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Overview of the Highly Pathogenic A(H5N1) Bird Flu Outbreak

Overview of the Outbreak
A(H5N1)

H5N1 was first detected at a goose farm in China in 1996. A big poultry outbreak in Hong Kong in 1997 led to the first documented human deaths and sparked the first pandemic fears. Around 2005, the virus spilled over into migratory birds, which have since spread it across the world in several big waves.

The H5N1 strain is a fast-mutating, highly pathogenic avian influenza virus (HPAI) found in multiple bird species. It is both epizootic (an epidemic in non-humans) and panzootic (a disease affecting animals of many species especially over a wide area).


HPAI A(H5N1) 2.3.4.4b Variant

A new variant named 2.3.4.4b that emerged in the Netherlands in October 2020 has spread faster and farther than any predecessor, dealing huge blows to the poultry industry in Europe and North America before arriving in Central and South America in the fall of 2022. “It seems this virus is just more adapted to all birds than any others have been,” says Richard Webby, an influenza researcher at St. Jude Children’s Research Hospital.

Because the receptors the virus binds to in the upper airways of birds are less common in mammalian upper airways, H5N1 largely spares mammals. But this time around many mammalian species have become infected, including foxes, cats, ferrets, seals, and dolphins, presumably through contact with infected birds.

In January 2021, an A(H5N1) related to the 2020–2021 European viruses was reported in West Africa and subsequently in South African countries. Since then, it has been persistently circulating in this geographic area, and in West Africa it has reassorted with the A(H9N2) subtype of the zoonotic G1 lineage.

From late 2021, different clade 2.3.4.4b A(H5N1) genotypes, one of them previously identified in Europe, have been detected in South and East Asia, including China. In December 2021, the A(H5N1) clade 2.3.4.4b strongly related to the A(H5N1) identified in Northern Europe during the 2020-2021 epidemic season was introduced in North America.

At the beginning of 2022, a new introduction in North America from the Pacific flyway of an A(H5N1) related to the viruses circulating in Japan was identified (Alkie et al., 2022). Since then the virus has spread all over North America undergoing reassortment events with LPAI viruses of the American lineages (Alkie et al., 2022).

In October 2022, A(H5N1) viruses spread for the first time to Mexico and soon after to South America, including Peru, Colombia, Ecuador and Venezuela, with mass mortality events reported in wild birds (BBC, online) and detections in poultry farms. The characterized viruses belong to clade 2.3.4.4b first detected in January 2022 in the Atlantic coast of North America (ProMed, online-a) and have been described as reassortant viruses between the Eurasian and American lineages (WOAH, 2022).

