Literature detail

Characterization of neurotropic HPAI H5N1 viruses with novel genome constellations and mammalian adaptive mutations in free-living mesocarnivores in Canada.

Tamiru N Alkie¹ Sherri Cox² Carissa Embury-Hyatt¹ Brian Stevens³ Neil Pople⁴ Margo J Pybus^5,6 Wanhong Xu¹ Tamiko Hisanaga¹ Matthew Suderman¹ Janice Koziuk¹ Peter Kruczkiewicz¹ Hoang Hai Nguyen¹ Mathew Fisher¹ Oliver Lung¹ Cassidy N G Erdelyan¹ Orie Hochman¹ Davor Ojkic⁷ Carmencita Yason⁸ Maria Bravo-Araya⁹ Laura Bourque¹⁰ Trent K Bollinger¹¹ Catherine Soos¹² Jolene Giacinti¹² Jennifer Provencher¹³ Sarah Ogilvie⁸ Amanda Clark¹⁴ Robyn MacPhee⁸ Glen J Parsons¹⁵ Hazel Eaglesome¹⁶ Sayrah Gilbert¹⁷ Kelsey Saboraki¹⁸ Richard Davis¹⁸ Alexandra Jerao¹⁹ Matthew Ginn²⁰ Megan E B Jones^10,15 Yohannes Berhane^1,11,21

Affiliations 21 institutions

National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada.
College of Biological Science, University of Guelph, Guelph, Canada.
Canadian Wildlife Health Cooperative, Guelph, Canada.
Veterinary Diagnostic Services, Manitoba Agriculture, Winnipeg, Canada.
Fish and Wildlife, Alberta Environment and Parks, Edmonton, Canada.
Department of Biological Sciences, University of Alberta, Edmonton, Canada.
Animal Health Laboratory, University of Guelph, Guelph, Canada.
Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada.
University of Saskatchewan, Saskatoon, Canada.
Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, Canada.
Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
Environment and Climate Change Canada, Saskatoon, Canada.
Environment and Climate Change Canada, Ottawa, Canada.
Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada.
Nova Scotia Department of Natural Resources and Renewables, Kentville, Canada.
National Wildlife Centre, Caledon, Canada.
Wildlife Haven Rehabilitation Centre, Île-des-Chênes, Canada.
Fish and Wildlife Branch, Manitoba Natural Resources and Northern Development, Gimli, Canada.
Office of the Chief Veterinarian, Manitoba Agriculture, Winnipeg, Canada.
Prince Edward Island Department of Environment, Energy and Climate Action, Charlottetown, Canada.
Department of Animal Science, University of Manitoba, Winnipeg, Canada.

PMID 36880345 2023 Emerg Microbes Infect eng ppublish

PubMed DOI Browse context

Article

Publication summary

The GsGd lineage (A/goose/Guangdong/1/1996) H5N1 virus was introduced to Canada in 2021/2022 through the Atlantic and East Asia-Australasia/Pacific flyways by migratory birds. This was followed by unprecedented outbreaks affecting domestic and wild birds, with spillover into other animals. Here, we report sporadic cases of H5N1 in 40 free-living mesocarnivore species such as red foxes, striped skunks, and mink in Canada. The clinical presentations of the disease in mesocarnivores were consistent with central nervous system infection. This was supported by the presence of microscopic lesions and the presence of abundant IAV antigen by immunohistochemistry. Some red foxes that survived clinical infection developed anti-H5N1 antibodies. Phylogenetically, the H5N1 viruses from the mesocarnivore species belonged to clade 2.3.4.4b and had four different genome constellation patterns. The first group of viruses had wholly Eurasian (EA) genome segments. The other three groups were reassortant viruses containing genome segments derived from both North American (NAm) and EA influenza A viruses. Almost 17 percent of the H5N1 viruses had mammalian adaptive mutations (E627 K, E627V and D701N) in the polymerase basic protein 2 (PB2) subunit of the RNA polymerase complex. Other mutations that may favour adaptation to mammalian hosts were also present in other internal gene segments. The detection of these critical mutations in a large number of mammals within short duration after virus introduction inevitably highlights the need for continually monitoring and assessing mammalian-origin H5N1 clade 2.3.4.4b viruses for adaptive mutations, which potentially can facilitate virus replication, horizontal transmission and posing pandemic risks for humans.

