Modeling malaria genomics reveals transmission decline and rebound in Senegal.
To study the effects of malaria-control interventions on parasite population genomics, we examined a set of 1,007 samples of the malaria parasite Plasmodium falciparum collected in Thiès, Senegal between 2006 and 2013. The parasite samples were genotyped using a molecular barcode of 24 SNPs. About 35% of the samples grouped into subsets with identical barcodes, varying in size by year and sometimes persisting across years. The barcodes also formed networks of related groups. Analysis of 164 completely sequenced parasites revealed extensive sharing of genomic regions. In at least two cases we found first-generation recombinant offspring of parents whose genomes are similar or identical to genomes also present in the sample. An epidemiological model that tracks parasite genotypes can reproduce the observed pattern of barcode subsets. Quantification of likelihoods in the model strongly suggests a reduction of transmission from 2006-2010 with a significant rebound in 2012-2013. The reduced transmission and rebound were confirmed directly by incidence data from Thiès. These findings imply that intensive intervention to control malaria results in rapid and dramatic changes in parasite population genomics. The results also suggest that genomics combined with epidemiological modeling may afford prompt, continuous, and cost-effective tracking of progress toward malaria elimination.
Departments of Immunology and Infectious Diseases and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; rdaniels@hsph.harvard.edu dhartl@oeb.harvard.edu dfwirth@hsph.harvard.edu.
Rachel F
RF
Daniels
Broad Institute, Cambridge, MA 02142;
Stephen F
SF
Schaffner
Institute for Disease Modeling, Bellevue, WA 98005;
Edward A
EA
Wenger
Institute for Disease Modeling, Bellevue, WA 98005;
Joshua L
JL
Proctor
Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115; Epidemiology and.
Hsiao-Han
HH
Chang
Departments of Immunology and Infectious Diseases and.
Wesley
W
Wong
Departments of Immunology and Infectious Diseases and.
Nicholas
N
Baro
Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal;
Daouda
D
Ndiaye
Senegal National Malaria Control Program, BP 25 270 Dakar-Fann, Senegal;
Fatou Ba
FB
Fall
Senegal National Malaria Control Program, BP 25 270 Dakar-Fann, Senegal;
Medoune
M
Ndiop
Senegal National Malaria Control Program, BP 25 270 Dakar-Fann, Senegal;
Mady
M
Ba
Departments of Immunology and Infectious Diseases and.
Danny A
DA
Milner
College of Osteopathic Medicine, Michigan State University, East Lansing, MI, 48824; Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi; and.
Terrie E
TE
Taylor
Broad Institute, Cambridge, MA 02142;
Daniel E
DE
Neafsey
Departments of Immunology and Infectious Diseases and Broad Institute, Cambridge, MA 02142; School of Nursing and Health Sciences, Simmons College, Boston, MA, 02115.
Sarah K
SK
Volkman
Institute for Disease Modeling, Bellevue, WA 98005;
Philip A
PA
Eckhoff
Departments of Immunology and Infectious Diseases and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; rdaniels@hsph.harvard.edu dhartl@oeb.harvard.edu dfwirth@hsph.harvard.edu.
Daniel L
DL
Hartl
Departments of Immunology and Infectious Diseases and Broad Institute, Cambridge, MA 02142; rdaniels@hsph.harvard.edu dhartl@oeb.harvard.edu dfwirth@hsph.harvard.edu.
Dyann F
DF
Wirth
D062665:Epidemiological Monitoring; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D006801:Humans; D008288:Malaria / Q000453:epidemiology* / Q000469:parasitology* / Q000635:transmission; D008957:Models, Genetic; D010963:Plasmodium falciparum / Q000235:genetics*; D012675:Senegal / Q000453:epidemiology
epidemiology; genomics; malaria