam has drastically reduced, prompting the National Malaria Control Program to officially engage in elimination efforts. Plasmodium vivax is becoming increasingly prevalent, remaining a major problem in the country's central and southern provinces. A better understanding of P. vivax genetic diversity and structure of local parasite populations will provide baseline data for the evaluation and improvement of current efforts for control and elimination. The aim of this study was to examine the population genetics and structure of P. vivax isolates from four communities in Tra Leng commune, Nam Tra My district in Quang Nam, Central Vietnam.

Methodology/Principal Findings

P. vivax mono infections collected from 234 individuals between April 2009 and December 2010 were successfully analyzed using a panel of 14 microsatellite markers. Isolates displayed moderate genetic diversity (He = 0.68), with no significant differences between study communities. Polyclonal infections were frequent (71.4%) with a mean multiplicity of infection of 1.91 isolates/person. Low but significant genetic differentiation (F_ST value from -0.05 to 0.18) was observed between the community across the river and the other communities. Strong linkage disequilibrium (IAS = 0.113, p < 0.001) was detected across all communities, suggesting gene flow within and among them. Using multiple approaches, 101 haplotypes were grouped into two genetic clusters, while 60.4% of haplotypes were admixed.

Conclusions/Significance

In this area of Central Vietnam, where malaria transmission has decreased significantly over the past decade, there was moderate genetic diversity and high occurrence of polyclonal infections. Local human populations have frequent social and economic interactions that facilitate gene flow and inbreeding among parasite populations, while decreasing population structure. Findings provide important information on parasites populations circulating in the study area and are relevant to current malaria elimination efforts.

In Vietnam, Plasmodium vivax (P. vivax) is the second most frequent human malaria parasite and a major obstacle to countrywide malaria elimination. Knowing the local parasite structure is useful for elimination efforts. Therefore, we analyzed, with a panel of 14 microsatellite markers, 234 P. vivax mono infections in blood samples collected from 4 communities in central Vietnam. Genetic diversity in the population was moderate; a high occurrence of polyclonal infections and significant linkage disequilibrium were detected, suggesting inbreeding or recombination between highly related haplotypes. In addition, both genetic differentiation and population structure was low and only detected between communities at each side of the river. Those results suggest gene flow between study communities with the river defining a moderate geographical barrier. Future studies should determine how this genetic variation is maintained in an area of extremely low transmission.

Plasmodium vivax Diversity and Population Structure across Four Continents

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (F_ST>0.2). Outside Central Asia F_ST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

Plasmodium vivax is the predominant malaria parasite in Latin America, Asia and the South Pacific. Different factors are expected to shape diversity and population structure across continents, e.g. transmission intensity which is much lower in South America as compared to Southeast-Asia and the South Pacific, or geographical isolation of P. vivax populations in the South Pacific. We have compiled data from 841 isolates from South and Central America, Africa, Central Asia, Southeast-Asia and the South Pacific typed with a panel of 11 microsatellite markers. Diversity was highest in Southeast-Asia, where transmission is intermediate-high and migration of infected hosts is high, and lowest in South America and Central Asia where malaria transmission is low and focal. Reducing the panel of microsatellites showed that 2–6 markers are sufficient for genotyping for most drug trials and epidemiological studies, as these markers can identify >90% of all haplotypes. Parasites clustered according to continental origin, with high population differentiation between South American and Central Asian populations and the other populations, and lowest differences between Southeast-Asia and the South Pacific. Current attempts to reduce malaria transmission might change this pattern, but only after transmission is reduced for an extended period of time.

Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in the Caribbean lizard malaria parasite Plasmodium floridense using 63 single-infection samples in lizards collected from across the parasite's range, and sequenced them at two mitochondrial, one apicoplast, and five nuclear genes. We identified 11 provisionally cryptic species within P. floridense, each of which exhibits low intraspecific variation and recent divergence times between species (some diverged approximately 110,000 years ago). Our results are consistent with the hypothesis that clonal reproduction can profoundly affect diversification of species capable of sexual recombination, and suggest that clonal reproduction may have led to a large number of unrecognized pathogen species. The factors that may influence the rates of clonal reproduction among pathogens are unclear, and we discuss how prevalence and virulence may relate to clonal reproduction.

