Live Poultry Trading Drives China's H7N9 Viral Evolution and Geographical Network Propagation

Abstract

The on-going reassortment, human-adapted mutations, and spillover events of novel A(H7N9) avian influenza viruses pose a significant challenge to public health in China and globally. However, our understanding of the factors that disseminate the viruses and drive their geographic distributions is limited. We applied phylogenic analysis to examine the inter-subtype interactions between H7N9 viruses and the closest H9N2 lineages in China during 2010–2014. We reconstructed and compared the inter-provincial live poultry trading and viral propagation network via phylogeographic approach and network similarity technique. The substitution rates of the isolated viruses in live poultry markets and the characteristics of localized viral evolution were also evaluated. We discovered that viral propagation was geographically-structured and followed the live poultry trading network in China, with distinct north-to-east paths of spread and circular transmission between eastern and southern regions. The epicenter of H7N9 has moved from the Shanghai–Zhejiang region to Guangdong Province was also identified. Besides, higher substitution rate was observed among isolates sampled from live poultry markets, especially for those H7N9 viruses. Live poultry trading in China may have driven the network-structured expansion of the novel H7N9 viruses. From this perspective, long-distance geographic expansion of H7N9 were dominated by live poultry movements, while at local scales, diffusion was facilitated by live poultry markets with highly-evolved viruses.

Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses

“…Considering evidence that H5N1 and H7N9 viruses were likely associated with the live poultry trade ( Bui et al. 2018 ; Li et al. 2018 ; Yang et al.…”

“…2020 ), in this study, based on the phylogeographic approach, we found that H5N6 viruses from Guangdong and Hunan provinces were more likely to have originated from, and migrated to, at least eleven locations and four locations, respectively, which implies that H5N6 viruses endemic in southern China might have jointly resulted from the gene flow through circular poultry movements. Livestock breeding is extensive in southern China, with many breeding poultry farms, particularly “free range” ducks that are raised in large amount of small backyard farms, and live poultry markets ( Li et al. 2018 ).…”

One health insights to prevent the next HxNy viral outbreak: learning from the epidemiology of H7N9

“…Initially, farmers and local authorities were reluctant to report avian influenza outbreaks, in particular, the asymptomatic LPAI virus H7N9 cases. Some farmers and small companies even transported infected poultry away from their premises once a viral infection had been identified, further facilitating the spread of the virus [49]. The difficulties associated with monitoring/preventing short distance, live poultry transportations potentially contributed to the repeated waves of H7N9 influenza virus outbreaks in China.…”

Delayed peak of human infections and ongoing reassortment of H7N9 avian influenza virus in the newly affected western Chinese provinces during Wave Five

“…Isolates from the western Chinese provinces clustered with isolates from various districts, while most of the isolates showed the highest homology with isolates from the neighboring provinces. This indicates that the majority of H7N9 viruses in the newly affected western Chinese provinces might have been imported from the neighboring provinces, most possibly by live poultry or poultry product transport, which has been shown to be a driver of China's H7N9 viral evolution and geographical network propagation (Gao, 2014;Li et al, 2018).…”