Schistosoma mansoni, ND

Confirmatory S. mansoni ND View in CoL 5 genotyping

All samples that successfully amplified all three target loci were subjected to a secondary singleplex PCR

to amplify only the S. mansoni ND 5 locus for Sanger sequencing [ 24]. Amplicons were visualised in the same manner as for the multiplex molecular xenomonitoring PCRs. Schistosoma mansoni ND 5 PCR products were purified as described above and Sanger sequenced in the forward direction using a dilution of the ND52 forward primer. Sequence data were visualised, trimmed, edited and identified as described above.

Templeton Crandall and Sing haplotype network To assess S. mansoni ND 5 diversity, we performed a haplotype analysis using all generated S. mansoni ND 5 sequence data. To do this, a MAFFT alignment was performed using sequence data within Geneious Prime (default MAFFT parameter settings). Te MAFFT alignment was then visualised, examined and edited as described above. Te alignment was then exported from Geneious Prime in Nexus file format and imported into PopART version 1.7. Within PopART, a TCS haplotype network was generated to allow examination of haplotype group structuring.