Plasmodium falciparum mating patterns and mosquito infectivity of natural isolates of gametocytes

Plasmodium falciparum infections in malaria endemic areas often harbor multiple clones of parasites. However, the transmission success of the different genotypes within the mosquito vector has remained elusive so far. The genetic diversity of malaria parasites was measured by using microsatellite markers in gametocyte isolates from 125 asymptomatic carriers. For a subset of 49 carriers, the dynamics of co-infecting genotypes was followed until their development within salivary glands. Also, individual oocysts from midguts infected with blood from 9 donors were genotyped to assess mating patterns. Multiplicity of infection (MOI) was high both in gametocyte isolates and sporozoite populations, reaching up to 10 genotypes. Gametocyte isolates with multiple genotypes gave rise to lower infection prevalence and intensity. Fluctuations of genotype number occurred during the development within the mosquito and sub-patent genotypes, not detected in gametocyte isolates, were identified in the vector salivary glands. The inbreeding coefficient Fis was positively correlated to the oocyst loads, suggesting that P. falciparum parasites use different reproductive strategies according to the genotypes present in the gametocyte isolate. The number of parasite clones within an infection affects the transmission success and the mosquito has an important role in maintaining P. falciparum genetic diversity. Our results emphasize the crucial importance of discriminating between the different genotypes within an infection when studying the A. gambiae natural resistance to P. falciparum, and the need to monitor parasite diversity in areas where malaria control interventions are implemented.

Patterns and dynamics of genetic diversity in Plasmodium falciparum: what past human migrations tell us about malaria

Plasmodium falciparum is the main agent of malaria, one of the major human infectious diseases affecting millions of people worldwide. The genetic diversity of P. falciparum populations is an essential factor in the parasite's ability to adapt to changes in its environment, enabling the development of drug resistance and the evasion from the host immune system through antigenic variation. Therefore, characterizing these patterns and understanding the main drivers of the pathogen's genetic diversity can provide useful inputs for informing control strategies. In this paper, we review the pioneering work led by Professor Kazuyuki Tanabe on the genetic diversity of P. falciparum populations. In a first part, we recall basic results from population genetics for quantifying within-population genetic diversity, and discuss the main mechanisms driving this diversity. Then, we show how these approaches have been used for reconstructing the historical spread of malaria worldwide, and how current patterns of genetic diversity suggest that the pathogen followed our ancestors in their journey out of Africa. Because these results are robust to different types of genetic markers, they provide a baseline for predicting the pathogen's diversity in unsampled populations, and some useful elements for predicting vaccine efficacy and informing malaria control strategies.

PCR/RFLP-based analysis of genetically distinct Plasmodium vivax population of Pvmsp-3α and Pvmsp-3β genes in Pakistan

Background

Plasmodium vivax is one of the widespread human malarial parasites accounting for 75% of malaria epidemics. However, there is no baseline information about the status and nature of genetic variation of Plasmodium species circulating in various parts of Pakistan. The present study was aimed at observing the molecular epidemiology and genetic variation of Plasmodium vivax by analysing its merozoite surface protein-3α (msp-3α) and merozoite surface protein-3β (msp-3β) genes, by using suballele, species-specific, combined nested PCR/RFLP detection techniques.

Methods

A total of 230 blood samples from suspected subjects tested slide positive for vivax malaria were collected from Punjab, Sindh, Khyber Pakhtunkhwa, and Balochistan during the period May 2012 to December 2013. Combined nested PCR/RFLP technique was conducted using Pvmsp-3α and Pvmsp-3β genetic markers to detect extent of genetic variation in clinical isolates of P. vivax in the studied areas of Pakistan.

Results

By PCR, P. vivax, 202/230 (87.82%), was found to be widely distributed in the studied areas. PCR/RFLP analysis showed a high range of allelic variations for both msp-3α and msp-3β genetic markers of P. vivax, i.e., 21 alleles for msp-3α and 19 for msp-3β. Statistically a significant difference (p ≤ 0.05) was observed in the genetic diversity of the suballelic variants of msp-3α and msp-3β genes of P. vivax.

