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Major subpopulations of Plasmodium falciparum in sub-Saharan Africa

  • Medical Research Council Unit The Gambia at LSHTM

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Understanding genomic variation and population structure of Plasmodium falciparum across Africa is necessary to sustain progress toward malaria elimination. Genome clustering of 2263 P. falciparum isolates from 24 malaria-endemic settings in 15 African countries identified major western, central, and eastern ancestries, plus a highly divergent Ethiopian population. Ancestry aligned to these regional blocs, overlapping with both the parasite’s origin and with historical human migration. The parasite populations are interbred and shared genomic haplotypes, especially across drug resistance loci, which showed the strongest recent identity-by-descent between populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives was evident in Ghana and Malawi. Such selection and the emerging substructure may affect treatment-based intervention strategies against P. falciparum malaria.
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Major subpopulations of Plasmodium
falciparum in sub-Saharan Africa
Alfred Amambua-Ngwa
, Lucas Amenga-Etego
, Edwin Kamau
, Roberto Amato
Anita Ghansah
, Lemu Golassa
, Milijaona Randrianarivelojosia
, Deus Ishengoma
Tobias Apinjoh
, Oumou Maïga-Ascofaré
, Ben Andagalu
, William Yavo
Marielle Bouyou-Akotet
, Oyebola Kolapo
, Karim Mane
, Archibald Worwui
David Jeffries
, Vikki Simpson
, Umberto DAlessandro
Dominic Kwiatkowski
, Abdoulaye A. Djimde
Understanding genomic variation and population structure of Plasmodium falciparum
across Africa is necessary to sustain progress toward malaria elimination. Genome
clustering of 2263 P. falciparum isolates from 24 malaria-endemic settings in
15 African countries identified major western, central, and eastern ancestries, plus a
highly divergent Ethiopian population. Ancestry aligned to these regional blocs,
overlapping with both the parasites origin and with historical human migration. The
parasite populations are interbred and shared genomic haplotypes, especially across drug
resistance loci, which showed the strongest recent identity-by-descent between
populations. A recent signature of selection on chromosome 12 with candidate resistance
loci against artemisinin derivatives was evident in Ghana and Malawi. Such selection
and the emerging substructure may affect treatment-based intervention strategies
against P. falciparum malaria.
The worldwide decline in malaria prevalence
is now stalling and additional knowledge,
new tools, and intervention strategies
will be needed for global malaria elimi-
nation and eradication (1). The burden of
Plasmodium falciparum malaria in particular
remains substantial in sub-Saharan Africa (sSA),
where it involves various vectors and human
populations (2,3). Although interventions have
reduced and disconnected malaria parasite pop-
ulations, they may be driving selection, adapta-
tion, and population fragmentation. Population
fragmentation and reduced diversity can be as-
sessed for refining approaches or tools for elim-
ination (4). Therefore, it is important to determine
the effect of large-scale control interventions on
the structure of the parasite population, which
until recently was considered to be highly diverse
and homogeneously interconnected in sSA (5).
The ancestry, current structure, and gene flow
between different P. falciparum populations
across sSA remain unclear. Previous studies
have used single-nucleotide polymorphism (SNP)
markers to characterize specific geographic
populations and describe genomic variation
and signatures of selection in sSA (6,7). Re-
cent higher-density genomic polymorphisms
from next-generation sequencing technologies
can further resolve African P. falciparum sub-
populations and population-specific genomic
The Plasmodium Diversity Network Africa
(PDNA) conducts P. falciparum genomic sur-
veillance across sSA, from the West Atlantic
coastal regions with their high rainfall and
perennial transmission; the Sahel with its short
rainy seasons and seasonal transmission; Central
Africa with its forest-covered areas and perennial
transmission; Eastern Africa with its perennial
and seasonal transmission; to Ethiopia and the
Amambua-Ngwa et al., Science 365, 813816 (2019) 23 August 2019 1of4
Medical Research Council Unit The Gambia at LSHTM,
Banjul, The Gambia.
West African Centre for Cell Biology of
Infectious Pathogens (WACCBIP), University of Ghana, Accra,
United States Army Medical Research Directorate-
Africa, Kenya Medical Research Institute/Walter Reed
Project, Kisumu, Kenya.
Walter Reed Army Institute of
Research, U.S. Military HIV Research Program, Silver Spring,
Wellcome Sanger Institute, Hinxton, UK.
Centre for Genomics and Global Health, Big Data Institute,
University of Oxford, Oxford, UK.
Noguchi Memorial Institute
for Medical Research (NMIMR), Accra, Ghana.
Aklilu Lemma
Institute of Pathobiology, Addis Ababa University, Addis
Ababa, Ethiopia.
Institut Pasteur of Madagascar, Antanarivo,
National Insti tute for Medical Research
(NIMR), Tanga, Tanzania.
Department of Biochemistry and
Molecular Biology, University of Buea, Buea, Cameroon.
Bernhard Nocht Institute for Topical Medicine (BNITM),
Hamburg, Germany.
Unite des Sciences Pharmaceutiques
et Biologiques, University Félix Houphouët-Boigny, Abidjan,
Côte dIvoire.
Faculty of Medicine, University of Health
Sciences, Libreville, Gabon.
Department of Zoology,
University of Lagos, Lagos, Nigeria.
Malaria Research and
Training Centre, University of Science, Techniques and
Technologies of Bamako, Bamako, Mali.
*Corresponding author. Email:
Fig. 1. Sites, sample sizes,
and genetic groupings
of P. falciparum isolates
across PDNA and Pf3K
studies in Africa.
(A)Sites,P. falciparum
(Pf) prevalence rate, and
studies from which
SNP data of 2263 isolates
were accessed. Map
was extracted from a
malaria atlas showing
P. falciparum prevalence
as brown density within
the ranges of the key
explorer/#/). (B)Com-
plexity of infections
by inbreeding coefficient
(Fws). (C) Scatter plot
from multidimensional
scaling of tess3r
ancestry coefficients
for six predicted
ancestral populations.
on August 24, 2019 from
island of Madagascar with their cotransmission
of P. vivax (8). Using high-resolution genome-
wide SNP variants of P. falciparum isolates
across sSA, we reveal the population structure,
admixture, markers of identity-by-descent (IBD),
differentiation, and signatures of selection.