Clade 2.3.4.4b H5N1 HPAI mammals mutation reassortment Influenza A Virus, H5N1 Subtype Influenza in Birds Animals Birds Canada Foxes Humans Mutation Phylogeny

Structured evidence records

Evidence records

8 total

Spillover Event 3 records

Spillover Event Extraction confidence 0.95

Key finding

Avian H5N1 clade 2.3.4.4b viruses spilled over from infected birds to free-living mesocarnivores, including red foxes, striped skunks, and mink in Canada.

Virus

Host

Location

Supporting text

Method: immunohistochemistry; phylogenetic analysis
Study design: field surveillance
Transmission direction: unknown
Geographic raw: Canada
Country inferred: Canada

Spillover Event Extraction confidence 0.95

Key finding

H5N1 infection occurred in striped skunks in Canada following avian outbreaks, consistent with spillover from infected birds.

Virus

Host

Location

Supporting text

Here, we report sporadic cases of H5N1 in 40 free-living mesocarnivore species such as red foxes, striped skunks, and mink in Canada.

Method: immunohistochemistry; phylogenetic analysis
Study design: field surveillance
Transmission direction: unknown
Geographic raw: Canada
Country inferred: Canada

Spillover Event Extraction confidence 0.95

Key finding

Free-living mink in Canada were infected with avian-origin H5N1 clade 2.3.4.4b viruses, implying spillover from avian hosts.

Virus

Host

Location

Supporting text

Here, we report sporadic cases of H5N1 in 40 free-living mesocarnivore species such as red foxes, striped skunks, and mink in Canada.

Method: immunohistochemistry; phylogenetic analysis
Study design: field surveillance
Transmission direction: unknown
Geographic raw: Canada
Country inferred: Canada

Genomic Evolution 1 records

Genomic Evolution Extraction confidence 0.90

Key finding

Clade 2.3.4.4b HPAI H5N1 viruses detected in free-living mesocarnivores in Canada showed distinct Eurasian and North American reassortment patterns and PB2 mutations (E627K, E627V, D701N) associated with mammalian adaptation.

Virus

Host

Location

Supporting text

Phylogenetically, the H5N1 viruses from the mesocarnivore species belonged to clade 2.3.4.4b and had four different genome constellation patterns. The first group of viruses had wholly Eurasian (EA) genome segments. The other three groups were reassortant viruses containing genome segments derived from both North American (NAm) and EA influenza A viruses. Almost 17 percent of the H5N1 viruses had mammalian adaptive mutations (E627K, E627V and D701N) in the polymerase basic protein 2 (PB2) subunit of the RNA polymerase complex.

Genes or proteins: PB2; RNA polymerase complex
Analysis methods: phylogenetic analysis; genome constellation analysis

Molecular Adaptation 1 records

Molecular Adaptation Extraction confidence 0.95

Key finding

HPAI H5N1 clade 2.3.4.4b viruses found in mesocarnivores carried PB2 E627K, E627V, and D701N mutations associated with mammalian host adaptation.

Virus

Host

Location

Supporting text

Almost 17 percent of the H5N1 viruses had mammalian adaptive mutations (E627 K, E627V and D701N) in the polymerase basic protein 2 (PB2) subunit of the RNA polymerase complex. Other mutations that may favour adaptation to mammalian hosts were also present in other internal gene segments.

Genes or proteins: PB2
Mutations: E627K; E627V; D701N
Mechanism types: polymerase_activity; replication_efficiency; host_adaptation

Recombination Or Reassortment 1 records

Recombination Or Reassortment Extraction confidence 0.90

Key finding

H5N1 clade 2.3.4.4b viruses detected in mesocarnivores in Canada were reassortants comprising genome segments from both Eurasian and North American influenza A viruses.

Virus

Host

Location

Supporting text

The other three groups were reassortant viruses containing genome segments derived from both North American (NAm) and Eurasian (EA) influenza A viruses.

Event type: reassortment

Serological Evidence 1 records

Serological Evidence Extraction confidence 0.85

Key finding

Red foxes infected with HPAI H5N1 in Canada showed serological evidence of exposure by developing anti-H5N1 antibodies.

Virus

Host

Location

Supporting text

Some red foxes that survived clinical infection developed anti-H5N1 antibodies.