Conclusion

It is concluded that P. vivax populations are highly polymorphic and diverse allelic variants of Pvmsp-3α and Pvmsp-3β are present in Pakistan.

New insights into clonality and panmixia in Plasmodium and toxoplasma

Until the 1990s, Plasmodium and Toxoplasma were widely considered to be potentially panmictic species, because they both undergo a meiotic sexual cycle in their definitive hosts. We have proposed that both parasites are able of clonal (nonrecombining) propagation, at least in some cycles. Toxoplasma was soon shown to be a paradigmatic case of clonal population structure in North American and in European cycles. But the proposal provoked an outcry in the case of Plasmodium and still appears as doubtful to many scientists. However, the existence of Plasmodium nonrecombining lines has been fully confirmed, although the origin of these lines is debatable. We discuss the current state of knowledge concerning the population structure of both parasites in the light of the recent developments of pathogen clonal evolution proposed by us and of new hypotheses presented here.

Kinase signalling in Plasmodium sexual stages and interventions to stop malaria transmission

The symptoms of malaria, one of the infectious diseases with the highest mortality and morbidity world-wide, are caused by asexual parasites replicating inside red blood cells. Disease transmission, however, is effected by non-replicating cells which have differentiated into male or female gametocytes. These are the forms infectious to mosquito vectors and the insects are the only hosts where parasite sexual reproduction can take place. Malaria is thus a complex infection in which pharmacological treatment of symptoms may still allow transmission for long periods, while pharmacological blockage of infectivity may not cure symptoms. The process of parasite sexual differentiation and development is still being revealed but it is clear that kinase-mediated signalling mechanisms play a significant role. This review attempts to summarise our limited current knowledge on the signalling mechanisms involved in the transition from asexual replication to sexual differentiation and reproduction, with a brief mention to the effects of current treatments on the sexual stages and to some of the difficulties inherent in developing pharmacological interventions to curtail disease transmission.

Genetic structure of Trypanosoma cruzi in Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach

BACKGROUND

Chagas disease is a systemic pathology caused by Trypanosoma cruzi. This parasite reveals remarkable genetic variability, evinced in six Discrete Typing Units (DTUs) named from T. cruzi I to T. cruzi VI (TcI to TcVI). Recently newly identified genotypes have emerged such as TcBat in Brazil, Colombia and Panama associated to anthropogenic bats. The genotype with the broadest geographical distribution is TcI, which has recently been associated to severe cardiomyopathies in Argentina and Colombia. Therefore, new studies unraveling the genetic structure and natural history of this DTU must be pursued.

RESULTS

We conducted a spatial and temporal analysis on 50 biological clones of T. cruzi I (TcI) isolated from humans with different clinical phenotypes, triatomine bugs and mammal reservoirs across three endemic regions for Chagas disease in Colombia. These clones were submitted to a nuclear Multilocus Sequence Typing (nMLST) analysis in order to elucidate its genetic diversity and clustering. After analyzing 13 nuclear housekeeping genes and obtaining a 5821 bp length alignment, we detected two robust genotypes within TcI henceforth named TcIDOM (associated to human infections) and a second cluster associated to peridomestic and sylvatic populations. Additionaly, we detected putative events of recombination and an intriguing lack of linkage disequilibrium.

CONCLUSIONS

These findings reinforce the emergence of an enigmatic domestic T. cruzi genotype (TcIDOM), and demonstrates the high frequency of recombination at nuclear level across natural populations of T. cruzi. Therefore, the need to pursue studies focused on the diferential virulence profiles of TcI strains. The biological and epidemiological implications of these findings are herein discussed.

