Characterization of within-host plasmodium falciparum diversity using next-generation sequence data

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Auburn, Sarah ^a,b   Campino, Susana ^a   Miotto, Olivo ^c,d   Djimde, Abdoulaye A ^e   Zongo, Issaka ^f   Manske, Magnus ^a   Maslen, Gareth ^a   Mangano, Valentina ^g   Alcock, Daniel ^a   MacInnis, Bronwyn ^a   Rockett, Kirk A ^a,h   Clark, Taane G ^a,i   Doumbo, Ogobara K ^e   Ouédraogo, Jean Bosco ^f   Kwiatkowski, Dominic P ^a,c,h  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b MENZIES SCHOOL OF HEALTH RESEARCH   (Australia)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d MAHIDOL UNIVERSITY   (Thailand)

^e UNIVERSITY OF BAMAKO   (Mali)

^f Public Health Research Institute for Health Sciences   (Burkina Faso)

^g SAPIENZA UNIVERSITY OF ROME   (Italy)

^h UNIVERSITY OF OXFORD   (United Kingdom)

ⁱ LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ARTICLE; CONTROLLED STUDY; GENE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HOST PARASITE INTERACTION; MOLECULAR CLONING; MSP 1 GENE; MSP 2 GENE; NONHUMAN; PARASITE IDENTIFICATION; PARASITE ISOLATION; PLASMODIUM FALCIPARUM; POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; ANIMAL; BIODIVERSITY; BIOLOGICAL MODEL; BURKINA FASO; DNA SEQUENCE; GENETICS; GENOME; HUMAN; MALI; METHODOLOGY; STATISTICAL MODEL;

PLASMODIUM FALCIPARUM;

PARASITE ANTIGEN;

ALLELES; ANIMALS; ANTIGENS, PROTOZOAN; BIODIVERSITY; BURKINA FASO; GENETIC VARIATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALI; MODELS, GENETIC; MODELS, STATISTICAL; PLASMODIUM FALCIPARUM; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84857678104     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032891     Document Type: Article

References (38)

