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. 2025 Jul 5;15(13):e5376.
doi: 10.21769/BioProtoc.5376.

Visualization of the Evolution and Transmission of Circulating Vaccine-Derived Poliovirus (cVDPV) Outbreaks in the African Region

Collins D Owuor  1 , Brook Tesfaye  1 , Arthur Yannick Doungmo Wakem  1 , Sakma Kabore  1 , Caroline Obianuju Ikeonu  1 , Mariette Egbonoumi Fifatin Glitho Epse Doussoh  1 , Priscilla Epse Mosoke Bobimwoh Sigala  1 , Idris Ibrahim Ibrahim  1 , Abdullateef Jimoh  1 , Idah Ndumba  1 , Jermaine Khumalo  1 , David O Oviaesu  1 , Cheroigin Kipchirchir  1 , Carolyne Gathenji  1 , John Kipterer  1 , Kebba Touray  1 , Hamisu Abdullahi  1 , Kathleen Rankin  2 , Ousmane M Diop  3 , Julius E Chia  1 , Ndoutabe Modjirom  1 , Jamal A Ahmed  3 , Anfumbom K W Kfutwah  1
Affiliations

Visualization of the Evolution and Transmission of Circulating Vaccine-Derived Poliovirus (cVDPV) Outbreaks in the African Region

Collins D Owuor et al. Bio Protoc. .

Abstract

Since the creation of the Global Polio Eradication Initiative (GPEI) in 1988, significant progress has been made toward attaining a poliovirus-free world. This has 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. However, the increased emergence of circulating vaccine-derived poliovirus (cVDPV) and the continued circulation of WPV1, although limited to two countries, pose a continuous threat of international spread of poliovirus. These challenges highlight the need to further strengthen surveillance and outbreak responses, particularly in the African Region (AFRO). 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. We created a comprehensive protocol for the phylogeographic analysis of polioviruses using Nextstrain, a powerful open-source tool for real-time interactive visualization of virus sequencing data. It is expected that this protocol will support poliovirus elimination strategies in AFRO and contribute significantly to global eradication strategies. These tools have been utilized for other pathogens of public health importance, for example, SARS-CoV-2, human influenza, Ebola, and Mpox, among others, through real-time tracking of pathogen evolution (https://nextstrain.org), harnessing the scientific and public health potential of pathogen genome data. Key features • Employs Nextstrain (https://nextstrain.org), which is an open-source tool for real-time interactive visualization of genome sequencing datasets. • First comprehensive protocol for the phylogeographic analysis of poliovirus sequences collected from countries in the World Health Organization (WHO) African Region (AFRO). • Phylogeographic visualization may provide insights into changes in poliovirus epidemiology, which can in turn guide the implementation of more strategic and effective vaccination campaigns. • This protocol can be deployed locally on a personal computer or on a Microsoft Azure cloud server for high throughput.

Keywords: African Region (AFRO); Poliovirus; VP1 gene; cVDPV; phylogeography.

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Conflict of interest statement

Competing interestsNo competing interests to be declared.

Figures

Figure 1.
Figure 1.. Different steps described in this protocol and the Augur modules used in each of the analysis steps
Figure 2.
Figure 2.. Sample record for poliovirus accession number PQ497685 strain in the sequences.fasta format
Figure 3.
Figure 3.. Summary screenshot of the lat_longs.tsv file required by Nextstrain for visualizing geographic traits
Figure 4.
Figure 4.. Nextstrain visualization output showing phylogeny and inferred transmissions
See this image and copyright information in PMC

References

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