Analysing malaria drug trials on a per-individual or per-clone basis: a comparison of methods

There are a variety of methods used to estimate the effectiveness of antimalarial drugs in clinical trials, invariably on a per-person basis. A person, however, may have more than one malaria infection present at the time of treatment. We evaluate currently used methods for analysing malaria trials on a per-individual basis and introduce a novel method to estimate the cure rate on a per-infection (clone) basis. We used simulated and real data to highlight the differences of the various methods. We give special attention to classifying outcomes as cured, recrudescent (infections that never fully cleared) or ambiguous on the basis of genetic markers at three loci. To estimate cure rates on a per-clone basis, we used the genetic information within an individual before treatment to determine the number of clones present. We used the genetic information obtained at the time of treatment failure to classify clones as recrudescence or new infections. On the per-individual level, we find that the most accurate methods of classification label an individual as newly infected if all alleles are different at the beginning and at the time of failure and as a recrudescence if all or some alleles were the same. The most appropriate analysis method is survival analysis or alternatively for complete data/per-protocol analysis a proportion estimate that treats new infections as successes. We show that the analysis of drug effectiveness on a per-clone basis estimates the cure rate accurately and allows more detailed evaluation of the performance of the treatment.

Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal

Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs), use of rapid diagnostic tests (RDTs) for malaria detection, and deployment of artemisinin combination therapy (ACT). Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.

Policy options for deploying anti-malarial drugs in endemic countries: a population genetics approach

Background

Anti-malarial drugs are constantly exposed to the threat of evolving drug resistance so good stewardship of existing therapy is an essential component of public health policy. However, the widespread availability of numerous different drugs through informal providers could undermine official drug deployment policies. A policy of multiple first-line therapy (MFT) is compared with the conventional policy of sequential drug deployment, i.e., where one drug is used until resistance evolves and then replaced by the next drug in the sequence.

Methods

Population genetic models of drug resistance are used to make the comparison; this methodology explicitly tracks the genetics of drug resistance (including, importantly, recombination in the sexual stage, intrahost dynamics, and direction of linkage disequilibrium).

Results

A policy of MFT outlasts sequential application providing drug usages are low to moderate, and appears not to drive widespread multi-drug resistance. Inadequate dosing is an even more potent driver of drug resistance than the MFT/sequential policy decision.

Conclusions

The provision of MFT as a deliberate policy can be encouraged provided overall treatment rates are low or moderate (less than around half of malaria infections are treated) and the ad hoc provision of MFT through the private sector may be tolerated. This must be fully supported by education to ensure people take adequate doses of each of the drugs.

Entomological indices of malaria transmission in Chikhwawa district, Southern Malawi

Background

Although malaria is highly prevalent throughout Malawi, little is known of its transmission dynamics. This paper describes the seasonal activity of the different vectors, human biting indices, sporozoite rates and the entomological inoculation rate in a low-lying rural area in southern Malawi.

Methods

Vectors were sampled over 52 weeks from January 2002 to January 2003, by pyrethrum knockdown catch in two villages in Chikhwawa district, in the Lower Shire Valley.

Results

In total, 7,717 anophelines were collected of which 55.1% were Anopheles gambiae sensu lato and 44.9% were Anopheles funestus. Three members of the An. gambiae complex were identified by PCR: Anopheles arabiensis (75%) was abundant throughout the year, An. gambiae s.s. (25%) was most common during the wet season and Anopheles quadriannulatus occurred at a very low frequency (n=16). An. funestus was found in all samples but was most common during the dry season.

Anopheles gambiae s.s. and An. funestus were highly anthropophilic with human blood indices of 99.2% and 96.3%, respectively. Anopheles arabiensis had fed predominantly on humans (85.0%) and less commonly on cattle (10.9%; 1.2% of blood meals were of mixed origin). Plasmodium falciparum (192/3,984) and Plasmodium malariae (1/3,984) sporozoites were detected by PCR in An. arabiensis (3.2%) and An. funestus (4.5%), and in a significantly higher proportion of An. gambiae s.s. (10.6%)(p<0.01). All three vectors were present throughout the year and malaria transmission occurred in every month, although with greatest intensity during the rainy season (January to April). The combined human blood index exceeded 92% and the P. falciparum sporozoite rate was 4.8%, resulting in estimated inoculation rates of 183 infective bites/ person per annum, or an average rate of ~15 infective bites/person/month.