SNP variants (29,998) were extracted from
whole-genome sequences of 2263 P. falciparum
isolates sampled from across 15 African coun-
tries (Fig. 1A and tables S1 and S2). At least 55%
of infections were polygenomic, with up to nine
clones in some infections from Ghana, Guinea,
and Malawi (fig. S1). The proportion of complex
infections [i.e., lower mean inbreeding coefficient
(Fws)] was highest in Kenya and lowest in
Ethiopia (Fig. 1B). Malaria transmission around
the sampling site in Kenya (Kisumu, Western
Kenya) was stable and high (9), probably driving
the high infection complexity. In West Africa,
isolates from The Gambia and Senegal were the
least complex, confirming earlier reports of a
decline in complexity with decreasing preva-
lence, probably due to the scale-up of inter-
ventions (10).
Standard principal components analysis, using
imputed genome haplotypes (fig. S2), resolved
three major groups: western (West Africa and the
more-central countries of Cameroon and Gabon),
eastern [Democratic Republic of the Congo (DR
Congo) and all other sites in East Africa], and a
Amambua-Ngwa et al., Science 365, 813816 (2019) 23 August 2019 2of4
Fig. 2. Genome-wide ancestry proportions. Ancestry proportions for P. falciparum isolates (admixture-like bar plots) or populations (pie charts)
modeled to include donors from all sites (incl. self) or excluding isolates from recipient sampling site (without self). (A) Ancestry per isolate (rows) from
each sampling site (left column). (B) Median ancestry from each sampling site. (C) Median ancestry proportions between isolates from each sampling
site, excluding donors from same site. Country colors are the same as in Fig. 1.
Fig. 3. Genome-wide ancestry proportions for P. falciparum populations in sSA. (A) Ancestry proportions for regional genetic blocs (left column).
Ancestry proportions for each genetic cluster (B) including self-copying and (C) without self-copying.
on August 24, 2019 from
distinct Ethiopian population (fig. S3). This sub-
structure was refined to six distinct clusters from
multidimensional scaling of ancestral member-
ship coefficients, splitting DR Congo from East
African populations (Fig. 1C and fig. S4). The six
retained genetic clusters were West African (WAF;
Senegal, Gambia, Guinea, Mali, Côte dIvoire,
Ghana, and Nigeria), Central African (CAF;
Cameroon and Gabon), South Central African
(SCAF; DR Congo), East African (EAF; Kenya
and Tanzania), Southeast African (SEAF; Malawi
and Madagascar), and the Horn of Africa (HAF;
Each cluster suggests an ancestral or trans-
mission connectivity supported by geographic
proximity and confirmed by significant isola-
tion by distance (P= 0.03, Mantel test) (fig. S5).
The major population continuums were within
West Africa and East Africa, with several-fold
difference in genetic distance [all fixation index
) values > 0.1] between them and Ethiopia.
Differentiation might also result from differences
in human and vector populations, the history
of interventions on spatial separation, and geo-
graphic barriers (e.g., western Cameroon forest,
the equatorial forest, Congo Basin rivers, and
highlands of Ethiopia). Isolates from DR Congo
and Ethiopia clustered away from geographically
proximal sites in CAF and EAF, respectively.
Human populations from Ethiopia and other
HAF sites, such as Djibouti, have a distinct an-
cestry from the rest of Africa, allowing sympat-
ric transmission of P. vivax, with earlier reports
of divergent P. falciparum populations (11,12).
As in Madagascar, HAF human populations have
higher frequencies of the Duffy antigen, allowing
P. vivax cotransmission. However, isolates from
Madagascar clustered with those from Malawi,
indicating mainland ancestry despite a high pro-
portion of human populations originating from
Southeast Asia and being separated by 1400 km
of land and the Indian Ocean. Therefore, it is not
likely that the divergence of HAF isolates is due
to co-prevalence with P. vivax but might be
driven by other factors such as differences in
vector populations. This could also explain the
differentiation between Congolese and other CAF
isolates where vector populations differ, with
Anopheles funestus being relatively dominant in
DR Congo (13).
Recent studies have shown that P. falciparum
from western great apes jumped into humans
about 10,000 years ago, prior to major human
migrations (14,15). The donation of ancestral
genome chunks from CAF to both western and
eastern P. falciparum populations aligns with
such an origin and the spread of malaria through
historical and more recent human migration in
Africa. Recent human migration brought on by
colonization and slavery may have resulted
in P. falciparum ancestral chunks shared be-
tween distal French colonies like Cameroon,
Mali, and Senegal, whereas ancestry from WAF
sites of Mali, Guinea, and Senegal are present in
DR Congo (Fig. 2 and fig. S6). However, historical
links prior to dispersal of humans and parasites
to West and East Africa may also account for the
shared ancestry between all major population
blocs (Fig. 3). The early human migration from
Central Africa, after the emergence of malaria
in humans, was dominated by Bantu popula-
tions moving westward and southeastward (16).
T-SNE and fineSTRUCTURE clustering of an-
cestral chunk matrices also maintained the
major West and East African subpopulations,
further indicating that isolates from DR Congo
share more eastern ancestry (figs. S7 and S8). Hu-
man population mixing could have facilitated
P. falciparum gene flow, IBD signatures, and
spread of adaptive alleles across Africa (17).
The proportions of isolates sharing IBD (<3%)
was weak and uneven across the genome, as ex-
pected for intensely recombining parasite pop-
ulations (Fig. 4A and fig. S9). However, relatively
high IBD proportions spanned 12 segments of the
genome, including regions coding for candidate
drug resistance loci; Pfaat1 (PF3D7_0629500) on
chromosome 6; known drug resistance genes
Pfmdr1, Pfcrt, and Pfdhps; anda cluster of genes
on chromosome 12 (Pfap2mu, PfATPase, and
Pfap2g2). These genes are involved in drug re-
sponses, transportation, and metabolism (fig. S10).