Sample type: serum

Zoonotic Surveillance 1 records

Zoonotic Surveillance Extraction confidence 0.95

Key finding

H5N1 was detected in free-living mesocarnivores including red foxes, striped skunks, and mink in Canada.

Virus

Host

Location

Supporting text

Here, we report sporadic cases of H5N1 in 40 free-living mesocarnivore species such as red foxes, striped skunks, and mink in Canada.

Method: immunohistochemistry; phylogenetic analysis; serology
Geographic raw: Canada
Country inferred: Canada

Citation context

References

60 references

Reference network

Force-directed citation graph. OmniVira-indexed references are prioritized and recursively expanded up to three steps.

260 nodes · 349 links · capped

Drag nodes to explore citation neighborhoods


PMID 5062472	On the structure of the influenza virus envelope	Klenk	1972
-	Orthomyxoviridae. In: Knipe D, Howley P, editor. Fields virology. Philadelphia, PA: Lippincott Williams & Wilkins; 2013. p. 1151–1185	Shaw	2013
PMID 1067600	Influenza virus genome consists of eight distinct RNA species	McGeoch	1976
PMID 19230160	The biology of influenza viruses	Bouvier	2008
PMID 9223507	Coinfection of wild ducks by influenza A viruses: distribution patterns and biological significance	Sharp	1997
PMID 8198436	Influenza virus subtypes in aquatic birds of eastern Germany	Süss	1994
PMID 10484749	Genetic characterization of the pathogenic influenza A/Goose/Guangdong/1/96 (H5N1) virus: Similarity of its hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks in Hong Kong	Xu	1999
PMID 16473931	Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control	Chen	2006
PMID 21734057	Antigenic drift in H5N1 avian influenza virus in poultry is driven by mutations in major antigenic sites of the hemagglutinin molecule analogous to those for human influenza virus	Cattoli	2011
PMID 31056053	A brief history of bird flu	Lycett	2019
PMID 27314845	Highly pathogenic avian influenza viruses and generation of novel reassortants, United States, 2014–2015	Lee	2016
PMID 31024736	Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18	Poen	2019
PMID 34557739	Dealing with highly pathogenic avian influenza: an impending crisis	Lin	2021
PMID 25855748	Intercontinental spread of Asian-origin H5N8 to North America through Beringia by migratory birds	Lee	2015
PMID 25804829	Reassortant highly pathogenic influenza A H5N2 virus containing gene segments related to Eurasian H5N8 in British Columbia, Canada, 2014	Pasick	2015
PMID 35821511	Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021	Caliendo	2022
PMID 36105667	A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways	Alkie	2022
PMID 17491066	Distribution of lesions and antigen of highly pathogenic avian influenza virus A/swan/Germany/R65/06 (H5N1) in domestic cats after presumptive infection by wild birds	Klopfleisch	2007
PMID 17283627	Fatal avian influenza A H5N1 in a dog	Songserm	2006
PMID 15663858 In OmniVira	Avian influenza H5N1 in tigers and leopards.	Keawcharoen	2004
PMID 27162026	Fatal influenza A (H5N1) virus infection in zoo-housed tigers in Yunnan Province, China	Hu	2016
PMID 34670656	Highly pathogenic avian influenza A(H5N1) virus in wild red foxes, The Netherlands, 2021	Rijks	2021
PMID 27122581 In OmniVira	Highly Pathogenic Avian Influenza H5N6 Viruses Exhibit Enhanced Affinity for Human Type Sialic Acid Receptor and In-Contact Transmission in Model Ferrets.	Sun	2016
PMID 30457524	Highly pathogenic avian influenza A(H5N6) in domestic cats, South Korea	Lee	2018
PMID 34670647	Encephalitis and death in wild mammals at a rehabilitation center after infection with highly pathogenic avian influenza A(H5N8) virus, United Kingdom	Floyd	2021
PMID 19046504	Highly pathogenic avian influenza virus (H5N1) infection in red foxes fed infected bird carcasses	Reperant	2008
PMID 12202562	Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes	Spackman	2002
PMID 20015998	Genetic and pathobiologic characterization of pandemic H1N1 2009 influenza viruses from a naturally infected swine herd	Weingartl	2010
PMID 28646651	Use of sequence-independent, single-primer-amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses	Chrzastek	2017
PMID 12136032	Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data	Drummond	2002