Bird Species Affected by Highly Pathgenic H5N1

  • Anas platyrhynchos domesticus (Duck)
  • Anserinae sp. (Goose)
  • Gallus gallus domesticus (Chicken)
  • Meleagris gallopavo (Turkey)
  • Alectura lathami (Australian bushturkey)
  • Ara ararauna × Ara macao (Catalina Macaw)
  • Ara macao (Scarlet Macaw)
  • Ara militaris (Military macaw)
  • Coturnix coturnix (Common Quail)
  • Cyanoliseus patagonus (Burrowing parrot)
  • Dromaius novaeollandiae (Emu)
  • Grus paradisea (Blue Crane)
  • Numida meleagris (Common Guineafowl)
  • Pavo cristatus (Peacock)
  • Perdix perdix (Grey Partridge)
  • Phasianus colchicus (Common Pheasant)
  • Phoenicopterus chilensis (Chilean flamingo)
  • Phoenicopterus minor (Lesser flamingo)
  • Struthio camelus (Ostrich)
  • Aix galericulata (Mandarin Duck)
  • Aix sponsa (Wood Duck)
  • Alopochen aegyptiaca (Egyptian Goose)
  • Amazonetta brasiliensis (Brazilian teal)
  • Anas acuta (Northern Pintail)
  • Anas carolinensis (American green-winged Teal)
  • Anas clypeata (Northern Shoveler)
  • Anas crecca (Common Teal)
  • Anas discors (Blue-winged Teal)
  • Anas falcata (Falcated Duck)
  • Anas penelope (Eurasian Wigeon)
  • Anas platyrhynchos (Mallard)
  • Anas poecilorhyncha (Indian spot-billed duck)
  • Anas querquedula (Garganey)
  • Anas rubripes (American Black Duck)
  • Anas strepera (Gadwall)
  • Anas undulata (Yellow-billed Duck)
  • Anas versicolor (Silver Teal)
  • Anser albifrons (Greater white-fronted Goose)
  • Anser anser (Greylag Goose)
  • Anser brachyrhynchus (Pink-footed Goose)
  • Anser caerulescens (Snow Goose)
  • Anser erythropus (Lesser white-fronted goose)
  • Anser fabalis (Bean Goose)
  • Anser rossii (Ross’s Goose)
  • Anser serrirostris (Bean Goose)
  • Aythya affinis (Lesser Scaup)
  • Aythya americana (Redhead Duck)
  • Aythya collaris (Ring-necked Duck)
  • Aythya ferina (Common Pochard)
  • Aythya fuligula (Tufted Duck)
  • Aythya marila (Greater Scaup)
  • Aythya nyroca (Ferruginous Pochard)
  • Aythyinae or Anatinae sp. (Wild Duck)
  • Branta bernicla (Brent Goose)
  • Branta canadensis (Canada Goose)
  • Branta hutchinsii (Cackling Goose)
  • Branta leucopsis (Barnacle Goose)
  • Branta ruficollis (Red breasted goose)
  • Branta sandvicensis (Nene)
  • Bucephala clangula (Common Goldeneye)
  • Cairina moschata (Muscovy Duck)
  • Chenonetta jubata (Maned Duck)
  • Coscoroba coscoroba (Coscoroba swan)
  • Cygnus atratus (Black Swan)
  • Cygnus buccinators (Trumpeter Swan)
  • Cygnus columbianus (Tundra Swan)
  • Cygnus cygnus (Whooper swan)
  • Cygnus olor (Mute Swan)
  • Dendrocygna eytoni (Plumed Whistling-Duck)
  • Lophodytes cucullatus (Hooded Merganser)
  • Mareca Americana (American wigeon)
  • Marmaronetta angustirostris (Marbled teal)
  • Mergus merganser. (Goosander)
  • Netta rufina (Red-crested Pochard)
  • Oxyura jamaicensis (Ruddy Duck)
  • Plectopterus gambensis (Spur-winged Goose)
  • Spatula clypeata (Northern Shoveler)
  • Spatula puna (Puna teal)
  • Tadorna tadorna (Common Shelduck)
  • Aechmophorus occidentalis (Western Grebe)
  • Agelaius phoeniceus (Red-winged Blackbird)
  • Alca torda (Razorbill)
  • Alectoris rufa (Red legged partridge)
  • Amazona farinose (Amazon Parrot)