Conclusions

The results demonstrate the importance of An. gambiae s.s., An. arabiensis and An. funestus in driving the high levels of malaria transmission in the south of Malawi. Sustained and high coverage or roll out of current approaches to malaria control (primarily insecticide-treated bed nets and indoor residual house spraying) in the area are likely to reduce the observed high malaria transmission rate and consequently the incidence of human infections, unless impeded by increasing resistance of vectors to insecticides.

Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

BACKGROUND

Malaria parasite population genetic structure varies among areas of differing endemicity, but this has not been systematically studied across Plasmodium falciparum populations in Africa where most infections occur.

METHODS

Ten polymorphic P. falciparum microsatellite loci were genotyped in 268 infections from eight locations in four West African countries (Republic of Guinea, Guinea Bissau, The Gambia and Senegal), spanning a highly endemic forested region in the south to a low endemic Sahelian region in the north. Analysis was performed on proportions of mixed genotype infections, genotypic diversity among isolates, multilocus standardized index of association, and inter-population differentiation.

RESULTS

Each location had similar levels of pairwise genotypic diversity among isolates, although there were many more mixed parasite genotype infections in the south. Apart from a few isolates that were virtually identical, the multilocus index of association was not significant in any population. Genetic differentiation between populations was low (most pairwise F(ST) values < 0.03), and an overall test for isolation by distance was not significant.

CONCLUSIONS

Although proportions of mixed genotype infections varied with endemicity as expected, population genetic structure was similar across the diverse sites. Very substantial reduction in transmission would be needed to cause fragmented or epidemic sub-structure in this region.

Analysis of malaria parasite phenotypes using experimental genetic crosses of Plasmodium falciparum

We review the principles of linkage analysis of experimental genetic crosses and their application to Plasmodium falciparum. Three experimental genetic crosses have been performed using the human malaria parasite P. falciparum. Linkage analysis of the progeny of these crosses has been used to identify parasite genes important in phenotypes such as drug resistance, parasite growth and virulence, and transmission to mosquitoes. The construction and analysis of genetic maps has been used to characterise recombination rates across the parasite genome and to identify hotspots of recombination.

Close kinship within multiple-genotype malaria parasite infections

Malaria infections containing multiple parasite genotypes are ubiquitous in nature, and play a central role in models of recombination, intra-host dynamics, virulence, sex ratio, immunity and drug resistance evolution in Plasmodium. While these multiple infections (MIs) are often assumed to result from superinfection (bites from multiple infected mosquitoes), we know remarkably little about their composition or generation. We isolated 336 parasite clones from eight patients from Malawi (high transmission) and six from Thailand (low transmission) by dilution cloning. These were genotyped using 384 single-nucleotide polymorphisms, revealing 22 independent haplotypes in Malawi (2–6 per MI) and 15 in Thailand (2–5 per MI). Surprisingly, all six patients from Thailand and six of eight from Malawi contained related haplotypes, and haplotypes were more similar within- than between-infections. These results argue against a simple superinfection model. Instead, the observed kinship patterns may be explained by inoculation of multiple related haploid sporozoites from single mosquito bites, by immune suppression of parasite subpopulations within infections, and serial transmission of related parasites between people. That relatedness is maintained in endemic areas in the face of repeated bites from infected mosquitoes has profound implications for understanding malaria transmission, immunity and intra-host dynamics of co-infecting parasite genotypes.

Sexual recombination is a signature of a persisting malaria epidemic in Peru

Background

The aim of this study was to consider the impact that multi-clone, complex infections have on a parasite population structure in a low transmission setting. In general, complexity of infection (minimum number of clones within an infection) and the overall population level diversity is expected to be minimal in low transmission settings. Additionally, the parasite population structure is predicted to be clonal, rather than sexual due to infrequent parasite inoculation and lack of recombination between genetically distinct clones. However, in this low transmission of the Peruvian Amazon, complex infections are becoming more frequent, in spite of decreasing infection prevalence. In this study, it was hypothesized that sexual recombination between distinct clonal lineages of Plasmodium falciparum parasites were altering the subpopulation structure and effectively maintaining the population-level diversity.

