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Background    Wolbachia  are intracellular bacteria found in arthropods and several filarial nematode species. The filarial  Wolbachia  have been proposed to be involved in the immunopathology associated with onchocerciasis. Higher  Wolbachia -to-nematode ratios have been reported in the savannah-ecotype compared to the forest-ecotype, and have been interpreted as consistent with a correlation between  Wolbachia  density and disease severity. However, factors such as geographic stratification and ivermectin drug exposure can lead to significant genetic heterogeneity in the nematode host populations, so we investigated whether  Wolbachia  copy number variation is also associated with these underlying factors.    Methods  Genomic DNA was prepared from single adult nematodes representing forest and savannah ecotypes sampled from Togo, Ghana, Côte d’Ivoire and Mali. A qPCR assay was developed to measure the number of  Wolbachia  genome(s) per nematode genome. Next-generation sequencing (NGS) was also used to measure relative  Wolbachia  copy number, and independently verify the qPCR assay.    Results  Significant variation was observed within the forest (range: 0.02 to 452.99; median: 10.58) and savannah (range: 0.01 to 1106.25; median: 9.10) ecotypes, however, no significant difference between ecotypes ( P =  0.645) was observed; rather, strongly significant  Wolbachia  variation was observed within and between the nine study communities analysed ( P  = 0.021), independent of ecotype. Analysis of ivermectin-treated and untreated nematodes by qPCR showed no correlation ( P =  0.869); however, an additional analysis of a subset of the nematodes by qPCR and NGS revealed a correlation between response to ivermectin treatment and  Wolbachia  copy number ( P  = 0.020).    Conclusions  This study demonstrates that extensive within and between population variation exists in the  Wolbachia  content of individual adult  O. volvulus . The origin and functional significance of such variation (up to ~ 100,000-fold between worms; ~10 to 100-fold between communities) in the context of the proposed mutualistic relationship between the worms and the bacteria, and between the presence of  Wolbachia  and clinical outcome of infection, remains unclear. These data do not support a correlation between  Wolbachia  copy number and forest or savannah ecotype, and may have implications for the development of anti- Wolbachia  drugs as a macrofilaricidal treatment of onchocerciasis. The biological significance of a correlation between variation in  Wolbachia  copy number and ivermectin response remains unexplained.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2126-4) contains supplementary material, which is available to authorized users.

Significant heterogeneity in Wolbachia copy number within and between populations of Onchocerca volvulus