Background

Significant progress has been made toward a poliovirus-free world since the creation of the Global Polio Eradication Initiative (GPEI) in 1988 [1]. GPEI efforts have resulted in the eradication of wild poliovirus (WPV) serotypes two (WPV2) and three (WPV3) and limited transmission of serotype one (WPV1) in Pakistan and Afghanistan [1]. However, the increased emergence of circulating vaccine-derived poliovirus (cVDPV) outbreaks and the continued circulation of WPV1 pose a continuous threat of international spread [2,3]. For example, WPV1 viruses showing a direct link to the viruses circulating in Pakistan have been isolated from stool samples collected in Malawi and Mozambique in November 2021 and March 2022, respectively (https://www.who.int/emergencies/disease-outbreak-news/item/wild-poliovirus-type-1-(WPV1)-malawi). Additionally, cVDPV serotype 2 (cVDPV2) isolates from environmental samples in five countries in the WHO European Region (EURO) have recently been genetically linked to cVDPV2 strains circulating in the World Health Organization (WHO) African Region (AFRO) [4].

The importation of WPV1 into WHO AFRO and the exportation of cVDPV2 from WHO AFRO to WHO EURO highlight the need to further strengthen surveillance and outbreak responses. Furthermore, there is a need for novel strategies to guide the implementation of more strategic and effective vaccination campaigns. Genetic sequencing of cVDPVs from stool and wastewater samples is a useful tool employed for the confirmation of poliovirus detection, identification of cVDPV origins, and tracking of geographic spreading patterns [5,6]. It is also important for the determination of appropriate and most effective vaccination strategies [6]. For example, it is possible to infer which cVDPV outbreak cases are due to local transmissions and which are more likely to be linked to chains of cVDPV transmission in other countries. Phylogeographic methods are based on Nextstrain real-time tracking of pathogen evolution (https://docs.nextstrain.org/en/latest/index.html) [7] and Bayesian evolutionary analysis sampling trees (BEAST) (https://beast.community/about) to infer the origins and geographic spread of cVDPVs between and within WHO AFRO countries [5]. These methods employ discrete trait analysis (DTA), which can provide information on the geographic history of viral spread and associated rates of transmission [5]. Starting from geolocated virus sequences, this approach allows inference of the location of internal nodes in phylogenetic trees [5,7]. DTA has previously been applied to inform viral diffusion for several infectious diseases, including SARS-CoV-2, human and animal influenza, Mpox, and Ebola (https://nextstrain.org), and is considered a powerful tool for molecular epidemiology of pathogens.

Regular updates of the cVDPV surveillance sequence data using phylogeographic visualization tools may provide insights into changes in poliovirus epidemiology, which can in turn guide the implementation of more strategic and effective supplementary immunization activities and improved outbreak response and surveillance. These analyses may be particularly relevant to halt the ongoing outbreaks of cVDPVs in WHO AFRO through improved surveillance and timely and effective outbreak response, possibly achieving the global poliovirus eradication efforts of the GPEI. With this goal in mind, we created a comprehensive protocol for the phylogenetic and phylogeographic analysis of poliovirus sequence datasets using Nextstrain [7], a powerful open-source tool for the real-time interactive visualization of genome sequencing data. Approaches for phylogeographic visualization of poliovirus in WHO AFRO are detailed in this protocol.