Methods

Fourteen microsatellite markers were chosen to describe the genetic diversity in 313 naturally occurring P. falciparum infections from Peruvian Amazon. The population and subpopulation structure was characterized by measuring: clusteredness, expected heterozygosity (H_e), allelic richness, private allelic richness, and linkage disequilibrium. Next, microsatellite haplotypes and alleles were correlated with P. falciparum merozoite surface protein 1 Block 2 (Pfmsp1-B2) to examine the presence of recombinant microsatellite haplotypes.

Results

The parasite population structure consists of six genetically diverse subpopulations of clones, called "clusters". Clusters 1, 3, 4, and 6 have unique haplotypes that exceed 70% of the total number of clones within each cluster, while Clusters 2 and 5 have a lower proportion of unique haplotypes, but still exceed 46%. By measuring the H_e, allelic richness, and private allelic richness within each of the six subpopulations, relatively low levels of genetic diversity within each subpopulation (except Cluster 4) are observed. This indicated that the number of alleles, and not the combination of alleles, are limited. Next, the standard index of association (I_A^S) was measured, which revealed a significant decay in linkage disequilibrium (LD) associated with Cluster 6, which is indicative of independent assortment of alleles. This decay in LD is a signature of this subpopulation approaching linkage equilibrium by undergoing sexual recombination. To trace possible recombination events, the two most frequent microsatellite haplotypes observed over time (defined by either a K1 or Mad20) were selected as the progenitors and then potential recombinants were identified in within the natural population.

Conclusions

Contrary to conventional low transmission models, this study provides evidence of a parasite population structure that is superficially defined by a clonal backbone. Sexual recombination does occur and even arguably is responsible for maintaining the substructure of this population.

Genetic exchange and emergence of novel strains in directly transmitted trypanosomatids

The breeding structure of protozoan infections, i.e. whether and how frequently parasites exchange genes ("sexual reproduction"), is a crucially important parameter for many important questions; it also matters for how new virulent strains might emerge. Whether protozoan parasites are clonal or sexual is therefore a hotly debated issue. For trypanosomatids, few experimental tests of breeding structure exist to date and are limited to the vector-borne human diseases Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. We infected the natural host (Bombus terrestris) of the monoxenous parasite Crithidia bombi (Trypanosomatida) either with a single strain of the parasite or in mixed infections and tested for genetic exchange among co-infecting strains using microsatellite markers. We show that strains regularly exchange genetic material, with occasional self-crossing during mixed infections. Most offspring clones fit the expected allelic pattern from a standard Mendelian segregation. In some cases, alleles are lost or gained, leading to an entirely new genotype different from either parent. Genetic exchange in C. bombi therefore does occur and the process also leads to allelic loss or gain that could result from slippage during recombination. The majority of novel offspring types correspond to a recombination of parental alleles. The case of C. bombi demonstrates that directly transmitted, monoxenic trypanosomatids can also exchange genes. Sex therefore seems to be found in very different lineages of the trypanosomatids. Furthermore, the data allowed estimating a frequency at which C. bombi shows genetic exchange in populations.

Environmental, pharmacological and genetic influences on the spread of drug-resistant malaria

Plasmodium falciparum malaria is subject to artificial selection from antimalarial drugs that select for drug-resistant parasites. We describe and apply a flexible new approach to investigate how epistasis, inbreeding, selection heterogeneity and multiple simultaneous drug deployments interact to influence the spread of drug-resistant malaria. This framework recognizes that different human 'environments' within which treatment may occur (such as semi- and non-immune humans taking full or partial drug courses) influence the genetic interactions between parasite loci involved in resistance. Our model provides an explanation for how the rate of spread varies according to different malaria transmission intensities, why resistance might stabilize at intermediate frequencies and also identifies several factors that influence the decline of resistance after a drug is removed. Results suggest that studies based on clinical outcomes might overestimate the spread of resistant parasites, especially in high-transmission areas. We show that when transmission decreases, prevalence might decrease without a corresponding change in frequency of resistance and that this relationship is heavily influenced by the extent of linkage disequilibrium between loci. This has important consequences on the interpretation of data from areas where control is being successful and suggests that reducing transmission might have less impact on the spread of resistance than previously expected.

