scholarly journals Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

2020 ◽  
Author(s):  
Jason A. Hendry ◽  
Dominic Kwiatkowski ◽  
Gil McVean
Keyword(s):  
Genetic Diversity ◽  
Malaria Control ◽  
Focal Point ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Malaria Surveillance ◽  
Related Factors ◽  
Malaria Epidemiology ◽  
Moran Model ◽  
Classical Models

AbstractThere is an abundance of malaria genetic data being collected from the field, yet using this data to understand features of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (~ months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.Author summaryKnowledge of how the prevalence of P.falciparum malaria varies, either between regions or through time, is critical to the operation of malaria control programs. Yet obtaining this information through traditional methods is fraught with challenges. Parasite genetic data is increasingly accessible, and may provide an alternative means to estimate P.falciparum prevalence in the field. However, our understanding of how the genetic diversity of parasite populations relates to prevalence is limited, and suitable models to guide our understanding are largely lacking. Here, we merge two classical models – the Ross-Macondald and the Moran – to produce a framework in which the relationships between parasite genetic diversity and prevalence can be explored. We find that several genetic diversity statistics are correlated with prevalence, although to differing degrees, and over different time scales. Overall, statistics related to mixed infection are robustly and rapidly responsive to changes in prevalence, suggesting they may be a useful focal point for the development of malaria surveillance methods that harness genetic data.

scholarly journals Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

2021 ◽  
Vol 17 (8) ◽  
pp. e1009287
Author(s):  
Jason A. Hendry ◽  
Dominic Kwiatkowski ◽  
Gil McVean
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Epidemiological Models ◽  
Related Factors ◽  
Malaria Epidemiology ◽  
Moran Model ◽  
Classical Models ◽  
Parasite Evolution

There is an abundance of malaria genetic data being collected from the field, yet using these data to understand the drivers of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (∼months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.

scholarly journals Modelling homogeneous regions of social vulnerability to malaria in Rwanda

2016 ◽  
Vol 11 (1s) ◽  
Author(s):  
Jean Pierre Bizimana ◽  
Stefan Kienberger ◽  
Michael Hagenlocher ◽  
Emmanuel Twarabamenye
Keyword(s):  
Social Vulnerability ◽  
Socioeconomic Development ◽  
Malaria Incidence ◽  
Spatially Explicit ◽  
Related Factors ◽  
Remote Areas ◽  
Malaria Epidemiology ◽  
Vulnerability Indicators ◽  
Applied Approach ◽  
Homogeneous Regions

Despite the decline in malaria incidence due to intense interventions, potentials for malaria transmission persist in Rwanda. To eradicate malaria in Rwanda, strategies need to expand beyond approaches that focus solely on malaria epidemiology and also consider the socioeconomic, demographic and biological/disease-related factors that determine the vulnerability of potentially exposed populations. This paper analyses current levels of social vulnerability to malaria in Rwanda by integrating a set of weighted vulnerability indicators. The paper uses regionalisation techniques as a spatially explicit approach for delineating homogeneous regions of social vulnerability to malaria. This overcomes the limitations of administrative boundaries for modelling the trans-boundary social vulnerability to malaria. The utilised approach revealed high levels of social vulnerability to malaria in the highland areas of Rwanda, as well as in remote areas where populations are more susceptible. Susceptibility may be due to the populations’ lacking the capacity to anticipate mosquito bites, or lacking resilience to cope with or recover from malaria infection. By highlighting the most influential indicators of social vulnerability to malaria, the applied approach indicates which vulnerability domains need to be addressed, and where appropriate interventions are most required. Interventions to improve the socioeconomic development in highly vulnerable areas could prove highly effective, and provide sustainable outcomes against malaria in Rwanda. This would ultimately increase the resilience of the population and their capacity to better anticipate, cope with, and recover from possible infection.

scholarly journals Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 306
Author(s):  
Maurizio Rossetto ◽  
Peter D. Wilson ◽  
Jason Bragg ◽  
Joel Cohen ◽  
Monica Fahey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
A Priori ◽  
Genetic Data ◽  
Environmental Data ◽  
Specific Data ◽  
Acacia Species ◽  
Simple Observation ◽  
Source Plant ◽  
Species Specific

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

scholarly journals The Impact of 3 Years of Targeted Indoor Residual Spraying With Pirimiphos-Methyl on Malaria Parasite Prevalence in a High-Transmission Area of Northern Zambia

