High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya

AbstractNovel interventions that leverage the heterogeneity of parasite transmission are needed to achieve malaria elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon next-generation sequencing of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From April 2013 to July 2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. Here, we evaluate genetic similarity between infected individuals using three indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly share haplotypes with their own household members. Furthermore, we observe robust temporal structuring of parasite genetic similarity and identify the unique molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures.

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High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya

10.1101/799312 ◽

2019 ◽

Author(s):

Cody S. Nelson ◽

Kelsey M. Sumner ◽

Elizabeth Freedman ◽

Joseph W. Saelens ◽

Andrew A. Obala ◽

...

Keyword(s):

Genetic Similarity ◽

Temporal Dynamics ◽

Control Measures ◽

Molecular Signature ◽

L1 Norm ◽

Transmission Setting ◽

Spatial And Temporal Dynamics ◽

Macro Scale ◽

Polymorphic Gene ◽

Household Members

ABSTRACTNovel interventions that leverage the heterogeneity of parasite transmission are needed to push malaria further towards elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon NGS of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From 4/2013–6/2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. We evaluated genetic similarity between infected individuals using three novel indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly shared haplotypes with their own household members. Furthermore, we identified robust temporal structuring of parasite genetic similarity that we exploited to identify the molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures.

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845. Children with Clinical Plasmodium falciparum Infection Have Increased Sharing of Haplotypes with Household Members as well as Temporally Proximal, Symptomatic Peers

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz359.030 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S14-S14

Author(s):

Cody S Nelson ◽

Kelsey Sumner ◽

Betsy Freedman ◽

Andrew Obala ◽

Jane Mangeni ◽

...

Keyword(s):

Genetic Relatedness ◽

Geographic Distance ◽

Population Level ◽

Illumina Miseq ◽

Molecular Signature ◽

Rank Test ◽

Haplotype Sharing ◽

L1 Norm ◽

Household Members ◽

Ring Testing

Abstract Background Falciparum malaria transmission has failed to decline in proportion to control efforts in certain regions such as Bungoma county, western Kenya. One proposed strategy to eradicate malaria is ring testing and treatment; however, it remains unknown whether infections spread locally or if asymptomatically infected household members are a risk factor for clinical disease. Methods From April 2013 to June 2014, we enrolled 442 cases (RDT+ children hospitalized with malaria) and 442 matched controls; all household members of cases and controls were also enrolled and tested, of which 13.6% (n = 608/4449) were RDT+. From each RDT+ participant, parasite gDNA was PCR-amplified at both Pf circumsporozoite protein (csp) and apical membrane antigen 1 (ama1) loci, amplicons sequenced on an Illumina Miseq, and haplotypes inferred using dada2. Results We identified 120 csp and 180 ama1 unique haplotypes (Figure 1). We evaluated the genetic distance between infected individuals using three novel indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Case children median [IQR] binary/proportional sharing of both csp and ama1 haplotypes was significantly increased with members of their origin household (e.g., csp binary sharing: origin = 50.3 [0–87.5] vs. similar household = 0 [0–50.3]; P = 0.01; Wilcoxon sign-rank test), indicating that cases are more likely to share haplotype-identical parasites with members of their own household (Figure 2). We also computed population-level haplotype sharing indices for all pairs of case children and observed no association between genetic relatedness and geographic distance. In contrast, we identified a strong inverse relationship between haplotype sharing and temporal distance, which we exploited to identify the molecular signature of an outbreak (Figure 3). Conclusion Overall, these findings suggest that, although haplotype sharing is more common within households, temporal rather than geographic proximity predicts parasite genetic similarity. The observation that identical haplotype combinations are found nearly simultaneously across the study area implies that ring testing approaches may not effectively reduce transmission. Disclosures All Authors: No reported Disclosures.

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Spatial and temporal dynamics of lexico-semantic processing in American Sign Language

PsycEXTRA Dataset ◽

10.1037/e512592013-575 ◽

2011 ◽

Author(s):

M. Leonard ◽

N. Ferjan Ramirez ◽

C. Torres ◽

M. Hatrak ◽

R. Mayberry ◽

...

Keyword(s):

American Sign Language ◽

Sign Language ◽

Semantic Processing ◽

Temporal Dynamics ◽

American Sign ◽

Spatial And Temporal Dynamics

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Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

Marine Ecology Progress Series ◽

10.3354/meps13211 ◽

2020 ◽

Vol 637 ◽

pp. 117-140 ◽

Cited By ~ 1

Author(s):

DW McGowan ◽

ED Goldstein ◽

ML Arimitsu ◽

AL Deary ◽

O Ormseth ◽

...

Keyword(s):

Temporal Dynamics ◽

Marine Ecosystem ◽

Gulf Of Alaska ◽

Data Series ◽

Limited Information ◽

Important Species ◽

Multiple Data ◽

Spatial And Temporal Dynamics ◽

Spawning Areas ◽

Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

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