Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation

Dhingra, Madhur S.; Artois, Jean; Robinson, Timothy P.; Linard, Catherine; Chaiban, Célia; Xénarios, Ioannis; Engler, Robin; Liechti, Robin; Kuznetsov, Dmitry; Xiao, Xiangming; Dobschuetz, Sophie von; Claes, Filip; Newman, Scott H.; Dauphin, Gwenae͏̈lle; Gilbert, Marius

doi:10.7554/elife.19571

Cited by 50 publications

(87 citation statements)

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“…In 1996, the highly pathogenic avian influenza (HPAI) H5N1 virus emerged in southern China, and persisted locally until it started spreading internationally in 2004 [10]. By 2006, the HPAI H5N1 virus had spread across over 60 countries in Asia, Europe and Africa [11]. Still today, the H5N6 and H5N8 HPAI viruses that caused important epizootics in the USA (winter 2014/2015) and Europe (winter 2014/2015 and 2016/2017) originated in China [12], and share an H5 genes with many HPAI H5N1 that were circulating in China in the previous years, and that reassorted with other avian influenza viruses in eastern Asia.…”

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confidence: 99%

Intensifying poultry production systems and the emergence of avian influenza in China: a ‘One Health/Ecohealth’ epitome

2017

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Several kinds of pressure can lead to the emergence of infectious diseases. In the case of zoonoses emerging from livestock, one of the most significant changes that has taken place since the mid twentieth century is what has been termed the “livestock revolution”, whereby the stock of food animals, their productivity and their trade has increased rapidly to feed rising and increasingly wealthy and urbanized populations. Further increases are projected in the future in low and middle-income countries. Using avian influenza as an example, we discuss how the emergence of avian influenza H5N1 and H7N9 in China was linked to rapid intensification of the poultry sector taking place in landscapes rich in wetland agriculture and wild waterfowls habitats, providing an extensive interface with the wild reservoir of avian influenza viruses. Trade networks and live-poultry markets further exacerbated the spread and persistence of avian influenza as well as human exposure. However, as the history of emergence of highly pathogenic avian influenza (HPAI) demonstrates in high-income countries such as the USA, Canada, Australia, the United Kingdom or the Netherlands, this is by no way specific to low and middle-income countries. Many HPAI emergence events took place in countries with generally good biosecurity standards, and the majority of these in regions hosting intensive poultry production systems. Emerging zoonoses are only one of a number of externalities of intensive livestock production systems, alongside antimicrobial consumption, disruption of nutrient cycles and greenhouse gases emissions, with direct or indirect impacts on human health. In parallel, livestock production is essential to nutrition and livelihoods in many low-income countries. Deindustrialization of the most intensive production systems in high-income countries and sustainable intensifications in low-income countries may converge to a situation where the nutritional and livelihood benefits of livestock production would be less overshadowed by its negative impacts on human an ecosystem health.

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Section: Main Textmentioning

confidence: 99%

Intensifying poultry production systems and the emergence of avian influenza in China: a ‘One Health/Ecohealth’ epitome

2017

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“…A standardized “clade” nomenclature was developed and first adopted in 2008, based on the evolution and divergence of H5N1 viruses that evolved from the original HA gene of the 1996 H5N1 virus (World Health Organization/World Organisation for Animal and Agriculture Organization, ). Although 10 distinct clades (0–9) were identified from 1996 to 2009, the H5 viruses responsible for most outbreaks in poultry were still almost of the N1 subtype (Dhingra et al., ). Since 2010, different H5Nx reassortant viruses, including H5N2, H5N5, H5N6 and H5N8 subtypes, were identified in live poultry markets in China (Bi et al., ; Gu et al., ; Zhao et al., , ).…”

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confidence: 99%

Compatibility between haemagglutinin and neuraminidase drives the recent emergence of novel clade 2.3.4.4 H5Nx avian influenza viruses in China

Qin

Zhu

et al. 2018

Transbound Emerg Dis

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Genetic reassortments between highly pathogenic avian influenza (HPAI) H5 subtype viruses with different neuraminidase (NA) subtypes have increased in prevalence since 2010 in wild birds and poultry from China. The HA gene slightly evolved from clade 2.3.4 to clade 2.3.4.4, raising the question of whether novel clade 2.3.4.4 HA broke the balance with N1 but is matched well with NAx to drive viral epidemics. To clarify the role of compatibility between HA and NA on the prevalence of H5Nx subtypes, we constructed 10 recombinant viruses in which the clade 2.3.4 or clade 2.3.4.4 HA genes were matched with different NA (N1, N2 and N8) genes and evaluated viral characteristics and pathogenicity. Combinations between clade 2.3.4 HA and N1 or between clade 2.3.4.4 HA and NAx, but not between clade 2.3.4.4 HA and N1, or between clade 2.3.4 HA and NAx, promoted viral growth, NA activity, thermostability, low-pH stability and pathogenicity in chicken and mice. These findings suggest that both clade 2.3.4 HA/N1 and clade 2.3.4.4 HA/NAx displayed a better match, which could promote the increased prevalence of clade 2.3.4 H5N1 AIV (prior to 2010) and clade 2.3.4.4 H5Nx AIV (since 2010) in China, respectively.

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“…Health/Food and Agriculture Organization (WHO/OIE/FAO) H5N1 Evolution Working Group, 2014). Viruses bearing HAs of the Gs/GD 2.3.4 lineage emerged around 2009 80 -2013 revealed an early propensity to reassort with NA subtypes other than N1, unlike 81 earlier clades, and showed unprecedented geographical range expansion via poultry 82 trade and wild bird migration (Claes et al, 2016;Dhingra et al, 2016;Lee et al, 2017). 83…”

Section: Introduction 49mentioning

confidence: 99%

Regional transmission and reassortment of 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses in Bulgarian poultry 2017/18

Venkatesh

Brouwer

Goujgoulova

et al. 2020

Preprint

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Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 HPAI viruses. In this study we use genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the North-Eastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates complete lack of reassortment in all segments but the MP, which presents as multiple smaller clusters associated with different European 2.3.4.4b viruses. Ancestral reconstruction of host states of the HA gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence we suggest that surveillance of domestic ducks as epidemiologically relevant species for subclinical infection. Monitoring spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks.

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Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation

Cited by 50 publications

References 56 publications

Intensifying poultry production systems and the emergence of avian influenza in China: a ‘One Health/Ecohealth’ epitome

Intensifying poultry production systems and the emergence of avian influenza in China: a ‘One Health/Ecohealth’ epitome

Compatibility between haemagglutinin and neuraminidase drives the recent emergence of novel clade 2.3.4.4 H5Nx avian influenza viruses in China

Regional transmission and reassortment of 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses in Bulgarian poultry 2017/18

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