2019 ◽  
Vol 188 (12) ◽  
pp. 2120-2130 ◽  
Author(s):  
Marisa A Hast ◽  
Mike Chaponda ◽  
Mbanga Muleba ◽  
Jean-Bertin Kabuya ◽  
James Lupiya ◽  
...  
Keyword(s):  
Malaria Transmission ◽  
Malaria Control ◽  
Malaria Parasite ◽  
Control Measure ◽  
Indoor Residual Spraying ◽  
Parasite Prevalence ◽  
Organophosphate Insecticide ◽  
Malaria Burden ◽  
Pirimiphos Methyl ◽  
The Impact

Abstract Malaria transmission in northern Zambia has increased in the past decade, despite malaria control activities. Evidence-based intervention strategies are needed to effectively reduce malaria transmission. Zambia’s National Malaria Control Centre conducted targeted indoor residual spraying (IRS) in Nchelenge District, Luapula Province, from 2014 to 2016 using the organophosphate insecticide pirimiphos-methyl. An evaluation of the IRS campaign was conducted by the Southern Africa International Centers of Excellence for Malaria Research using actively detected malaria cases in bimonthly household surveys carried out from April 2012 to July 2017. Changes in malaria parasite prevalence after IRS were assessed by season using Poisson regression models with robust standard errors, controlling for clustering of participants in households and demographic, geographical, and climatological covariates. In targeted areas, parasite prevalence declined approximately 25% during the rainy season following IRS with pirimiphos-methyl but did not decline during the dry season or in the overall study area. Within targeted areas, parasite prevalence declined in unsprayed households, suggesting both direct and indirect effects of IRS. The moderate decrease in parasite prevalence within sprayed areas indicates that IRS with pirimiphos-methyl is an effective malaria control measure, but a more comprehensive package of interventions is needed to effectively reduce the malaria burden in this setting.

Conservation genetics of Pitcher’s thistle (Cirsium pitcheri), an endangered Great Lakes endemic

Botany ◽  
2010 ◽  
Vol 88 (3) ◽  
pp. 250-257 ◽  
Author(s):  
Martha Gauthier ◽  
Emily Crowe ◽  
Lindsey Hawke ◽  
Neil Emery ◽  
Paul Wilson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Great Lakes ◽  
Genetic Data ◽  
Nuclear Data ◽  
Population Connectivity ◽  
Chloroplast Microsatellite ◽  
Management Plans ◽  
Low Levels ◽  
Cirsium Pitcheri ◽  
Pitcher's Thistle

Pitcher's thistle ( Cirsium pitcheri Torr. ex Eaton (Torr. & Gray)) is a Great Lakes endemic that in Canada is designated as threatened at both the provincial (Ontario) and national levels. Management plans will benefit from conservation genetic data, which can provide insight into population genetic diversity and differentiation. We obtained genetic data from nuclear and chloroplast microsatellite markers from 17 populations of C. pitcheri around the Great Lakes. The nuclear data revealed overall low levels of diversity, high levels of inbreeding, and low levels of population connectivity. The chloroplast data identified a single haplotype, which is consistent with reduced genetic diversity following postglacial colonization. The high levels of inbreeding within populations will likely pose a serious threat to populations in the short term; these have resulted from a combination of low connectivity between populations, and small and fluctuating population sizes. Future management of C. pitcheri populations should consider human-mediated dispersal of plants or seeds among sites.

scholarly journals Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia

AoB Plants ◽  
2020 ◽  
Vol 12 (4) ◽  
Author(s):  
Elizabeth A Sinclair ◽  
Jane M Edgeloe ◽  
Janet M Anthony ◽  
John Statton ◽  
Martin F Breed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Western Australia ◽  
Reproductive Effort ◽  
Genetic Data ◽  
Fruit Production ◽  
Mixed Mating ◽  
Mixed Mating System ◽  
Shark Bay ◽  
Range Edge

Abstract Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.

scholarly journals The role of improved housing and living environments in malaria control and elimination

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Richard Carter ◽  
Nadira D. Karunaweera
Keyword(s):  
Sri Lanka ◽  
Malaria Transmission ◽  
Malaria Control ◽  
Housing Stock ◽  
Blood Feeding ◽  
Malaria Risk ◽  
Living Environment ◽  
George Macdonald ◽  
Malaria Epidemiology

