Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia

Lycett, Samantha; Pohlmann, Anne; Staubach, Christoph; Caliendo, Valentina; Woolhouse, Mark; Beer, Martin; Kuiken, Thijs; Viruses, Related Influenza

doi:10.1073/pnas.2001813117

Cited by 84 publications

(99 citation statements)

References 53 publications

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“…Similar sequences to genotype A viruses were identified in Croatia, Italy, Belgium, Poland, and the Czech Republic; they also were found in domestic ducks in Hungary (19). France and Hungary are the main producers of foie gras in Europe.…”

Section: Discussionsupporting

confidence: 62%

“…The 2016–17 HPAI A(H5N8) outbreak in Europe affected 1,576 wild birds and 1,134 domestic birds ( 18 ). In France, we identified 3 genotypes that had previously been described elsewhere in Europe ( 19 , 35 – 37 ), indicating that H5N8 was introduced into France > 3 times during November 2016–April 2017. We found sporadic cases of genotypes B and C, mostly in wild birds.…”

Section: Discussionmentioning

confidence: 55%

“…Only 2 viruses of genotype A were in backyard poultry, an observation that corresponds to the findings of Souvestre et al ( 39 ), which showed the minor role of backyards in the H5N8 transmission dynamic. Of the 6 genotypes characterized during this outbreak in Europe, 3 genotypes resemble the sequences now described in France (i.e., genotype A corresponds with reassortants 6-like, B with reassortants 3-like, and C with reassortants 7-like) ( 19 ).…”

Section: Discussionmentioning

confidence: 84%

“…We chose the best model on the basis of Akaike’s Information Criterion value ( 29 ). We applied the uncorrelated lognormal molecular clock with the SDR06 model of nucleotide substitution and Bayesian Skygrid coalescent model ( 30 ) as in previous studies ( 8 , 19 ). We ran the model for 40 million generations with sampling evolutionary parameters every 4,000 generations.…”

Section: Methodsmentioning

confidence: 99%

“…During this outbreak, researchers identified 6 HPAI A(H5N8) genotypes in Europe; 2 of these genotypes were identified using 6 sequences from infected birds in France ( 19 ). France had 539 cases of HPAI A(H5N8) infections, 51 in wild birds and 488 in poultry flocks, most of which occurred at duck farms producing foie gras ( 18 ).…”

mentioning

confidence: 99%

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Highly Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016–17

Briand¹,

Niqueux²,

Schmitz³

et al. 2021

Emerg. Infect. Dis.

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I nfluenza A viruses are enveloped viruses of the Alphainfluenzavirus genus in the Orthomyxoviridae family. Their negative-stranded RNA genome consists of 8 segments encoding a total of 10-14 proteins. Avian influenza viruses (AIVs) are classified on the basis of antigenic differences in their surface glycoproteins, hemagglutinin (H1-H16) and neuraminidase (N1-N9) (1). H5 and H7 subtypes can become highly pathogenic avian influenza (HPAI) viruses after the evolution of multiple basic amino acids in the cleavage site of hemagglutinin protein (2,3). This mutation enables the virus to replicate efficiently in all organs, causing a severe and often fatal systemic disease. In contrast, the cleavage site of hemagglutinin in low pathogenicity AIVs lacks these multiple amino acids, restricting viral replication to the respiratory and digestive tracts. Low pathogenicity AIVs cause subclinical or mild disease that can be aggravated by secondary infections (4,5). Because H5 and H7 AIVs can evolve to be highly pathogenic, the diseases caused by these subtypes are notifiable to national and international bodies (6). Since 1996, highly pathogenic H5 viruses of the A/goose/Guangdong/1/96 (Gs/GD/96) lineage have caused recurrent outbreaks with high death rates in birds. These HPAIs are categorized into 10 distinct clades (0-9) on the basis of hemagglutinin sequences (7). These clades are found in Asia; a few have spread to Africa, Europe, and North America (8-10). Europe experienced major introductions of H5N1 of clade 2.2 during 2005-2007 and H5N8 of clade 2.3.4.4 during 2014-2020 (11-14). Many reassortments were observed on Gs/Gd/1/96-like viruses, especially within clade 2.3.4.4. The reassortments generated several subtypes including H5N1, H5N2, H5N5, H5N6, and H5N8 (11,15-17). During winter 2016-17, twenty-nine countries in Europe reported 1,576 cases of Gs/Gd/1/96like H5N8 infections in wild birds and 1,134 in poultry, especially domestic ducks (18). During this outbreak, researchers identified 6 HPAI A(H5N8) genotypes in Europe; 2 of these genotypes were identified using 6 sequences from infected birds in France (19). France had 539 cases of HPAI A(H5N8) infections, 51 in wild birds and 488 in poultry flocks, most of which occurred at duck farms producing foie gras (18). A previous study used spatiotemporal analysis of clinical cases comprising 2 distinct epizootic periods in southwestern France (20). The first period spanned November 28, 2016-February 2, 2017 and comprised 4 spatiotemporal clusters (20). The second period spanned February 3-March 23, 2017 and comprised a single spatiotemporal cluster (20).

