Integrating contact tracing and whole-genome sequencing to track the elimination of dog-mediated rabies: an observational and genomic study

Authors: Kennedy Lushasi*, Kirstyn Brunker*, Malavika Rajeev, Elaine A Ferguson, Gurdeep Jaswant, Laurie Baker, Roman Biek, Joel Changalucha, Sarah Cleaveland, Anna Czupryna, Anthony R Fooks, Nicodemus Govella, Daniel T Haydon, Paul Johnson, Rudovick Kazwala✢, Tiziana Lembo, Denise Marston, Msanif Masoud, Mathew Maziku, Eberhard Mbunda✢, Geofrey Mchau, Ally Z Mohamed, Emmanuel Mpolya, Chanasa Ngeleja, Kija Ng’abhi, Hesron Nonga, Khasim Omar, Kristyna Rysava, Maganga Sambo, Lwitiko Sikana, Rachel Steenson & Katie Hampson. * Equal contributions, ✢ Deceased

This repository contains all the code and de-identified data in this study.

Geographic masking was used to de-identify the spatial data on rabies transmission (mostly localized to households of either dog owners or persons bitten by rabid animals), by jittering XY locations within a 1km radius. Running the transmission tree code on these jittered data will therefore not generate precisely the same inferred progenitors as from the raw data because the very localized spatial structure is masked. The resulting (transmission) consensus trees are provided from the original raw data.

For more information: katie.hampson@glasgow.ac.uk