  • Amazona ochrocephala (Yellow-crowned Parrot)
  • Antigone canadensis (Sandhill Crane)
  • Antigone vipio (White-naped crane)
  • Ara cloropterus (Green and red macaw)
  • Ardea alba (Great Egret)
  • Ardea cinerea (Grey Heron)
  • Ardea herodias (Great Blue Heron)
  • Ardea melanocephala (Black-headed Heron)
  • Aythya baeri (Baer's pochard)*
  • Balearica regulorum (Crowned crane)
  • Bonasa umbellus (Ruffed grouse)
  • Botaurus stellaris (Eurasian bittern)
  • Bubulcus ibis (Western Cattle Egret)
  • Bucephala islandica (Barrow's goldeneye) *
  • Butorides virescens (Green Heron)
  • Calidris alba (Sanderling)
  • Calidris alpine (Dunlin)
  • Calidris canutus (Red Knot)
  • Calidris ferruginea (Curlew sandpiper)
  • Calidris maritima (Purple sandpiper)
  • Calidris minuta (Little stint)
  • Calidris pusilla (Semipalmated sandpiper)
  • Cepphus grille (Black Guillemot)
  • Charadrius alexandrines (Kentish Plover)
  • Charadrius dubius (Little ringed plover)
  • Charadrius hiaticula (Common ringed plover)
  • Charadrius mongolus (Lesser Sand Plover)
  • Charadrius nivosus (Snowy plover )
  • Charadrius pallidus (Chestnut-banded Plover)
  • Chlidonias hybrid (Whiskered Tern)
  • Chlidonias leucoptera (White-winged Black Tern)
  • Ciconia boyciana (Oriental stork )
  • Ciconia ciconia (White Stork)
  • Ciconiidae sp. (Stork)
  • Coloeus monedula (Eurasian Jackdaw)
  • Columba guinea (African rock pigeon)
  • Columba livia (Rock Pigeon)
  • Columba palumbus (Common Wood-Pigeon)
  • Columbidae sp. (Pigeon)
  • Corvus monedula (Western jackdaw)
  • Cyanocitta cristata (Blue Jay)
  • Cyrtonyx montezumae (Montezuma Quail)
  • Dendrocopos major (Great spotted woodpecker)
  • Egretta garzetta (Little Egret)
  • Egretta thula (Snowy Egret)
  • Eudocimus albus (American White Ibis)
  • Eudocimus ruber (Scarlet Ibis)
  • Fringilla coelebs (Common chaffinch)
  • Fratercula arctica (Atlantic Puffin)
  • Fulica americana (American coot)
  • Fulica atra (Common Coot)
  • Fulmarus glacialis (Northern Fulmar)
  • Gallinula chloropus (Common Moorhen)
  • Garrulus glandarius (Eurasian jay)
  • Gavia immer (Common Loon)
  • Gavia pacifica (Pacific loon)
  • Gavia stellata (Red-throated loon)
  • Geronticus eremita (Northern Bald Ibis)
  • Grus grus (Common Crane)
  • Grus japonensis (Red-crowned Crane)
  • Grus monacha (Hooded Crane)
  • Haematopus moquini (African Black Oystercatcher)
  • Haematopus ostralegus (Eurasian oystercatcher)
  • Himantopus himantopus (Black-winged Stilt)
  • Hirundo sp. (Swallow)
  • Hydrocoloeus minutus (Little Gull)
  • Hydroprogne caspia (Caspian Tern)
  • Junco hyemalis (Dark-eyed Junco)
  • Leucophaeus atricilla (Laughing Gull)
  • Lonchura sp. (Munia)
  • Mergellus albellus (Smew)*
  • Mergus squamatus (Scaly-sided merganser)*
  • Motacilla alba (Pied Wagtail)
  • Mycteria americana (American Wood Stork)
  • Mycteria leucocephala (Painted Stork)
  • Nannopterum auritum (Double-crested cormorant)
  • Nannopterum brasilianum (Neotropic Cormorant)
  • Numenius arquata (Eurasian Curlew)
  • Numenius sp.(Curlew)
  • Nycticorax nycticorax (Black-Crowned Heron)
  • Passer domesticus (House Sparrow)
  • Pelecanus crispus (Dalmatian pelican)
