Modeling malaria genomics reveals transmission decline and rebound in Senegal

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 22, 2015, Pages 7067-7072

  Daniels, Rachel F ^a,b   Schaffner, Stephen F ^c   Wenger, Edward A ^d   Proctor, Joshua L ^d   Chang, Hsiao Han ^a   Wong, Wesley ^a   Baro, Nicholas ^a   Ndiaye, Daouda ^e   Fall, Fatou Ba ^f   Ndiop, Medoune ^f   Ba, Mady ^f   Milner, Danny A ^a   Taylor, Terrie E ^g,h   Neafsey, Daniel E ^c   Volkman, Sarah K ^a,c,i   Eckhoff, Philip A ^d   Hartl, Daniel L ^a,b   Wirth, Dyann F ^a,c  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b HARVARD UNIVERSITY   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d INSTITUTE FOR DISEASE MODELING   (United States)

^e UNIVERSITÉ CHEIKH ANTA DIOP   (Senegal)

^f Senegal National Malaria Control Program   (Senegal)

^g MICHIGAN STATE UNIVERSITY   (United States)

^h UNIVERSITY OF MALAWI   (Malawi)

ⁱ SIMMONS COLLEGE   (United States)

Author keywords

Epidemiology; Genomics; Malaria

Indexed keywords

GENOMIC DNA; MITOCHONDRIAL DNA;

ARTICLE; CHROMOSOME 3; CHROMOSOME 9; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA BARCODING; EFFECTIVE POPULATION SIZE; FEMALE; GENE FREQUENCY; GENETIC DRIFT; GENETIC MODEL; GENETIC RECOMBINATION; GENOME; GENOME SIZE; GENOMICS; GENOTYPE; HUMAN; INBREEDING; INCIDENCE; MAJOR CLINICAL STUDY; MALARIA CONTROL; MALARIA FALCIPARUM; NONHUMAN; PARASITE TRANSMISSION; PLASMODIUM FALCIPARUM; POPULATION SIZE; PRIORITY JOURNAL; PROGRAM COST EFFECTIVENESS; REPRODUCTIVE SUCCESS; SENEGAL; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; EPIDEMIOLOGICAL MONITORING; GENETIC VARIABILITY; GENETICS; MALARIA; PARASITOLOGY; POPULATION GENETICS; PROCEDURES; TRANSMISSION;

PLASMODIUM FALCIPARUM;

EPIDEMIOLOGICAL MONITORING; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; HUMANS; MALARIA; MODELS, GENETIC; PLASMODIUM FALCIPARUM; SENEGAL;

EID: 84930618454     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1505691112     Document Type: Article

References (19)

1. Noor AM, et al. (2014) The changing risk of Plasmodium falciparum malaria infection in Africa: 2000-10: A spatial and temporal analysis of transmission intensity. Lancet 383(9930):1739-1747.
2. Mouzin E, Thior PM, Diouf MB, Sambou B (2010) Focus on Senegal Roll Back Malaria: Progress and Impact Series (World Health Organization, Geneva), Vol 4.
3. Daniels R, et al. (2008) A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking. Malar J 7:223.
4. Daniels R, et al. (2012) Rapid, field-deployable method for genotyping and discovery of single-nucleotide polymorphisms associated with drug resistance in Plasmodium falciparum. Antimicrob Agents Chemother 56(6):2976-2986.
5. Daniels R, et al. (2013) Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. PLoS ONE 8(4):e60780.
6. Chang HH, et al. (2013) Malaria life cycle intensifies both natural selection and random genetic drift. Proc Natl Acad Sci USA 110(50):20129-20134.
7. Eckhoff PA (2012) Malaria parasite diversity and transmission intensity affect development of parasitological immunity in a mathematical model. Malar J 11:419.
8. Steele SJ, Raftery AE, Emond MJ (2006) Computing normalizing constants for finite mixture models via incremental mixture importance sampling (IMIS). J Comput Graph Stat 15(3):712-734.
9. Raftery AE, Bao L (2010) Estimating and projecting trends in HIV/AIDS generalized epidemics using Incremental Mixture Importance Sampling. Biometrics 66(4):1162-1173.
10. Branch OH, et al. (2011) Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon. Mol Biol Evol 28(7):1973-1986.
11. Obaldia N, et al. (2015) Clonal Outbreak of Plasmodium falciparum Infection in Eastern Panama. J Infect Dis 211(7):1087-1096.
12. Nkhoma SC, et al. (2013) Population genetic correlates of declining transmission in a human pathogen. Mol Ecol 22(2):273-285.
13. Trape JF, et al. (2011) Malaria morbidity and pyrethroid resistance after the introduction of insecticide-treated bednets and artemisinin-based combination therapies: A longitudinal study. Lancet Infect Dis 11(12):925-932.
14. Kelly-Hope LA, McKenzie FE (2009) The multiplicity of malaria transmission: A review of entomological inoculation rate measurements and methods across sub-Saharan Africa. Malar J 8:19.
15. Ndiaye D, et al. (2013) Polymorphism in dhfr/dhps genes, parasite density and ex vivo response to pyrimethamine in Plasmodium falciparum malaria parasites in Thies, Senegal. Int. J. Parasitol. Drugs Drug. Resist 3:135-142.
16. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25:1754-1760.
17. Aurrecoechea CJ, et al. (2009) PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 37:D539-D543.
18. DePristo MA, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491-498.
19. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101(30):11030-11035.