These results confirm links between Pfcrt and
Pfaat1, which together with Pfap2g2 and PfAT-
Pase2 have been identified as part of the malaria
druggablegenome(18). Pfap2mu in particular
has been linked to artemisinin tolerance in
Africa (19). Strong IBD around Pfap2mu in Ghana
and Malawi (Fig. 4B) may have emerged inde-
pendently and calls for increased vigilance
against artemisinin-based combination therapy
(ACT) efficacy. The introduction or local emer-
gence and sharing of candidate drug resistance
haplotypes would be recent, as IBD detection
was limited to 25 generations. Haplotype paint-
ing across drug resistance loci (table S6) empha-
sized bidirectional gene flow across these loci
(fig. S11). Multiple origins of antifolate markers
were confirmed (20) but also seen for Pfmdr1,
which showed two ancestral lineages dominant
in West and East African populations, respec-
tively (fig. S12). Multiple emergence for a major
quinolone resistance mediator such as Pfmdr1
Amambua-Ngwa et al., Science 365, 813816 (2019) 23 August 2019 3of4
Fig. 4. Pairwise IBD between isolates across sites. (A) Manhattan plot of median IBD between
pairs of P. falciparum isolates, showing each chromosome as numbered on the xaxis. IBD segment
peaks labeled for dihydrofolate reductase (dhfr), multidrug resistance protein 1 (mdr1), amino
acid transporter 1 (aat1), chloroquine resistance transporter (crt), dihydropteroate synthetase
(dhps), AP2 domain transcription factors (ap2-g2 and ap2-mu), and aminophospholipid-
transp orting P-ATPase (atpase2). (B) Heatmap of pairwise IBD between sampled populations
clustered on rows for similar patterns between populations. SNP values are in columns
separated by chromosomes for each pair of populations in rows. Low to high values are color
graded from blue to red on RGB color wheel.
on August 24, 2019 from
has not been previously reported. Selection,
emergence, and spread of resistance to drugs is
therefore possible in all malaria endemic sites
across sSA. These findings are important because
artemisinin resistance may emerge independently
in sSA and not necessarily spread from Southeast
Asia. This calls for careful surveillance of artemis-
inin resistance in sSA, where drug pressure from
ACT and seasonal malaria chemoprevention with
sulfadoxine-pyrimethamine and amodiaquine are
being scaled up for elimination. These would also
lead to population differentiation (fig. S13) and
positive selection that could facilitate the devel-
opment of clinical drug resistance.
SNPs related to drug resistance, erythrocyte
invasion, gametocytogenesis, oocyst development,
and antigenic loci were the most differentiated
between populations (fig. S14, A and B, and tables
S7 and S8). These could be due to different envi-
ronmental conditions and varying human and
mosquito populations. Known drug loci (Pfaat1,
Pfmdr1, Pfcrt, Pfdhfr, and Pfdhps) and the IBD
cluster on chromosome 12 showed signatures of
positive selection and haplotype differentiation
across sampled populations (figs. S14, C and D,
S15, and S16, and tables S9 and S10). It would be
important to determine whether variants at these
loci can compromise the efficacy of artemisinins
and/or ACTs.
P. falciparum in sSA is clustered into major
western, central, and eastern subgroups and a
highly divergent Ethiopian subpopulation. These
endogenous genomic lineages are the ancestral
backbone on which adaptive loci such as drug
resistance mutations may have emerged, recom-
bined, and been shared both westerly and easterly
across sSA. This may occur again against current
artemisinin-based treatments, which are already
directionally selecting loci on chromosome 12.
These signal the need for broader molecular
and phenotypic surveillance of P. falciparum in
sSA, including the large swathes of endemic pop-
ulations in Central Africa, where civil strife and
other global health pathogen epidemics could
maintain malaria and threaten elimination efforts.
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We thank the participants and local health workers from PDNA
sites. Special thanks to G. Busby for discussion and advising on
admixture analyses. Genome sequencing was done at the
Wellcome Sanger Institute as part of the MalariaGEN Plasmodium
falciparum Community Project (
We thank the MalariaGEN P. falciparum Community Project and
Pf3K Project for allowing access to non-PDNA data. We thank
K. Rockett, J. Stalker, R. Pearson, and other members of the
MalariaGEN resource center and the staff of Wellcome Sanger
Institute Sample Logistics, Sequencing, and Informatics facilities
for their contributions to sample processing, sequence data
generation, and variant calling pipelines. Funding: A.A.-N., L.A.-E.,
A.G., L.G., D.I., T.A., O.M.-A., B.A., Y.W., M.B.-A., and A.A.D. are
currently supported through the DELTAS Africa Initiative, an
independent funding scheme of the African Academy of Sciences
(AAS)s Alliance for Accelerating Excellence in Science in Africa
(AESA), and are also supported by the New Partnership for Africas
Development Planning and Coordinating Agency (NEPAD Agency)
with funding from Wellcome (DELGEME grant 107740/Z/15/Z) and
the U.K. government. Sample collection in Kenya was funded by
Armed Forces Health Surveillance Center (AFHSB) and its Global
Emerging Infections Surveillance (GEIS) Section, Grant P0209_15_
KY. The views expressed in this publication are those of the
authors and not necessarily those of AAS, NEPAD Agency,
Wellcome, the U.S. Army or the Department of Defense, or the U.K.