1. Hastings IM, D'Alessandro U, (2000) Modelling a predictable disaster: the rise and spread of drug-resistantmalaria. Parasitol Today 16: 340-347.
2. Contamin H, Fandeur T, Rogier C, Bonnefoy S, Konate L, et al. (1996) Different genetic characteristics of Plasmodium falciparum isolates collected during successive clinical malaria episodes in Senegalese children. Am J Trop Med Hyg 54: 632-643.
3. Forsyth KP, Philip G, Smith T, Kum E, Southwell B, et al. (1989) Diversity of antigens expressed on the surface of erythrocytes infected with mature Plasmodium falciparum parasites in Papua New Guinea. Am J Trop Med Hyg 41: 259-265.
4. Marsh K, Otoo L, Hayes RJ, Carson DC, Greenwood BM, (1989) Antibodies to blood stage antigens of Plasmodium falciparum in rural Gambians and their relation to protection against infection. Trans R Soc Trop Med Hyg 83: 293-303.
5. Newbold CI, Pinches R, Roberts DJ, Marsh K, (1992) Plasmodium falciparum: the human agglutinating antibody response to the infected red cell surface is predominantly variant specific. Exp Parasitol 75: 281-292.
6. Bell AS, de Roode JC, Sim D, Read AF, (2006) Within-host competition in genetically diverse malaria infections: parasite virulence and competitive success. Evolution 60: 1358-1371.
7. de Roode JC, Culleton R, Bell AS, Read AF, (2004) Competitive release of drug resistance following drug treatment of mixed Plasmodium chabaudi infections. Malar J 3: 33.
8. de Roode JC, Pansini R, Cheesman SJ, Helinski ME, Huijben S, et al. (2005) Virulence and competitive ability in genetically diverse malaria infections. Proc Natl Acad Sci U S A 102: 7624-7628.
9. Mackinnon MJ, Read AF, (2004) Virulence in malaria: an evolutionary viewpoint. Philos Trans R Soc Lond B Biol Sci 359: 965-986.
10. al-Yaman F, Genton B, Reeder JC, Anders RF, Smith T, et al. (1997) Reduced risk of clinical malaria in children infected with multiple clones of Plasmodium falciparum in a highly endemic area: a prospective community study. Trans R Soc Trop Med Hyg 91: 602-605.
11. Engelbrecht F, Togel E, Beck HP, Enwezor F, Oettli A, et al. (2000) Analysis of Plasmodium falciparum infections in a village community in Northern Nigeria: determination of msp2 genotypes and parasite-specific IgG responses. Acta Trop 74: 63-71.
12. Felger I, Smith T, Edoh D, Kitua A, Alonso P, et al. (1999) Multiple Plasmodium falciparum infections in Tanzanian infants. Trans R Soc Trop Med Hyg 93 (Suppl 1): 29-34.
13. Mayor A, Saute F, Aponte JJ, Almeda J, Gomez-Olive FX, et al. (2003) Plasmodium falciparum multiple infections in Mozambique, its relation to other malariological indices and to prospective risk of malaria morbidity. Trop Med Int Health 8: 3-11.
14. Owusu-Agyei S, Smith T, Beck HP, Amenga-Etego L, Felger I, (2002) Molecular epidemiology of Plasmodium falciparum infections among asymptomatic inhabitants of a holoendemic malarious area in northern Ghana. Trop Med Int Health 7: 421-428.
15. Smith T, Beck HP, Kitua A, Mwankusye S, Felger I, et al. (1999) Age dependence of the multiplicity of Plasmodium falciparum infections and of other malariological indices in an area of high endemicity. Trans R Soc Trop Med Hyg 93 (Suppl 1): 15-20.
16. Taylor LH, Walliker D, Read AF, (1997) Mixed-genotype infections of malaria parasites: within-host dynamics and transmission success of competing clones. Proc Biol Sci 264: 927-935.
17. Zwetyenga J, Rogier C, Tall A, Fontenille D, Snounou G, et al. (1998) No influence of age on infection complexity and allelic distribution in Plasmodium falciparum infections in Ndiop, a Senegalese village with seasonal, mesoendemic malaria. Am J Trop Med Hyg 59: 726-735.
18. Druilhe P, Daubersies P, Patarapotikul J, Gentil C, Chene L, et al. (1998) A primary malarial infection is composed of a very wide range of genetically diverse but related parasites. J Clin Invest 101: 2008-2016.
19. Portugal S, Carret C, Recker M, Armitage AE, Goncalves LA, et al. (2011) Host-mediated regulation of superinfection in malaria. Nat Med 17: 732-737.
20. Snounou G, Beck HP, (1998) The use of PCR genotyping in the assessment of recrudescence or reinfection after antimalarial drug treatment. Parasitol Today 14: 462-467.
21. Viriyakosol S, Siripoon N, Petcharapirat C, Petcharapirat P, Jarra W, et al. (1995) Genotyping of Plasmodium falciparum isolates by the polymerase chain reaction and potential uses in epidemiological studies. Bull World Health Organ 73: 85-95.
22. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
23. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
24. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732.
25. Bereczky S, Dolo A, Maiga B, Hayano M, Granath F, et al. (2006) Spleen enlargement and genetic diversity of Plasmodium falciparum infection in two ethnic groups with different malaria susceptibility in Mali, West Africa. Trans R Soc Trop Med Hyg 100: 248-257.
26. Soulama I, Nebie I, Ouedraogo A, Gansane A, Diarra A, et al. (2009) Plasmodium falciparum genotypes diversity in symptomatic malaria of children living in an urban and a rural setting in Burkina Faso. Malar J 8: 135.
27. Coene J, (1993) Malaria in urban and rural Kinshasa: the entomological input. Med Vet Entomol 7: 127-137.
28. Omumbo JA, Guerra CA, Hay SI, Snow RW, (2005) The influence of urbanisation on measures of Plasmodium falciparum infection prevalence in East Africa. Acta Trop 93: 11-21.
29. Kiwanuka GN, (2009) Genetic diversity in Plasmodium falciparum merozoite surface protein 1 and 2 coding genes and its implications in malaria epidemiology: a review of published studies from 1997-2007. J Vector Borne Dis 46: 1-12.
30. Havryliuk T, Ferreira MU, (2009) A closer look at multiple-clone Plasmodium vivax infections: detection methods, prevalence and consequences. Mem Inst Oswaldo Cruz 104: 67-73.
31. Anderson TJ, Haubold B, Williams JT, Estrada-Franco JG, Richardson L, et al. (2000) Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol Biol Evol 17: 1467-1482.
32. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, et al. (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
33. Forbes SH, Hogg JT, Buchanan FC, Crawford AM, Allendorf FW, (1995) Microsatellite evolution in congeneric mammals: domestic and bighorn sheep. Mol Biol Evol 12: 1106-1113.
34. Levinson G, Gutman GA, (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221.
35. Schlotterer C, (1998) Genome evolution: are microsatellites really simple sequences? Curr Biol 8: R132-134.
36. Juliano JJ, Porter K, Mwapasa V, Sem R, Rogers WO, et al. (2010) Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing. Proc Natl Acad Sci U S A 107: 20138-20143.
37. Auburn S, Campino S, Clark TG, Djimde AA, Zongo I, et al. (2011) An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing. PLoS One 6: e22213.
38. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.