Serigne-Fallu/Recent-molecular-epidemiology-of-non-polio-enteroviruses-in-Africa
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# 🧬 Recent Molecular Epidemiology of Human Non-Polio Enteroviruses in Africa
## 🧾 Overview
This repository contains all datasets, scripts, and analyses associated with our study on the **molecular epidemiology, circulation dynamics, and evolutionary patterns** of **human non-polio enteroviruses (NPEVs)** in Africa.
The project integrates:
* **Genomic sequences from GenBank**, and
* **Sequences generated by the Intercountry Reference Laboratory for Poliomyelitis at the Institut Pasteur de Dakar (IPD)**.
We applied a **Bayesian phylodynamic framework** to infer:
* Evolutionary rates
* Spatiotemporal diffusion
* Host-associated transmission
* Recombination dynamics
Our findings highlight **Africa’s central role in the global circulation** of NPEVs, as well as persistent gaps in surveillance across the continent.
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# 🌟 Highlights
• Circulation dynamics of human non-polio enteroviruses across Africa.
• Clear discrepancy in NPEV sequence submissions between global regions and Africa.
• EV-B exhibited a significantly higher substitution rate than other species.
• EV-A displayed the highest root height; EV-D emerged as the most recent lineage.
• The number of recombinant non-polio enterovirus sequences increased sharply after 1988.
• All NPEVs show evidence of **interspecies recombination**; EV-B and EV-C show **high rates of intra-species recombination**.
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# 📄 Abstract
Human non-polio enteroviruses (NPEVs) are major public health concerns due to frequent outbreaks and wide clinical manifestations. This study used genomic data to analyze the molecular epidemiology and circulation patterns of NPEVs in Africa, assess their host-associated dynamics, and investigate recombination events.
**Methods:**
Genomic data were obtained from GenBank and the Intercountry Reference Laboratory for Poliomyelitis (Institut Pasteur de Dakar). A Bayesian phylodynamic framework was used to infer temporal, spatial, and host-associated evolutionary patterns. Whole-genome se …
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