government. The investigators have adhered to the policies for
protection of human subjects as prescribed in AR-70. Sequencing
was undertaken in partnership with MalariaGEN and the
Parasites and Microbes program at the Wellcome Sanger Institute
with funding from Wellcome (206194; 090770/Z/09/Z) and by
the MRC Centre for Genomics and Global Health which is jointly
funded by the Medical Research Council and the Department
for International Development (DFID) (G0600718 to D.K.;
M006212). Author contributions: A.G., L.G., M.R., D.I., T.A.,
O.M.-A., B.A., Y.W., O.K., and M.B.-A. contributed samples and
reviewed the manuscript. A.A.-N. and L.A.-E. contributed samples,
conceived of the manuscript, executed data analysis, and
participated in the writing (A.A.-N.) and revision (L.A.-E.) of the
manuscript. E.K. reviewed the analysis and manuscript. R.A.
provided analytical support. K.M., A.W., and D.J. conducted data
analysis and reviewed the manuscript. V.S. coor dinated the
collaboration an d reviewed the m anuscript. U.D. read and
reviewed the manu script. D.K. led the team that generated data,
conceived of the m anuscript, and reviewed the analysis an d
manuscript. A.A .D. coordinated the consortium, contr ibuted
samples conceived of the manuscript, and read and reviewed the
manuscript. Competing interests: The authors declare no
competi ng interest. Data and materials availability: The short-
read sequences used in this publication are available in the ENA
and SRA databases (see table S2 for accession numbers). The
views expressed are those of the authors and should not be
construed to represent the positions of the U.S. Army or the
Department of Defense. The investigators have adhered to the
policies for protection of human subjects as prescribed in AR-70.
Materials and Methods
Figs. S1 to S16
Tables S1 to S10
References (2131)
27 September 2018; accepted 5 July 2019
Amambua-Ngwa et al., Science 365, 813816 (2019) 23 August 2019 4of4
on August 24, 2019 from
in sub-Saharan AfricaPlasmodium falciparumMajor subpopulations of
Dominic Kwiatkowski and Abdoulaye A. Djimde
Bouyou-Akotet, Oyebola Kolapo, Karim Mane, Archibald Worwui, David Jeffries, Vikki Simpson, Umberto D'Alessandro,
Randrianarivelojosia, Deus Ishengoma, Tobias Apinjoh, Oumou Maïga-Ascofaré, Ben Andagalu, William Yavo, Marielle
Alfred Amambua-Ngwa, Lucas Amenga-Etego, Edwin Kamau, Roberto Amato, Anita Ghansah, Lemu Golassa, Milijaona
DOI: 10.1126/science.aav5427
(6455), 813-816.365Science
, this issue p. 813; see also p. 752Science P. vivax.malaria parasite, , which may be indicative of coexistence with anotherP. falciparumand that Ethiopia has a distinctive population of
slavery. Furthermore, whole-genome sequencing showed that there is extensive gene flow among the different regions
signatures of selection by antimalarial drugs were detected, along with indications of the effect of colonization and
within Africa that is consistent with human and vector population divergence (see the Perspective by Sibley). Specific
of the Plasmodium Diversity Network Africa found substantial population structureet al.genomics, Amambua-Ngwa
important to know for grasping the risks and dynamics of the spread of drug resistance. Harnessing the power of
across Africa is poorly understood butPlasmodium falciparumThe population genetics of the malaria parasite
Ebb and flow of parasite populations
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on August 24, 2019 from
... Human migration is one of the main drivers of spread of P. falciparum [83][84][85], making human movement across Angola an important factor to consider in understanding the dynamics of malaria in the region. Of the current population of ~ 36 million, about two thirds live in urban centres, including 2.8 million in the capital city, Luanda, and 9.1 million in the overall Luanda province [86]. ...
... Broadly speaking, in countries of high transmission intensity, infections are often polyclonal and parasite populations are highly diverse and panmictic [107,108]. In contrast, at the edges of the malaria distribution or in regions where malaria is epidemic, the parasite population is fragmented, infections often contain a single genotype, and clonal expansion is more common [85,109,110]. The spatial distribution of malaria transmission is stratified as low (light green), medium (medium green) and high (dark green) [10] Across Angola these two extremes, as well as variations in between, can all be found. ...
... The presence of genetically distinct P. falciparum populations in east and west African countries is well established, contributing to the high genetic diversity of P. falciparum in Africa [111,112], and the most comprehensive study of P. falciparum genetic variation in Africa to date demonstrated the existence of several genetically distinct parasite populations south of the Sahara [85]. Angola, which encompasses the southwestern-most edge of the African P. falciparum distribution, is surrounded by distinct P. falciparum populations; one, in Central Africa, is represented by parasites from Gabon and Cameroon, and another, in south-central Africa, is composed of parasites from the DRC [85]. ...
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Over the past two decades, a considerable expansion of malaria interventions has occurred at the national level in Angola, together with cross-border initiatives and regional efforts in southern Africa. Currently, Angola aims to consolidate malaria control and to accelerate the transition from control to pre-elimination, along with other country members of the Elimination 8 initiative. However, the tremendous heterogeneity in malaria prevalence among Angolan provinces, as well as internal population movements and migration across borders, represent major challenges for the Angolan National Malaria Control Programme. This review aims to contribute to the understanding of factors underlying the complex malaria situation in Angola and to encourage future research studies on transmission dynamics and population structure of Plasmodium falciparum , important areas to complement host epidemiological information and to help reenergize the goal of malaria elimination in the country.
... Unsurprisingly, the DBLa-var relationship was weak when relationships were explored in relation to var exon 1 sourced from a larger geographical region (i.e., country-or continentspecific var exon 1, see Methods), showcasing the underlying effects of spatial variation that are also seen with other molecular markers such as SNPs (Amambua-Ngwa et al., 2019). This was evident from substantially reduced proportions of DBLa types with 1-to-1 DBLa-var relationships and increased proportions of DBLa types with 1-to-many DBLa-var relationships within these larger spatial contexts ( Figure S10 in Data Sheet 1). ...
