Evolution and Transmission Dynamics of Wild Poliovirus in Pakistan and Afghanistan (2012-2023): implications for global polio eradication

Abstract Despite concerted global vaccination efforts, wild poliovirus remains endemic in two countries in 2024, Pakistan and Afghanistan. This study uses phylogeographic analysis of poliovirus genetic and epidemiological data from clinical and wastewater surveillance to identify the causes of poliovirus persistence and routes of spread over the last decade (2012 to 2023). Poliovirus genetic diversity declined post-2020, with the die-out of one of two major genetic clusters and recent detections are now close genetic relatives. We find that high-risk and hard-to-access regions have been key to persistent polio transmission over the past decade, supporting transmission when it had stopped elsewhere. Karachi, one of the most densely populated cities globally, has acted as a major hub for the amplification and spread of poliovirus to other regions, many of which we show to be dead-end for onwards transmission despite frequent virus detection. This information has been used to guide polio vaccination and surveillance.