Abstract Malaria risk and endemicity is often associated with the nature of human habitation and living environment. The disappearance of malaria from regions where it had been endemic for centuries, such as coastal areas of southern England, has been attributed, at least in part, to improvement in the quality of housing. Moreover, indigenous malaria transmission ceased throughout England without the necessity to eliminate the vector mosquitoes. The principles of malaria transmission, as formulated following the thinking of the pioneers of malaria epidemiology, Ronald Ross and George Macdonald, show how this may happen. Malaria ceases to be sustainable where its reproduction number, R0, the number of new cases generated on average for each existing case of malaria, falls below 1. In the terms of a Ross/Macdonald analysis the reduced contact between humans and blood-feeding mosquitoes that is achieved through housing that is secure against mosquito entry can have a powerful effect in reducing malaria R0. The island of Sri Lanka, where malaria had been endemic probably for centuries previously, has reported no indigenous cases of malaria since 2012. The disappearance of malaria from Sri Lanka followed an effective attack upon malaria transmission by the Sri Lanka Anti Malaria Campaign. The targeted and enhanced efforts of this campaign launched in 1999, drove the malaria R0 below 1 for most of the period up to 2012, leading to a nearly continuous decline in malaria cases until their extinction. The decades leading up to the launch of these efforts were ones of general improvement of living environment and notably in the quality of housing stock. Studies in the late 1980s had shown that quality of housing in a highly malarious district of Sri Lanka was a strong determinant of malaria risk. Through its effects on malaria R0, improved housing is likely to have facilitated the malaria control and cessation of indigenous malaria transmission in Sri Lanka and that it will help reduce the risk of the re-introduction of malaria to the island.

scholarly journals Genetic, morphological and spatial characterization of two populations of Mabea fistulifera Mart. (Euphorbiaceae), in different successional stages

2005 ◽  
Vol 48 (2) ◽  
pp. 275-284 ◽  
Author(s):  
Maíra Figueiredo Goulart ◽  
Sérvio Pontes Ribeiro ◽  
Maria Bernadete Lovato
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Data ◽  
Ecological Traits ◽  
Spatial Characterization ◽  
Shannon’S Index ◽  
Successional Stages ◽  
Morphologic Data ◽  
Two Populations

Two populations of Mabea fistulifera (Euphorbiaceae) located at Rio Doce State Park (Minas Gerais, Brazil) in places characterized as in different successional stages, were investigated through genetic and ecological traits. Twenty randomly chosen individuals from each population had its genetic data assessed by 43 RAPD markers and were also evaluated through five morphologic traits and its spatial distribution. Both Shannon's index and AMOVA reveled that most of the genetic variation was found between individuals within populations and about 9% of variation was located between populations. Moreover, populations differed genetically, but presented similar values of genetic diversity. Morphologic data showed differences between populations. Significant correlations among matrix of genetic, geographic and morphologic distances were obtained considering both populations, and spatially closer individuals were more similar genetically, characterizing genetic substructured populations.

Microsatellite loci over a thirty-three year period for a malaria parasite (Plasmodium mexicanum): bottleneck in effective population size and effect on allele frequencies

Parasitology ◽  
2012 ◽  
Vol 140 (1) ◽  
pp. 21-28 ◽  
Author(s):  
J. J. SCHALL ◽  
K. M. ST. DENIS
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Malaria Parasite ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Allele Frequencies ◽  
The Other ◽  
Effective Population ◽  
Blood Smears ◽  
Parasite Plasmodium

SUMMARYChanges in population allele frequencies may be driven by several forces, including selection and drift, and are revealed only by sampling over many generations. Such studies, however, are rare for protist parasites. Microsatellite allele frequencies for 4 loci were followed in a population of Plasmodium mexicanum, a malaria parasite of lizards in California USA at 1 site from 1978 to 2010. Rapid turnover of the lizards indicates the parasite was studied for a minimum of 33 transmission cycles and possibly twice that number. Sample sizes ranged from 841 to 956 scored parasite clones per locus. DNA was extracted from frozen dried blood and blood removed from stained blood smears from the earliest years, and a verification study demonstrated DNA from the blood smears provided valid genetic data. Parasite prevalence and effective population size (Ne) dropped after 2000, remaining lower for the next decade. For 2 loci, allele frequencies appeared stable for the first 2 decades of the study, but changed more rapidly after the decline in prevalence. Allele frequencies changed more gradually for the other 2 loci. Genetic drift could account for changes in allele frequencies, especially after the drop in prevalence and Ne, but the force of selection could also have driven the observed patterns.

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