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The enormous diversity and complexity of var genes that diversify rapidly by recombination has led to the exclusion of assembly of these genes from major genome initiatives (e.g., Pf6). A scalable solution in epidemiological surveillance of var genes is to use a small ‘tag’ region encoding the immunogenic DBLα domain as a marker to estimate var diversity. As var genes diversify by recombination, it is not clear the extent to which the same tag can appear in multiple var genes. This relationship between marker and gene has not been investigated in natural populations. Analyses of in vitro recombination within and between var genes have suggested that this relationship would not be exclusive. Using a dataset of publicly-available assembled var sequences, we test this hypothesis by studying DBLα- var relationships for four study sites in four countries: Pursat (Cambodia) and Mae Sot (Thailand), representing low malaria transmission, and Navrongo (Ghana) and Chikwawa (Malawi), representing high malaria transmission. In all study sites, DBLα- var relationships were shown to be predominantly 1-to-1, followed by a second largest proportion of 1-to-2 DBLα- var relationships. This finding indicates that DBLα tags can be used to estimate not just DBLα diversity but var gene diversity when applied in a local endemic area. Epidemiological applications of this result are discussed.
... A second chloroquine-associated peak found on chromosome 6 is a novel result in this geographic region. The peak contains (in the case of Ecuador) or is adjacent to (for Colombia) amino acid transporter 1 (aat1, Pf3D7_0629500), which has been identified as mediating resistance to chloroquine and other drugs [43,44] and as being under selection in natural populations [45,46]. In this data set, we observe a high-frequency derived allele that causes a nonsynonymous serine to leucine change at amino acid 258 (S258L), which falls within the protein's predicted transmembrane domain. ...
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The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P . falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring less genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to changes in drug regime. Using newly sequenced whole genomes, we measure relatedness between 166 parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore past selection events in the region. Two genes associated with chloroquine resistance, crt and aat1 , show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci ( dhps , mdr1 , and dhfr ). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in small populations, as will occur in any region nearing malaria elimination.
... Resistance to Sulfadoxine-pyrimethamine (SP), caused by mutations in the target genes dhfr and dhps [21][22][23][24][25], threatens the efficacy of intermittent preventive therapy in pregnancy (SP-IPTp) and seasonal malaria chemoprevention (SMC) in young children (used in combination with amodiaquine, SP+AQ) [26]; these are important public health interventions to protect vulnerable populations in hyperendemic regions. Parasite genome sequencing, incorporated into surveillance programmes, can provide key information to guide National Malaria Control Programme (NMCP) decision-making; for example, describing the geospatial distribution and longitudinal trends of antimalarial resistance markers [27][28][29][30] and P. falciparum population structure and relatedness [31][32][33][34][35]. ...
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Malaria is a global public health priority causing over 600,000 deaths annually, mostly young children living in Sub-Saharan Africa. Molecular surveillance can provide key information for malaria control, such as the prevalence and distribution of antimalarial drug resistance. However, genome sequencing capacity in endemic countries can be limited. Here, we have implemented an end-to-end workflow for Plasmodium falciparum genomic surveillance in Ghana using Oxford Nanopore Technologies, targeting antimalarial resistance markers and the leading vaccine antigen circumsporozoite protein (csp). The workflow was rapid, robust, accurate, affordable and straightforward to implement. We found that P. falciparum parasites in Ghana had become largely susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine (SP) resistance, and no evidence of artemisinin resistance. Multiple Single Nucleotide Polymorphism (SNP) differences from the vaccine csp sequence were identified, though their significance is uncertain. This study demonstrates the potential utility and feasibility of malaria genomic surveillance in endemic settings using Nanopore sequencing.
... Previous reports had also indicated that malaria parasites in Ethiopia have moderate levels of genetic diversity and a similar population structure of the parasite [32]. They presented the lowest levels of heterozygosity in a continent-wide P. falciparum genomic analysis [33], indicating the need to further determine how they have evolved and are responding to the general interventions recommended for all malaria populations. ...
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Background Genetic diversity of malaria parasites can inform the intensity of transmission and poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity would provide essential information about the ongoing control efforts. This study aimed to explore allelic polymorphism of merozoite surface protein 1 ( msp1 ) and merozoite surface protein 2 ( msp2 ) to determine the genetic diversity and multiplicity of Plasmodium falciparum infections circulating in high and low transmission sites in western Ethiopia. Methods Parasite genomic DNA was extracted from a total of 225 dried blood spots collected from confirmed uncomplicated P. falciparum malaria-infected patients in western Ethiopia. Of these, 72.4% (163/225) and 27.6% (62/225) of the samples were collected in high and low transmission areas, respectively. Polymorphic msp1 and msp2 genes were used to explore the genetic diversity and multiplicity of falciparum malaria infections. Genotyping of msp1 was successful in 86.5% (141/163) and 88.7% (55/62) samples collected from high and low transmission areas, respectively. Genotyping of msp2 was carried out among 85.3% (139/163) and 96.8% (60/62) of the samples collected in high and low transmission sites, respectively. Plasmodium falciparum msp1 and msp2 genes were amplified by nested PCR and the PCR products were analysed by QIAxcel ScreenGel Software. A P-value of less or equal to 0.05 was considered significant. Results High prevalence of falciparum malaria was identified in children less than 15 years as compared with those ≥ 15 years old (AOR = 2.438, P = 0.005). The three allelic families of msp1 (K1, MAD20, and RO33) and the two allelic families of msp2 (FC27 and 3D7), were observed in samples collected in high and low transmission areas. However, MAD 20 and FC 27 alleles were the predominant allelic families in both settings. Plasmodium falciparum isolates circulating in western Ethiopia had low genetic diversity and mean MOI. No difference in mean MOI between high transmission sites (mean MOI 1.104) compared with low transmission area (mean MOI 1.08) (p > 0.05). The expected heterozygosity of msp1 was slightly higher in isolates collected from high transmission sites (He = 0.17) than in those isolates from low transmission (He = 0.12). However, the heterozygosity of msp 2 was not different in both settings ( Pfmsp2 : 0.04 in high transmission; pf msp2 : 0.03 in low transmission). Conclusion Plasmodium falciparum from clinical malaria cases in western Ethiopia has low genetic diversity and multiplicity of infection irrespective of the intensity of transmission at the site of sampling. These may be signaling the effectiveness of malaria control strategies in Ethiopia; although further studies are required to determine how specific intervention strategies and other parameters that drive the pattern.
