Population genomics of ancient and modern Trichuris trichiura

Doyle, S. R.; Soe, M. J.; Nejsum, P.; Betson, M.; Cooper, P. J.; Peng, L.; Zhu, X.-Q.; Sanchez, A.; Matamoros, G.; Sandoval, G. A. F.; Cutillas, C.; Tchuem Tchuente, L.-A.; Mekonnen, Z.; Ame, S. M.; Namwanje, H.; Levecke, B.; Berriman, M.; Fredensborg, B. L.; Kapel, C. M. O.

doi:10.1101/2021.10.21.464505

bioRxiv · 10.1101/2021.10.21.464505

Population genomics of ancient and modern Trichuris trichiura

Doyle, S. R.·Soe, M. J.·Nejsum, P.·Betson, M.·Cooper, P. J.·Peng, L.·Zhu, X.-Q.·Sanchez, A.·Matamoros, G.·Sandoval, G. A. F.·Cutillas, C.·Tchuem Tchuente, L.-A.·Mekonnen, Z.·Ame, S. M.·Namwanje, H.·Levecke, B.·Berriman, M.·Fredensborg, B. L.·Kapel, C. M. O.

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Abstract

The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.

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Doyle, S. R., Soe, M. J., Nejsum, P., Betson, M., Cooper, P. J., Peng, L., Zhu, X.-Q., Sanchez, A., Matamoros, G., Sandoval, G. A. F., Cutillas, C., Tchuem Tchuente, L.-A., Mekonnen, Z., Ame, S. M., Namwanje, H., Levecke, B., Berriman, M., Fredensborg, B. L., Kapel, C. M. O.. 2021-10-21. Population genomics of ancient and modern Trichuris trichiura. https://doi.org/10.1101/2021.10.21.464505

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