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Section: Discussionsupporting

confidence: 62%

Section: Discussionmentioning

confidence: 55%

Section: Discussionmentioning

confidence: 84%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Highly Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016–17

Briand¹,

Niqueux²,

Schmitz³

et al. 2021

Emerg. Infect. Dis.

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Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America

et al. 2022

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Prior to the emergence of the A/goose/Guangdong/1/1996 (Gs/GD) H5N1 influenza A virus, the long‐held and well‐supported paradigm was that highly pathogenic avian influenza (HPAI) outbreaks were restricted to poultry, the result of cross‐species transmission of precursor viruses from wild aquatic birds that subsequently gained pathogenicity in domestic birds. Therefore, management agencies typically adopted a prevention, control, and eradication strategy that included strict biosecurity for domestic bird production, isolation of infected and exposed flocks, and prompt depopulation. In most cases, this strategy has proved sufficient for eradicating HPAI. Since 2002, this paradigm has been challenged with many detections of viral descendants of the Gs/GD lineage among wild birds, most of which have been associated with sporadic mortality events. Since the emergence and evolution of the genetically distinct clade 2.3.4.4 Gs/GD lineage HPAI viruses in approximately 2010, there have been further increases in the occurrence of HPAI in wild birds and geographic spread through migratory bird movement. A prominent example is the introduction of clade 2.3.4.4 Gs/GD HPAI viruses from East Asia to North America via migratory birds in autumn 2014 that ultimately led to the largest outbreak of HPAI in the history of the United States. Given the apparent maintenance of Gs/GD lineage HPAI viruses in a global avian reservoir; bidirectional virus exchange between wild and domestic birds facilitating the continued adaptation of Gs/GD HPAI viruses in wild bird hosts; the current frequency of HPAI outbreaks in wild birds globally, and particularly in Eurasia where Gs/GD HPAI viruses may now be enzootic; and ongoing dispersal of AI viruses from East Asia to North America via migratory birds, HPAI now represents an emerging disease threat to North American wildlife. This recent paradigm shift implies that management of HPAI in domestic birds alone may no longer be sufficient to eradicate HPAI viruses from a given country or region. Rather, agencies managing wild birds and their habitats may consider the development or adoption of mitigation strategies to minimize introductions to poultry, to reduce negative impacts on wild bird populations, and to diminish adverse effects to stakeholders using wildlife resources. The main objective of this review is, therefore, to provide information that will assist wildlife managers in developing mitigation strategies or approaches for dealing with outbreaks of Gs/GD HPAI in wild birds in the form of preparedness, surveillance, research, communications, and targeted management actions. Resultant outbreak response plans and actions may represent meaningful steps of wildlife managers toward the use of collaborative and multi‐jurisdictional One Health approaches when it comes to the detection, investigation, and mitigation of emerging viruses at the human‐domestic animal‐wildlife interface.

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Approaches for Spatial and Temporal-Spatial Clustering Analysis in Avian Influenza Outbreaks

Huang

Wu²,

Chao

2023

Earth Data Analytics for Planetary Health

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Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia

Cited by 84 publications

References 53 publications

Highly Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016–17

Highly Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016–17

Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America

Approaches for Spatial and Temporal-Spatial Clustering Analysis in Avian Influenza Outbreaks

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