  • Pelecanus erythrorhynchos (American White Pelican)
  • Pelecanus occidentalis (Brown Pelican)
  • Pelecanus onocrotalus (Great White Pelican)
  • Pelecanus thagus (Peruvian Pelican)
  • Phalacrocorax auritus (Double-crested Cormorant)
  • Phalacrocorax capensis (Cape Cormorant)
  • Phalacrocorax carbo (Great Cormorant)
  • Phalacrocorax pygmaeus (Pygmy Cormorant)
  • Phasianus colchicus (Common Pheasant)
  • Phalacrocorax gaimardi (Red-legged cormorant)
  • Phoenicopterus roseus (Greater Flamingo)
  • Platalea leucorodia (Eurasian Spoonbill)
  • Platalea minor (Black-faced Spoonbill)
  • Plegadis chihi (White-faced ibis)
  • Plegadis falcinellus (Glossy Ibis)
  • Ploceus velatus (Southern Masked-Weaver)
  • Podiceps auritus (Horned Grebe)
  • Podiceps cristatus (Great Cested Grebe)
  • Podiceps grisegena (Red-necked Grebe)
  • Podiceps nigricollis (Eared Grebe)
  • Puffinus gravis (Great shearwater)
  • Puffinus puffinus (Manx Shearwater)
  • Quiscalus major (Boat-tailed Grackle)
  • Quiscalus quiscula (Common Grackle)
  • Rallus aquaticus (Water Rail)
  • Recurvirostra avosetta (Pied avocet)
  • Rhea Americana (Greater Rhea)
  • Rissa tridactyla (Black-legged Kittiwake)
  • Rynchops niger (Black skimmer)
  • Scolopax rusticola (Eurasian Woodcock)
  • Somateria mollissima (Eider)
  • Somateria spectabilis (King Eider)
  • Spheniscus demersus (Jackass Penguin)
  • Stercorarius parasiticus (Arctic Skua)
  • Stercorarius skua (Great Skua)
  • Sterna dougallii (Roseate Tern)
  • Sterna forsteri (Forster's tern)
  • Sterna hirundo (Common Tern)
  • Sterna paradisaea (Acrtic Tern)
  • Streptopella decaocto (Eurasian Collared Dove)
  • Streptopella senegalensis (Laughing Dove)
  • Sturnus vulgaris (Common Starling)
  • Tachybaptus ruficollis (Little Grebe)
  • Tachycineta bicolor (Tree Swallow)
  • Thalasseus bergii (Swift tern)
  • Thalasseus elegans (Elegant tern)
  • Thalasseus maximus (Royal Tern)
  • Thalasseus sandvicensis (Sandwich Tern)
  • Threskiornis aethiopicus (Sacred Ibis)
  • Tringa glareola (Wood Sandpiper)
  • Tringa melanoleuca (Greater Yellowlegs)
  • Tringa ochropus (Green Sandpiper)
  • Turdus merula (Eurasian Blackbird)
  • Turdus migratorius (American Robin)
  • Turdus philomelos (Song Thrush)
  • Turdus pilaris (Fieldfare)
  • Uria aalge (Common Murre)
  • Uria lomvia (Thick-billed Murre)
  • Vanellus vanellus (Northern Lapwing)
  • Accipiter cooperii (Cooper’s Hawk)
  • Accipiter gentilis (Northern Goshawk)
  • Accipiter nisus (Eurasian Sparrowhawk)
  • Accipiter striatus (Sharp-shinned Hawk)
  • Aegolius acadicus (Northern Saw-whet Owl)
  • Aquila chrysaetos (Golden Eagle)
  • Asio flammeus (Short-Eared owl)
  • Asio otus (Long Eared Owl)
  • Athene noctua (Little Owl)
  • Bonaparte's gull (Larus philadelphia)
  • Bubo africanus (Spotted Eagle-Owl)
  • Bubo bubo (Eurasian Eagle-Owl)
  • Bubo scandiacus (Snowy Owl)
  • Bubo virginianus (Great Horned Owl)
  • Buteo buteo (Common Buzzard)
  • Buteo jamaicensis (Red-tailed Hawk)
  • Buteo japonicus (Eastern buzzard)
  • Buteo lagopus (Rough-legged Hawk)
  • Buteo lineatus (Red-shouldered Hawk)
  • Buteo platypterus (Broad-winged Hawk)
  • Buteo rufofuscus (Jackal Buzzard)