Le paludisme est une maladie parasitaire causée par diverses espèces de Plasmodium ; P. falciparum étant l'espèce la plus répandue et responsable des cas mortels de la maladie. Les enfants âgés de moins de cinq ans et les femmes enceintes représentent les couches les plus vulnérables de la population en raison de l'acquisition progressive de l'immunité protectrice chez les enfants et de la susceptibilité accrue des femmes enceintes primigestes aux infections palustres. En l'absence d'un vaccin homologué par l'OMS pour lutter contre la maladie, une stratégie de lutte définie en trois axes a été mise en oeuvre pour aider à l'élimination du paludisme. Il s'agit de la lutte anti-vectorielle, le diagnostic et le traitement (l'utilisation des TDRs et combinaisons thérapeutiques à base d'artémisinine (CTAs)) et enfin, les traitements préventifs intermittents (TPI) pour les populations à risque. La mise en place globale de ces stratégies a contribué à la diminution importante de la mortalité liée au paludisme. Cependant, ces efforts se heurtent à l'émergence et à la propagation de la résistance à la SP (recommandée dans le TPI) ainsi qu'à celle de l'artémisinine et ses composés partenaires (recommandé en première intention dans le traitement du paludisme). La résistance aux antipaludiques a été d'abord observée au Cambodge, puis s'est étendue à une grande partie de l'Asie du Sud-Est pour enfin apparaître de façon spontanée en Afrique l'Est. Si cette perte de l'efficacité des CTAs venait à se répandre dans toute l'Afrique, les conséquences seraient dramatiques en termes de santé publique. C'est pourquoi des outils de surveillance permettant la détection précoce de la résistance à l'artémisinine doivent être mises en place pour mieux orienter les mesures d'interventions. Cette thèse vise à utiliser les technologies de séquençage, pour évaluer la pression de sélection exercée par deux traitements recommandés par l'OMS en zone d'endémie palustre (le TPI et les CTAs). La première partie de ce travail est subdivisée en deux sous parties. Dans un premier temps, il s'est agi de confirmer les effets bénéfiques sur les nouveau-nés de la prise d'un nombre supérieur ou égal à 3 doses de traitement préventif intermittent avec la sulfadoxine pyriméthamine (TPI-SP) par les femmes enceintes. Ensuite, de montrer grâce à la technologie de séquençage Sanger que cette prise de TPI-SP exerçait une sélection sur des parasites porteurs de mutations associées à la résistance à cette combinaison thérapeutique. L'essentiel des travaux de cette partie a été menée au Ghana, pays endémique au paludisme et qui très tôt a adopté la nouvelle politique d'utilisation du TPI-SP qui consiste en une prise mensuelle de la SP après le troisième mois de grossesse. La deuxième partie de ce manuscrit de thèse nous a permis dans un premier temps de comparer le génome entier des parasites collectés avant et après traitement aux dérivés d'artémisinine ; et dans un second temps de montrer grâce à la méthode du targeted amplicon deep sequencing la possibilité d'une sélection des parasites porteurs de mutations associées à la résistance aux dérivés d'artémisinine quelques heures après un traitement aux CTAs. Pour aider à l'atteinte des objectifs visés, une méthode de filtration visant à améliorer la qualité des résultats de séquençage d'ADN grâce à la technologie illumina a été mise en place. Les travaux issus de cette deuxième partie ont été menés grâce aux échantillons collectés au Bénin chez des enfants souffrant de paludisme simple et de paludisme grave. L'ensemble des travaux présentés dans ce manuscrit s'inscrit dans une stratégie de surveillance de la résistance aux antipaludiques pouvant permettre de mieux adapter les traitements antipaludiques afin de limiter la sélection de parasites résistants.
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Over the past 15 years, Zanzibar has made great strides toward malaria elimination; yet progress has stalled. Parasite genetic data of Plasmodium falciparum may inform strategies for malaria elimination by helping to identify contributory factors to parasite persistence. Here we elucidate fine-scale parasite population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. We sequenced 518 P. falciparum samples from 5 districts covering both main islands using a novel, highly multiplexed droplet digital PCR (ddPCR)-based amplicon deep sequencing method targeting 35 microhaplotypes and drug-resistance loci. Despite high genetic diversity, we observe strong fine-scale spatial and temporal structure of local parasite populations, including isolated populations on Pemba Island and genetically admixed populations on Unguja Island, providing evidence of ongoing local transmission. We observe a high proportion of highly related parasites in individuals living closer together, including between clinical index cases and the mostly asymptomatic cases surrounding them, consistent with isolation-by-distance. We identify a substantial fraction (2.9%) of related parasite pairs between Zanzibar, and mainland Tanzania and Kenya, consistent with recent importation. We identify haplotypes known to confer resistance to known antimalarials in all districts, including multidrug-resistant parasites, but most parasites remain sensitive to current first-line treatments. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and reveals actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination.
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Plasmodium malariae , a neglected human malaria parasite, contributes up to 10% of malaria infections in sub-Saharan Africa (sSA). Though P. malariae infection is considered clinically benign, it presents mostly as coinfections with the dominant P. falciparum . Completion of its reference genome has paved the way to further understand its biology and interactions with the human host, including responses to antimalarial interventions. We characterized 75 P. malariae isolates from seven endemic countries in sSA using highly divergent microsatellites. The P. malariae infections were highly diverse and five subpopulations from three ancestries (independent of origin of isolates) were determined. Sequences of 11 orthologous antimalarial resistance genes, identified low frequency single nucleotide polymorphisms (SNPs), strong linkage disequilibrium between loci that may be due to antimalarial drug selection. At least three sub-populations were detectable from a subset of denoised SNP data from mostly the mitochondrial cytochrome b coding region. This evidence of diversity and selection calls for including P. malariae in malaria genomic surveillance towards improved tools and strategies for malaria elimination.
