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. 2019 Nov 28;9:17790. doi: 10.1038/s41598-019-54203-0

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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PCR-correction outcomes by AmpSeq for three sample pairs from Day 0/Day X. Within-host haplotype frequencies are shown for AmpSeq markers ama1-D3, cpmp, and cpp, quantified in three replicates (Rep1 to Rep3) for each of the Day 0 and Day X samples. Different haplotypes of a marker are represented by different shapes and colours. Left panel represents a clear recrudescence because of concordant results by all 3 markers; middle panel: clear new infection; right panel: discordant results whereby result from marker ama1-D3 (NI) contrasts with that from cpmp (R) and cpp (R).