PMID 30958812	BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis	Bouckaert	2019
PMID 18006085	Development and application of monoclonal antibodies against avian influenza virus nucleoprotein	Yang	2008
PMID 19699764	Production and diagnostic application of monoclonal antibodies against influenza virus H5	Yang	2009
PMID 20181719	PB2 residue 271 plays a key role in enhanced polymerase activity of influenza A viruses in mammalian host cells	Bussey	2010
PMID 24371069	Virulence-affecting amino acid changes in the PA protein of H7N9 influenza A viruses	Yamayoshi	2014
PMID 29553313	Enhanced replication of highly pathogenic influenza A(H7N9) virus in humans	Yamayoshi	2018
PMID 23732876	Adaptive mutations in the H5N1 polymerase complex	Gabriel	2013
PMID 26082035	Identification of mammalian-adapting mutations in the polymerase complex of an avian H5N1 influenza virus	Taft	2015
PMID 19393699	Single mutation at the amino acid position 627 of PB2 that leads to increased virulence of an H5N1 avian influenza virus during adaptation in mice can be compensated by multiple mutations at other sites of PB2	Li	2009
PMID 27926816	Identification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from Pigeons	Elgendy	2017
PMID 26656683	Glycine at position 622 in PB1 contributes to the virulence of H5N1 avian influenza virus in mice	Feng	2016
PMID 16339318	The viral polymerase mediates adaptation of an avian influenza virus to a mammalian host	Gabriel	2005
PMID 18248089	Interaction of polymerase subunit PB2 and NP with importin α1 Is a determinant of host range of influenza A virus	Gabriel	2008
-	Highly Pathogenic avian influenza is an emerging disease threat to wild birds in North America	Ramey	2022
PMID 27812044	Surveillance for highly pathogenic H5 avian influenza virus in synanthropic wildlife associated with poultry farms during an acute outbreak	Shriner	2016
PMID 28284614	Characterization of H5N1 highly pathogenic mink influenza viruses in eastern China	Jiang	2017
PMID 20392847	In vitro assessment of attachment pattern and replication efficiency of H5N1 influenza A viruses with altered receptor specificity	Chutinimitkul	2010
PMID 11546875	Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses	Hatta	2001
PMID 32873642	Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation	Liu	2020
PMID 35172704	Infections with highly pathogenic avian influenza A virus (HPAIV) H5N8 in harbor seals at the German North Sea coast, 2021	Postel	2022
PMID 29299528	Human clade 2.3.4.4 A/H5N6 influenza virus lacks mammalian adaptation markers and does not transmit via the airborne route between ferrets. mSphere. 2018;3:e00405–17	Herfst	2018
PMID 21816827	Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex	Aggarwal	2011
PMID 21216958	Interaction of the influenza A virus polymerase PB2 C-terminal region with importin α isoforms provides insights into host adaptation and polymerase assembly	Boivin	2011
PMID 26424125	Large-scale conformational dynamics control H5N1 influenza polymerase PB2 binding to importin α	Delaforge	2015
PMID 19066626 In OmniVira	The host-dependent interaction of alpha-importins with influenza PB2 polymerase subunit is required for virus RNA replication.	Resa-Infante	2008
PMID 25704008	Influenza virus adaptation PB2-627K modulates nucleocapsid inhibition by the pathogen sensor RIG-I	Weber	2015
PMID 31265471 In OmniVira	PB2 mutations arising during H9N2 influenza evolution in the Middle East confer enhanced replication and growth in mammals.	Arai	2019
PMID 26202239 In OmniVira	Transmission of H7N9 Influenza Viruses with a Polymorphism at PB2 Residue 627 in Chickens and Ferrets.	Luk	2015
PMID 19119420	Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N	Steel	2009
PMID 24403592	Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts	Mok	2014

Evidence overview

Evidence 8

Types 6

Virus 2

Host 4

Evidence types

Spillover Event 3 Genomic Evolution 1 Molecular Adaptation 1 Recombination Or Reassortment 1 Serological Evidence 1 Zoonotic Surveillance 1

Linked entities

Viruses

Hosts

Locations

Publication metadata

Journal: Emerging microbes & infections
Volume / Issue / Pages: 12 / 1 / 2186608
ISSN: 2222-1751
Journal country: United States
DOI: 10.1080/22221751.2023.2186608