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Longitudinal tracking of Plasmodium falciparum clones in complex infections by amplicon deep sequencing

View ORCID ProfileAnita Lerch, View ORCID ProfileCristian Koepfli, Natalie E. Hofmann, View ORCID ProfileJohanna H. Kattenberg, Anna Rosanas-Urgell, Inoni Betuela, Ivo Mueller, View ORCID ProfileIngrid Felger
doi: https://doi.org/10.1101/306860
Anita Lerch
1Swiss Tropical and Public Health Institute, Basel, Switzerland
2University of Basel, Basel, Switzerland
3Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
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  • ORCID record for Anita Lerch
Cristian Koepfli
3Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
4University of Melbourne, Parkville, Australia
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  • ORCID record for Cristian Koepfli
Natalie E. Hofmann
1Swiss Tropical and Public Health Institute, Basel, Switzerland
2University of Basel, Basel, Switzerland
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Johanna H. Kattenberg
5Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
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  • ORCID record for Johanna H. Kattenberg
Anna Rosanas-Urgell
5Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
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Inoni Betuela
5Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
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Ivo Mueller
3Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
4University of Melbourne, Parkville, Australia
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Ingrid Felger
1Swiss Tropical and Public Health Institute, Basel, Switzerland
2University of Basel, Basel, Switzerland
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  • ORCID record for Ingrid Felger
  • For correspondence: ingrid.felger@unibas.ch
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Abstract

Background Longitudinal tracking of individual Plasmodium falciparum strains in multi-clonal infections is essential for investigating infection dynamics of malaria. The traditional genotyping techniques did not permit tracking changes in individual clone density during persistent natural infections. Amplicon deep sequencing (Amp-Seq) offers a tool to address this knowledge gap.

Methods The sensitivity of Amp-Seq for relative quantification of clones was investigated using three molecular markers, ama1-D2, ama1-D3, and cpmp. Amp-Seq and length-polymorphism based genotyping were compared for their performance in following minority clones in longitudinal samples from Papua New Guinea.

Results Amp-Seq markers were superior to length-polymorphic marker msp2 in detecting minority clones (sensitivity Amp-Seq: 95%, msp2: 85%). Multiplicity of infection (MOI) by Amp-Seq was 2.32 versus 1.73 for msp2. The higher sensitivity had no effect on estimates of force of infection because missed minority clones were detected in preceding or succeeding bleeds. Individual clone densities were tracked longitudinally by Amp-Seq despite MOI>1, thus providing an additional parameter for investigating malaria infection dynamics.

Conclusion Amp-Seq based genotyping of longitudinal samples improves detection of minority clones and estimates of MOI. Amp-Seq permits tracking of clone density over time to study clone competition or the dynamics of specific, i.e. resistance-associated genotypes.

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    Posted April 30, 2018.
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    Longitudinal tracking of Plasmodium falciparum clones in complex infections by amplicon deep sequencing
    Anita Lerch, Cristian Koepfli, Natalie E. Hofmann, Johanna H. Kattenberg, Anna Rosanas-Urgell, Inoni Betuela, Ivo Mueller, Ingrid Felger
    bioRxiv 306860; doi: https://doi.org/10.1101/306860
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    Longitudinal tracking of Plasmodium falciparum clones in complex infections by amplicon deep sequencing
    Anita Lerch, Cristian Koepfli, Natalie E. Hofmann, Johanna H. Kattenberg, Anna Rosanas-Urgell, Inoni Betuela, Ivo Mueller, Ingrid Felger
    bioRxiv 306860; doi: https://doi.org/10.1101/306860

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