A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity

Table 1 Summary of DRC individual samples and population cluster samples PCR and amplicon deep sequencing results

Sample type	Number of samples	No. of pfldh qPCR positive samples (%)^a	No. of pfama1 PCR positive samples (%)	No. of samples with analysable deep sequence reads (%)^b
Individual	115	99 (86.1)	81 (70.4)	79 (68.7)
Population cluster	84	–	79 (94.0)	73 (86.9)

^aConcentrations of pfldh based on qPCR standard curve analysis ranged from less than 0.1 ng/ml to over 1000 ng/ml for individual samples
^bThe number of samples with analysable deep sequence reads was determined using the SeekDeep targeted amplicon analysis pipeline criteria and a 2.5% minimum haplotype frequency cutoff requirement for inclusion in analysis. The SeekDeep analysis pipeline excludes reads based on missing barcodes, short reads (< 50 bp), and poor quality/chimeric reads

ISSN: 1475-2875