Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing

Jonathan J. Juliano, Kimberly Porter, Victor Mwapasa, Rithy Sem, William O. Rogers, Frédéric Ariey, Chansuda Wongsrichanaiai, Andrew Fraser Read, Steven R. Meshnick

Research output: Contribution to journalArticle

68 Citations (Scopus)

Abstract

Malaria infections commonly contain multiple genetically distinct variants. Mathematical and animal models suggest that interactions among these variants have a profound impact on the emergence of drug resistance. However, methods currently used for quantifying parasite diversity in individual infections are insensitive to low-abundance variants and are not quantitative for variant population sizes. To more completely describe the in-host complexity and ecology of malaria infections, we used massively parallel pyrosequencing to characterize malaria parasite diversity in the infections of a group of patients. By individually sequencing single strands of DNA in a complex mixture, this technique can quantify uncommon variants in mixed infections. The in-host diversity revealed by this method far exceeded that described by currently recommended genotyping methods, with as many as sixfold more variants per infection. In addition, in paired pre-and posttreatment samples, we show a complex milieu of parasites, including variants likely up-selected and down-selected by drug therapy. As with all surveys of diversity, sampling limitations prevent full discovery and differences in sampling effort can confound comparisons among samples, hosts, and populations. Here, we used ecological approaches of species accumulation curves and capture-recapture to estimate the number of variants we failed to detect in the population, and show that these methods enable comparisons of diversity before and after treatment, as well as between malaria populations. The combination of ecological statistics and massively parallel pyrosequencing provides a powerful tool for studying the evolution of drug resistance and the in-host ecology of malaria infections.

Original languageEnglish (US)
Pages (from-to)20138-20143
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number46
DOIs
StatePublished - Nov 16 2010

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Malaria
Infection
Population
Parasites
Ecology
Drug Resistance
Population Density
Complex Mixtures
Coinfection
Theoretical Models
Animal Models
Drug Therapy
DNA

All Science Journal Classification (ASJC) codes

  • General

Cite this

Juliano, Jonathan J. ; Porter, Kimberly ; Mwapasa, Victor ; Sem, Rithy ; Rogers, William O. ; Ariey, Frédéric ; Wongsrichanaiai, Chansuda ; Read, Andrew Fraser ; Meshnick, Steven R. / Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing. In: Proceedings of the National Academy of Sciences of the United States of America. 2010 ; Vol. 107, No. 46. pp. 20138-20143.
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Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing. / Juliano, Jonathan J.; Porter, Kimberly; Mwapasa, Victor; Sem, Rithy; Rogers, William O.; Ariey, Frédéric; Wongsrichanaiai, Chansuda; Read, Andrew Fraser; Meshnick, Steven R.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 107, No. 46, 16.11.2010, p. 20138-20143.

Research output: Contribution to journalArticle

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