TY - JOUR
T1 - Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa
AU - Omedo, Irene
AU - Mogeni, Polycarp
AU - Bousema, Teun
AU - Rockett, Kirk A.
AU - Amambua-Ngwa, Alfred
AU - Oyier, Isabella
AU - Stevenson, Jennifer C.
AU - Baidjoe, Amrish Y.
AU - de Villiers, Etienne P.
AU - Fegan, Greg
AU - Ross, Amanda
AU - Hubbart, Christina
AU - Jeffreys, Anne
AU - Williams, Thomas N.
AU - Kwiatkowski, Dominic
AU - Bejon, Philip
N1 - Funding Information:
The paper is published with the permission of the Director of KEMRI.
Funding Information:
Grant information: Sample collection at the Rachuonyo South site was supported by the Bill and Melinda Gates Foundation, under the
Funding Information:
Sample collection at the Rachuonyo South site was supported by the Bill and Melinda Gates Foundation, under the Malaria Transmission Consortium, Grant No.45114 and the Grand Challenge Grant No. OPP1024438. Thomas N. Williams is funded by the Wellcome Trust, grant number 091758. Philip Bejon, Polycarp Mogeni and Irene Omedo are funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement. Polycarp Mogeni is funded by the Gottfied und Julia Bangerter-Rhyner Stiftung and the Novartis Foundation for Medical Biological Research project 13A13. Sample collection in Kilifi was supported by core funding from the Wellcome Trust to the Kenya Programme.
Funding Information:
Malaria Transmission Consortium, Grant No.45114 and the Grand Challenge Grant No. OPP1024438. Thomas N. Williams is funded by the Wellcome Trust, grant number 091758. Philip Bejon, Polycarp Mogeni and Irene Omedo are funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement. Polycarp Mogeni is funded by the Gottfied und Julia Bangerter-Rhyner Stiftung and the Novartis Foundation for Medical Biological Research project 13A13. Sample collection in Kilifi was supported by core funding from the Wellcome Trust to the Kenya Programme.
Publisher Copyright:
© 2017 Omedo I et al.
PY - 2017
Y1 - 2017
N2 - Background: The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites. Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models. Methods: Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites (Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal districts) to determine the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA) and linear regression to examine the relationship between genetic relatedness and distance in space and time for parasite pairs. Results: Using 107, 177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show that there are no discrete geographically restricted parasite sub-populations, but instead we see a diffuse spatio-temporal structure to parasite genotypes. Genetic relatedness of sample pairs is predicted by relatedness in space and time. Conclusions: Our findings suggest that targeted malaria control will benefit the surrounding community, but unfortunately also that emerging drug resistance will spread rapidly through the population.
AB - Background: The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites. Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models. Methods: Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites (Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal districts) to determine the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA) and linear regression to examine the relationship between genetic relatedness and distance in space and time for parasite pairs. Results: Using 107, 177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show that there are no discrete geographically restricted parasite sub-populations, but instead we see a diffuse spatio-temporal structure to parasite genotypes. Genetic relatedness of sample pairs is predicted by relatedness in space and time. Conclusions: Our findings suggest that targeted malaria control will benefit the surrounding community, but unfortunately also that emerging drug resistance will spread rapidly through the population.
KW - Genotyping
KW - Malaria
KW - Micro-epidemiological
KW - Parasite mixing
KW - Plasmodium falciparum
KW - Population structure
KW - Principal component analysis
KW - Targeted control
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U2 - 10.12688/wellcomeopenres.10784.2
DO - 10.12688/wellcomeopenres.10784.2
M3 - Article
AN - SCOPUS:85091254393
VL - 2
JO - Wellcome Open Research
JF - Wellcome Open Research
SN - 2398-502X
M1 - 10
ER -