  • Buteo swainsoni (Swainson's Hawk)
  • Caracara cheriway (Northern Crested Caracara)
  • Cathartes aura (Turkey Vulture)
  •  Chroicocephalus brunnicephalus (Brown-headed gull)
  • Chroicocephalus cirrocephalus (Grey Headed Gull)
  • Chroicocephalus hartlaubii (Hartlaub’s Gull)
  • Chroicocephalus ridibundus (Black-headed Gull)
  • Circus aeruginosus (Western Marsh Harrier)
  • Circus cyaneus (Hen Harrier)
  • Circus hudsonius (Northern Harrier) 
  • Coragyps atratus (Black Vulture)
  • Corvus albidae (Pied Crow)
  • Corvus brachyrhynchos (American Crow) 
  • Corvus corax (Common Raven)
  • Corvus cornix (Hooded Crow)
  • Corvus corone (Carrion Crow)
  • Corvus frugilegus (Rook)
  • Corvus macrorhynchos (Large-billed Crow)
  • Corvus ossifragus (Fish Crow) 
  • Corvus splendens (House Crow)
  • Falco cherrug (Saker Falcon)
  • Falco columbarius (Merlin)
  • Falco mexicanus (Prairie falcon)
  • Falco peregrinus (Peregrine Falcon)
  • Falco tinnunculus (Common Kestrel)
  • Falco rusticolus (Gryfalcon)
  • Falco sparverius (American Kestrel)
  • Falco tinnunculus (Common Kestrel)
  • Falco vespertinus (Red-footed Falcon)
  • Geranoaetus polyosoma (Variable Hawk)
  • Gypaetus barbatus (Bearded vulture) 
  • Gyps africanus (White-backed vulture)
  • Gyps fulvus (Griffon Vulture)
  • Haematopus palliatus (American oystercatcher)
  • Haliaeetus albicilla (White Tailed Eagle)
  • Haliaeetus leucocephalus (Bald Eagle)
  • Haliaeetus pelagicus (Steller’s Sea Eagle)
  • Haliaeetus vocifer (African Fish Eagle)
  • Hieraaetus fasciatus (Bonelli’s Eagle)
  • Ichthyaetus ichthyaetus (Pallas's Gull) 
  • Ichthyaetus melanocephalus (Mediterranean Gull)
  • Larosterna inca (Inca tern)
  • Larus argentatus (Herring Gull)
  • Larus armenicus (Armenian Gull)
  • Larus brachyrhynchus (Short-billed Gull)
  • Larus brachyrhynchus (Short-billed Gull)
  • Larus cachinnans (Caspian gull)
  • Larus belcheri (Belcher's gull)
  • Larus californicus (California Gull)
  • Larus canus (Mew Gull)
  • Larus delawarensis (Ring-billed Gull) 
  • Larus dominicanus (Kelp Gull)
  • Larus fuscus (Lesser Black-backed Gull)
  • Larus glaucoides (Iceland Gull)
  • Larus marinus (Great black-backed Gull)
  • Larus michahellis (Yellow-legged Gull)
  • Larus novaehollandiae (Silver Gull)
  • Larus schistisagus (Slaty-backed Gull)
  • Larus thayeri (Thayer's gull)
  • Leucophaeus pipixcan (Franklin's Gull)
  • Megascops asio (Eastern Screech Owl)
  • Megascops kennicottii (Western Screech-Owl)
  • Milvus milvus (Red Kite)
  • Milvus migrans (Black Kite)
  • Morus bassanus (Northern Gannet)
  • Nisaetus nipalensis (Mountain Hawk Eagle)
  • Otus scops (Scops Owl)
  • Pagophila eburnean (Ivory Gull)
  • Pandion haliaetus (Osprey)
  • Parabuteo unicinctus (Harris's Hawk) 
  • Pica hudsonia (Black-billed magpie)
  • Pica pica (Common Magpie)
  • Sagittarius serpentarius (Secretary Bird)
  • Spilornis cheela (Crested Serpent Eagle)
  • Strigiformes (Owl)
  • Strix aluco (Tawny owl)
  • Strix uralensis (Ural Owl)
  • Strix varia (Barred owl) 
  • Sula capensis (Cape Gannet)
  • Thalasseus elegans (Elegant tern)
  • Tyto alba (Common Barn-Owl)
  • Xema sabini (Sabine’s Gull)

Global Updates on A(H5N1)