# Using homologous network to identify reassortment risk in H5Nx avian influenza viruses

## TL;DR

This paper introduces a network-based method to assess reassortment risk in H5Nx avian influenza viruses, identifying key hosts and providing a framework for better surveillance and prevention.

## Contribution

A novel network approach is introduced to quantify and rank H5Nx reassortment risk using genomic data and community detection.

## Key findings

- An IAVs homologous network was constructed to embed reassortment history and estimate reassortment risk.
- Domestic poultry in China and wild birds in North America and Europe were identified as primary hosts contributing to reassortment.
- The study provides a framework for quantifying reassortment risk across different H5Nx viruses.

## Abstract

The resurgence of H5Nx reassortment has caused multiple epidemics resulting in severe disease even death in wild birds and poultry. Assessing H5Nx reassortment risk is crucial for designing targeted interventions and enhancing preparedness efforts to manage H5Nx outbreaks effectively. However, the complexity in H5Nx reassortment, driven by the diversity of influenza A viruses (IAVs) and wide range of hosts, has hindered the effective quantification of reassortment risk. In this study, we utilized a network approach to explore the reassortment history using a large-scale dataset. By inferring genomic homogeneity among IAVs, we constructed an IAVs homologous network with reassortment history embedded within it. We estimated the communities within the IAVs homologous network to represent the reassortment risk of various viruses, revealing diverse reassortment risks across different H5Nx viruses. Our analysis also identified the primary hosts contributing to reassortment: domestic poultry in China, and wild birds in North America and Europe. These primary hosts are critical targets for future H5Nx reassortment interventions. Our study provides a framework for quantifying and ranking H5Nx reassortment risk, contributing to enhanced preparedness and prevention efforts.

As an important evolutionary process, H5Nx reassortment has caused frequent epidemics, resulting in severe disease and even death in various species of wild birds and domestic poultry. Therefore, it is highly important to design effective prevention strategies against future potential H5Nx reassortment. Assessing reassortment risk may be one helpful strategy. However, it is still challenging to evaluate reassortment risk due to the sporadic nature and complexity inherent in the reassortment process. Here, we developed a network-based approach to quantify reassortment risk by collecting all whole genome sequences from the IAVs dataset and constructing an IAVs homologous network embedded with a reassortment history. We then identified network communities to quantify reassortment risk across various viruses and revealed diverse reassortment risks among different H5Nx viruses. By analysing viruses from different hosts, we also identified the primary hosts contributing to reassortment: domestic poultry in China and wild birds in North America and Europe. These primary hosts are critical targets for future H5Nx reassortment interventions. Our study provides a new method for quantifying and ranking reassortment risk in H5Nx, thereby facilitating an effective reassortment surveillance program with a more clearly defined host target.