Effect of heterogeneous mixing and vaccination on the dynamics of anthelmintic resistance: a nested model

Anthelmintic resistance is a major threat to current measures for helminth control in humans and animals. The introduction of anthelmintic vaccines, as a complement to or replacement for drug treatments, has been advocated as a preventive measure. Here, a computer-based simulation, tracking the dynamics of hosts, parasites and parasite-genes, shows that, depending on the degree of host-population mixing, the frequency of totally recessive autosomes associated with anthelmintic resistance can follow either a fast dynamical regime with a low equilibrium point or a slow dynamical regime with a high equilibrium point. For fully dominant autosomes, only one regime is predicted. The effectiveness of anthelminthic vaccines against resistance is shown to be strongly influenced by the underlying dynamics of resistant autosomes. Vaccines targeting adult parasites, by decreasing helminth fecundity or lifespan, are predicted to be more effective than vaccines targeting parasite larvae, by decreasing host susceptibility to infection, in reducing the spread of resistance. These results may inform new strategies to prevent, monitor and control the spread of anthelmintic resistance, including the development of viable anthelmintic vaccines.

Genetic structure of Plasmodium vivax and Plasmodium falciparum in the Bannu district of Pakistan

BACKGROUND

Plasmodium vivax and Plasmodium falciparum are the major causative agents of malaria. While knowledge of the genetic structure of malaria parasites is useful for understanding the evolution of parasite virulence, designing anti-malarial vaccines and assessing the impact of malaria control measures, there is a paucity of information on genetic diversity of these two malaria parasites in Pakistan. This study sought to shed some light on the genetic structure of P. vivax and P. falciparum in this understudied region.

METHODS

The genetic diversities of P. vivax and P. falciparum populations from the densely populated, malaria-endemic Bannu district of Pakistan were evaluated by analysis of their merozoite surface protein (msp) genes by PCR-RFLP. Specifically, the Pvmsp-3alpha and Pvmsp-3beta genes of P. vivax and the Pfmsp-1 and Pfmsp-2 genes of P. falciparum were analysed.

RESULTS

In P. vivax, genotyping of Pvmsp-3alpha and Pvmsp-3beta genes showed a high level of diversity at these loci. Four distinct allele groups: A (1.9 kb), B (1.5 kb), C (1.2 kb), and D (0.3 kb) were detected for Pvmsp-3alpha, type A being the most prevalent (82%). Conversely, amplification of the P. vivax msp-3beta locus produced two allele groups: A (1.7-2.2 kb, 62%) and B (1.4-1.5 kb, 33%), with 5% mixed-strain infections. Restriction analysis of Pvmsp-3alpha and Pvmsp-3beta yielded 12 and 8 distinct alleles, respectively, with a combined mixed genotype prevalence of 20%. In P. falciparum, all three known genotypes of Pfmsp-1 and two of Pfmsp-2 were observed, with MAD20 occurring in 67% and 3D7/IC in 65% of the isolates, respectively. Overall, 24% P. falciparum samples exhibited mixed-strain infections.

CONCLUSION

These results indicate that both P. vivax and P. falciparum populations in Pakistan are highly diverse.

Apparent high recombination rates in clonal parasitic organisms due to inappropriate sampling design

Sampling design is of primary importance for empirical studies, in particular, population genetics. For parasitic organisms, a rather frequent way of sampling individuals from local populations is to collect and genotype only one randomly chosen parasite (or isolate) per host individual (or subpopulation), although each host (subpopulation) harbors a set of parasites belonging to the same species (that is, an infrapopulation). Here, we investigate, using simulations, the consequences of such sampling design regarding the estimates of linkage disequilibrium and departure from the Hardy-Weinberg expectations (H-WE) in clonal parasites with an acyclic life cycle. We show that collecting and genotyping only one individual pathogen per host individual (or per subpopulation) and pooling them to form one 'artificial' subpopulation may generate strongly misleading patterns of genetic variations that may lead to false conclusions regarding their reproduction mode. In particular, we show that when subpopulations (or infrapopulations) are genetically differentiated, (i) the level of linkage disequilibrium is significantly reduced and (ii) the departure from the H-WE is strongly modified, sometimes giving a forged picture of a strongly recombining organism despite high levels of clonal reproduction.

