Polio surveillance
The R code behind WHO AFRO's weekly polio surveillance bulletin, and the analysis tools I built with the Nigeria National Polio Emergency Operations Centre.
Automated polio surveillance reporting at WHO AFRO
Automated polio surveillance reporting at WHO AFRO
Problem
The WHO African Region reviews polio surveillance indicators every week across 47 Member States. The data sit in several systems, including POLIS, ACLED, the IOM Displacement Tracking Matrix, campaign records and modelled immunity estimates. Each source needs cleaning and checking before the data can be combined.
My contribution
I worked as an epidemiologist and data scientist at the WHO Regional Office for Africa from 2023 to 2025. I designed and built the weekly bulletin pipeline, which runs overnight in R. I wrote poliprep with Derrick Demeveng and contributed code to the US CDC packages sirfunctions and tidypolis. I also spent two months at the National Polio Emergency Operations Centre in Abuja, working with the WHO Nigeria Country Office. There I built an analytical platform and trained the national data team to maintain it.
Output
The pipeline produces a weekly bulletin of more than 60 pages, sent to over 500 recipients across the 47 AFRO Member States, GPEI, US CDC and the Gates Foundation.
The bulletin and the Nigeria platform contain operational surveillance data and are not reproduced here.