Le paludisme est une maladie infectieuse parasitaire causée par diverses espèces de Plasmodium, P. falciparum étant l'espèce la plus répandue et responsable des cas mortels de la maladie. Les traitements actuels reposent sur des combinaisons thérapeutiques à base d'artémisinine (CTA), couplant un dérivé d'artémisinine (ARTD) à une autre molécule antipaludique. Des parasites résistants aux ARTDs ont émergé en Asie du sud-est ; ceux-ci sont encore non détectés en Afrique. La résistance se traduit par une durée d'élimination des parasites allongée, et est conférée par des mutations non-synonymes localisées sur le domaine Kelch-repeat propeller (KREP) de la protéine P. falciparum K13 (PfK13). Similairement, de multiples mutations non-synonymes sur le transporteur P. falciparum Chloroquine Resistance Transporter (PfCRT) confèrent la résistance à la chloroquine (CQ, ancien traitement) et à la pipéraquine (PPQ, une des molécules partenaires dans les CTAs actuels). Le rôle physiologique de ces protéines, essentielles durant le développement du parasite, demeure mal connu. Ce travail de thèse a donc pour objectif de mieux caractériser PfK13 et PfCRT : i) en prédisant les positions qui seraient impliquées dans des interactions protéine-substrat ; et ii) en étudiant les altérations structurales et physico-chimiques induites par les mutations de résistance. Selon les concepts liés à la théorie de l'évolution moléculaire, les mutations touchant des sites exerçant une fonction critique au sein d'une protéine essentielle sont éliminées par la sélection purificatrice. Ces sites sont donc plus conservés que le reste de la protéine. Par des approches bioinformatiques couplant évolution et structure tertiaire, nous avons mis en évidence des régions extrêmement conservées au sein de PfK13 et PfCRT. En comparant ces résultats avec les données expérimentales de protéines / domaines appartenant aux mêmes familles structurales, nous avons identifié plusieurs sites de PfK13 et PfCRT que nous proposons comme candidats pour des interactions protéine-substrat. À notre surprise, les mutations de résistance aux ARTDs ne sont pas localisées à la surface d'interaction que nous avons prédite sur le domaine KREP de PfK13. Les dynamiques moléculaires que nous avons réalisées sur deux mutations de résistance (C580Y et R539T) ont révélé des déstabilisations structurales locales du domaine KREP. Nous supposons que ces mutations pourraient perturber la stabilité du domaine KREP et ainsi diminuer l'abondance cellulaire de PfK13. Concernant PfCRT, les deux modèles de structure tertiaire, prédits par homologie structurale, montrent que la majorité des mutations de résistance à la CQ et à la PPQ sont localisées au niveau d'une poche probable de liaison que nous avons identifiée au coeur du transporteur. Ces mutations altèrent fortement le potentiel électrostatique à la surface de cette poche, passant d'un potentiel neutre à un potentiel électronégatif. Ce changement de propriété physico-chimique de la poche du transporteur est probablement un déterminant majeur de l'acquisition de la propriété de transport de la CQ di-protonée de la vacuole digestive vers le cytoplasme du parasite. Les sites fonctionnels candidats de PfCRT et PfK13 identifiés doivent maintenant être validés par des approches expérimentales. Nous avons initié des approches biochimiques dites de pull-down différentiels pour le domaine KREP de PfK13. Dans un premier temps, certains domaines PfK13, fusionnés à la glutathion S-transférase (GST), ont été exprimés dans la bactérie Escherichia coli, purifiés, puis incubés avec un lysat parasitaire total afin de caractériser des protéines interagissant avec PfK13. Les mises au point de ces expériences se poursuivent. Dans un second temps, des approches génétiques directement chez le parasite, par des techniques de transfection et d'édition de gènes, seront mises en place pour tester l'importance des sites fonctionnels candidats.
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Transmission dynamics is an important indicator for malaria control and elimination. As we move closer to eliminating malaria in Sub-Saharan Africa (sSA), transmission indices with higher resolution (genomic approaches) will complement our current measurements of transmission. Most of the present programmatic knowledge of malaria transmission patterns are derived from assessments of epidemiologic and clinical data, such as case counts, parasitological estimates of parasite prevalence, and Entomological Inoculation Rates (EIR). However, to eliminate malaria from endemic areas, we need to track changes in the parasite population and how they will impact transmission. This is made possible through the evolving field of genomics and genetics, as well as the development of tools for more in-depth studies on the diversity of parasites and the complexity of infections, among other topics. If malaria elimination is to be achieved globally, country-specific elimination activities should be supported by parasite genomic data from regularly collected blood samples for diagnosis, surveillance and possibly from other programmatic interventions. This presents a unique opportunity to track the spread of malaria parasites and shed additional light on intervention efficacy. In this review, various genetic techniques are highlighted along with their significance for an enhanced understanding of transmission patterns in distinct topological settings throughout Sub-Saharan Africa. The importance of these methods and their limitations in malaria surveillance to guide control and elimination strategies, are explored.
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Abstract Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3′-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.
