Population genomics of Onchocerca volvulus
Nodules containing nematodes were surgically extracted pre-ivermectin treatment or 80 days post-ivermectin treatment. Nodules were treated with collagenase and individual females removed. DNA was extracted from the posterior end of each worm (i.e., from non-reproductive tissue). Worms from Cameroon (N = 96) were sequenced using reduced representation enrichment. A design for NuGEN Allegro Targeted Genotyping (Tecan Genomics, Redwood City, California, USA) was developed based on regions identified as associated with sub-optimal response. Regions identified and not identified as associated with SOR were both included in the probe design, with an attempt to relatively evenly distribute the number of bp and the placement of target regions across each of the major chromosomes, excluding regions identified as containing repetitive sequence. Enriched libraries were prepared and sequenced at AGRF (Melbourne, Victoria, Australia) following manufacturers protocols.