Effective size of the hierarchically structured populations of the agent of malaria: a coalescent-based model

Using the coalescence theory, we derived a simple expression for the asymptotic inbreeding effective population size of Plasmodium falciparum, the most malignant agent of malaria, in relationship to F-statistics at different hierarchical levels. We consider the effective size of malaria parasites, both for the intrinsic interest of the result for the study of this medically important organism and as an example illustrating general arguments that should clarify effective size calculations in a wide range of organisms with complex life cycles and a hierarchical population structure. We consider in this study a model with four hierarchical levels (villages, oocyst infrapopulations, oocysts within infrapopulations and the oocyst). The derived expression is applicable to both island and isolation by distance models and is a function of three F-statistics: the genetic differentiation among villages (F(VT)), the genetic differentiation among oocyst infrapopulations (F(MV)) and, finally, the departure from panmixia (F(IM)) within oocyst infrapopulations. The logic of the derivation of effective size presented in this study is applicable to any organism showing the same levels of subdivision.

Clonal diversity of a malaria parasite, Plasmodium mexicanum, and its transmission success from its vertebrate-to-insect host

Infections of the lizard malaria parasite Plasmodium mexicanum are often genetically complex within their fence lizard host (Sceloporus occidentalis) harbouring two or more clones of parasite. The role of clonal diversity in transmission success was studied for P. mexicanum by feeding its sandfly vectors (Lutzomyia vexator and Lutzomyia stewarti) on experimentally infected lizards. Experimental infections consisted of one, two, three or more clones, assessed using three microsatellite markers. After 5days, vectors were dissected to assess infection status, oocyst burden and genetic composition of the oocysts. A high proportion (92%) of sandflies became infected and carried high oocyst burdens (mean of 56 oocysts) with no influence of clonal diversity on these two measures of transmission success. Gametocytemia was positively correlated with transmission success and the more common vector (L. vexator) developed more oocysts on midguts. A high proportion ( approximately 74%) of all alleles detected in the lizard blood was found in infected vectors. The relative proportion of clones within mixed infections, determined by peak heights on pherograms produced by the genetic analyser instrument, was very similar for the lizard's blood and infections in the vectors. These results demonstrate that P. mexicanum achieves high transmission success, with most clones making the transition from vertebrate-to-insect host, and thus explains in part the high genetic diversity of the parasite among all hosts at the study site.

Discovery of mating in the major African livestock pathogen Trypanosoma congolense

The protozoan parasite, Trypanosoma congolense, is one of the most economically important pathogens of livestock in Africa and, through its impact on cattle health and productivity, has a significant effect on human health and well being. Despite the importance of this parasite our knowledge of some of the fundamental biological processes is limited. For example, it is unknown whether mating takes place. In this paper we have taken a population genetics based approach to address this question. The availability of genome sequence of the parasite allowed us to identify polymorphic microsatellite markers, which were used to genotype T. congolense isolates from livestock in a discrete geographical area of The Gambia. The data showed a high level of diversity with a large number of distinct genotypes, but a deficit in heterozygotes. Further analysis identified cryptic genetic subdivision into four sub-populations. In one of these, parasite genotypic diversity could only be explained by the occurrence of frequent mating in T. congolense. These data are completely inconsistent with previous suggestions that the parasite expands asexually in the absence of mating. The discovery of mating in this species of trypanosome has significant consequences for the spread of critical traits, such as drug resistance, as well as for fundamental aspects of the biology and epidemiology of this neglected but economically important pathogen.

Triggers and tricks of Plasmodium sexual development

Irrespective of the tremendous suffering caused by malaria, a Plasmodium infection by pathogenic blood stages is only transient and an obligate step toward the Anopheles vector where sexual reproduction and genetic recombination of the unicellular parasite takes place. Recent expression profiling studies identified the molecular make-up of female and male gametocytes. Differential promoters and translational repression through mRNA binding by a female-specific helicase help to fine-tune the expression of these sexual stage-specific genes. However, we are only just beginning to discover the triggers that initiate gametocytogenesis and the developmental programs that drive sexual development.