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Background: Passive surveillance of malaria in health facilities remains vital for implementation of control and elimination programs. It is therefore essential understanding current age profile of clinical malaria morbidity, mortality and presentations in areas with variant infection susceptibility. This study aimed at understanding the current malaria morbidity and mortality in Western Kenya. Methods: Surveillance of clinical and asymptomatic parasitological positivity rates of all malaria suspected patients and school children were respectively determined from June 2015 to August 2016. From 2014 to 2016, register books in hospitals were referred and the confirmed malaria cases in conjunction with total number of monthly outpatient visits (OPD) counted. All registered malaria admissions were counted together with other causes of admissions. Moreover, outcome of malaria admissions in terms of discharge or death was recorded using inpatient charts within the same time frame. Prospective surveillance of severe malaria collected information on clinical features of the disease. Giemsa stained blood slides confirmed existence of malaria parasitemia. Chi-square and analysis of variance tests were used, respectively, to compute proportions and means; then a comparison was made between different age groups, periods, and study areas. Results: During the survey of asymptomatic infections among school children, overall blood slide positivity ranged from 6.4% at the epidemic prone site to 38.3% at the hyperendemic site. During the clinical malaria survey, school age children (5-14) presented with overall the highest (45%) blood slide positivity rate among those suspected to have the infection at the epidemic prone study site. The survey of all malaria confirmed and registered cases at OPD found 17% to 27% of all consultations among <5 children and 9.9% to 20.7% of all OPD visits among the ≥5 patients were due to malaria. Moreover, survey of all registered causes of admission in hospitals found 47% of admissions were due to malaria. The disease was a major cause of admission in epidemic prone setting where 63.4% of the <5 children and 62.8% of the ≥5 patients were admitted due to malaria (p>0.05) and 40% of all malaria admissions were school age children. Malaria related death rate was highest among <5 years at the hyperendemic site, that is 60.9 death per 1000 malaria <5 admissions. Conversely, the epidemic prone setting experienced highest malaria related death among ≥15 years (18.6 death per 1000 admissions) than the < 15 years (5.7 death per 1000 admissions of the <15 years) (p< 0.001). Surveillance of severe form of the disease found that hyperpyrexia, hyperparastemia, prostration and convulsions as common presentations of severe disease. Conclusion: Malaria is still the major cause of hospital consultations in Western Kenya with an alarming number of severe forms of the disease among the school aged children at the epidemic prone setting. Mortalities were higher among <5 children years in high infection transmission setting and among ≥15 years in low and moderate transmission settings. Surveillance of asymptomatic and symptomatic malaria along with evaluation of current interventions in different age groups should be implemented in Kenya.
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Genome sequences of 247 Plasmodium falciparum isolates collected in The Gambia in 2008 and 2014 were analysed to identify changes possibly related to the scale-up of antimalarial interventions that occurred during this period. Overall, there were 15 regions across the genomes with signatures of positive selection. Five of these were sweeps around known drug resistance and antigenic loci. Signatures at antigenic loci such as thrombospodin related adhesive protein (Pftrap) were most frequent in eastern Gambia, where parasite prevalence and transmission remain high. There was a strong temporal differentiation at a non-synonymous SNP in a cysteine desulfarase (Pfnfs) involved in iron-sulphur complex biogenesis. During the 7-year period, the frequency of the lysine variant at codon 65 (Pfnfs-Q65K) increased by 22% (10% to 32%) in the Greater Banjul area. Between 2014 and 2015, the frequency of this variant increased by 6% (20% to 26%) in eastern Gambia. IC50 for lumefantrine was significantly higher in Pfnfs-65K isolates. This is probably the first evidence of directional selection on Pfnfs or linked loci by lumefantrine. Given the declining malaria transmission, the consequent loss of population immunity, and sustained drug pressure, it is important to monitor Gambian P. falciparum populations for further signs of adaptation.
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Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections. Using the inferred IBD status at genomic locations, we have also developed a novel statistic for identifying loci under positive selection and propose relatedness networks as a means of exploring shared haplotypes within populations. We evaluate the performance of our methodologies for detecting IBD and selection, including comparisons with existing tools, then perform an exploratory analysis of whole genome sequencing data from a global Plasmodium falciparum dataset of more than 2500 genomes. This analysis identifies Southeast Asia as having many highly related isolates, possibly as a result of both reduced transmission from intensified control efforts and population bottlenecks following the emergence of antimalarial drug resistance. Many signals of selection are also identified, most of which overlap genes that are known to be associated with drug resistance, in addition to two novel signals observed in multiple countries that have yet to be explored in detail. Additionally, we investigate relatedness networks over the selected loci and determine that one of these sweeps has spread between continents while the other has arisen independently in different countries. IBD analysis of microorganisms using isoRelate can be used for exploring population structure, positive selection and haplotype distributions, and will be a valuable tool for monitoring disease control and elimination efforts of many diseases.
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Dissecting Plasmodium drug resistance Malaria is a deadly disease with no effective vaccine. Physicians thus depend on antimalarial drugs to save lives, but such compounds are often rendered ineffective when parasites evolve resistance. Cowell et al. systematically studied patterns of Plasmodium falciparum genome evolution by analyzing the sequences of clones that were resistant to diverse antimalarial compounds across the P. falciparum life cycle (see the Perspective by Carlton). The findings identify hitherto unrecognized drug targets and drug-resistance genes, as well as additional alleles in known drug-resistance genes. Science , this issue p. 191 ; see also p. 159
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The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease. To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa, and identified over 50 million single nucleotide polymorphisms within the accessible genome. These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size. Strong signals of recent selection were observed in insecticide-resistance genes, with several sweeps spreading over large geographical distances and between species. The design of new tools for mosquito control using gene-drive systems will need to take account of high levels of genetic diversity in natural mosquito populations.
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Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.
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The t-distributed stochastic neighbor embedding t-SNE is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot. We conclude that the ability for t-SNE to reveal population stratification at different scales could be useful for human genetic association studies.
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Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with local populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans. © 2017, American Association for the Advancement of Science. All rights reserved.
Dramatic changes in transmission intensity can impact Plasmodium population diversity. Using samples from 2 distant time-points in the Dielmo/Ndiop longitudinal cohorts from Senegal, we applied a molecular barcode tool to detect changes in parasite genotypes and complexity of infection that corresponded to changes in transmission intensity. We observed a striking statistically significant difference in genetic diversity between the 2 parasite populations. Furthermore, we identified a genotype in Dielmo and Ndiop previously observed in Thiès, potentially implicating imported malaria. This genetic surveillance study validates the molecular barcode as a tool to assess parasite population diversity changes and track parasite genotypes.