Avian influenza virus

Influenza A virus is an Orthomyxovirus; a family of segmented negative-sense RNA viruses that also includes Influenza types B, C and D, Thogotovirus and Infectious Salmon Anaemia virus. Influenza A viruses are primarily a virus of birds and only in birds have all the different subtypes been found, defined by their surface glycoproteins Haemagglutinin (HA1-16) and Neuraminidase (NA1-9) 1,2. The closely related Influenza A-like viruses of Bats have also recently been described (H17-18 and N10-11) 3. Certain subtypes have evolved and been maintained in humans as seasonal influenza, such as H1N1, H3N2 and H2N2.

Avian Influenza (AI) is described as low pathogenic (LP) or highly pathogenic (HP). LPAI is generally described as an acute mild infection of the intestinal tract of aquatic birds, or as a respiratory infection of poultry, associated with few or no clinical signs 4. HPAI on the other hand is able to cause high mortality in poultry with some strains capable of significant clinical signs in wild birds. Previously regarded as ‘fowl plague’, HPAI was first recognised as the ‘filterable’ infective agent to cause ‘fowl plague’ in 1901 by Centanni and Savonuzzi, later characterised as influenza virus by Schäfer 1955 5.

Virus genome and proteins

Influenza A virus particles are pleomorphic, that is to say they may be spherical (~100nm) or filamentous (up to 20µm), depending on the virus strain, cell origin, passage history and Matrix protein 1 (M1) 6. A lipid membrane encases the virion and harbours three transmembrane proteins HA, NA and Matrix protein 2 (M2) (Figure 1A). HA and NA are glycoproteins, present as a homotrimer and homotetramer, respectively, involved in cell attachment by sialic acid receptors (HA) and release (NA). Positioned beneath the envelope, M1 protein acts as a structural case that protects the virus genome. Genome release from the cell endosome after virus entry is facilitated by the M2 ion channel and pH mediated membrane fusion by the HA.

Eight negative-sense RNA segments make up the virus genome. Each segment exists as a ribonucleoprotein (RNP) complex, consisting of the gene segment together with nucleoprotein (NP) and the polymerase complex (Polymerase Basic 2 [PB2], Polymerase Basic 1 [PB1] and Polymerase Acidic [PA] protein). Each gene segment is flanked by un-translated regions (UTR) at the 5’ and 3’ ends including the virus gene promoter sequences. Virus transcription (by a cap-snatching mechanism) and replication (by a complimentary RNA intermediate) are carried out by the virus RNA-dependent RNA polymerase in the cell nucleus. Influenza utilises a number of genetic tricks to encode multiple protein products from a gene segment. So far, the PB1, PA, M and NS (non-structural) gene segments have been found to encode more than one protein product. The PB1 gene encodes proteins PB1-F2 and PB1-40 by an alternative open reading frame 7,8. Similarly the PA gene also contains alternative initiation codons to generate two N-terminal truncated forms of PA, PA-N155 and PA-N182, together with PA-X which carries a C-terminus in a different reading frame as a result of a ribosomal frameshift 9,10. As well as coding for M1 and NS1 (Non-structural protein 1) the M and NS gene segments use alternative splicing as a mechanism to generate M2 and M42 and NEP/NS2 (Nuclear Export Protein/Non-structural protein 2) respectively 11,12. It appears that not all influenza A viruses encode the recently discovered protein products and each genome must be considered strain by strain.

Virus exit is by budding at the cell surface and is known to involve scission by M1, but the mechanism of this and genome packaging remains poorly understood 13.

Epidemiology and host range

Wild birds are considered the primordial source of influenza, in particular influenza is most frequently found in the Anseriformes (ducks, geese and swans) and the Charadriiformes (gulls, terns and shorebirds). The natural site of replication is the intestinal tract and high titres of virus can be shed and transmitted by the faecal/oral route 14, although experimental infections show other routes, such as intracloacal inoculation, can be successful 15.

Certain subtypes can pass from wild birds into domestic Galliformes such as chickens and turkeys: H1, H4-5, H7 and H9 subtypes are isolated most frequently 1. Galliformes are generally more susceptible to influenza infection suffering a respiratory disease and may present clinical signs, depending on the virus subtype or strain 16. Poultry are particularly vulnerable to HPAI, and the recent emergence of the H5 and H7 strains have caused great economic loss and concern about zoonosis. Migratory birds are thought to play an important role in the global spread of AI and introduction into poultry 17.

Influenza viruses have also been described in a number of other animals including swine, equine, deer, big cats, dogs, ferrets, seals, whales and bats 1. Similarly to humans, influenza viruses that have crossed the species barrier maintain preferred subtypes in certain hosts. The H1N1, H1N2 and H3N2 subtypes are endemic in swine 18,19 and the H3N8 subtype is commonly found in horses and dogs 20,21.

There are several barriers influenza faces when crossing from one species to another. Be it cell receptor preference between birds and mammals (α-2,3 linked sialic acids to α-2,6 linked sialic acids, respectively); pH of HA fusion (higher for AI than human seasonal influenza); or mutations in the virus polymerase in order to co-opt human cellular protein ANP32A/B instead of chicken ANP32A 22,23.

The ability of the virus to adapt to these different hosts is aided by its error prone virus RNA-dependent RNA-polymerase, facilitating frequent mutation of its genome, and by the ability of its segmented genome to reassort between different strains in a co-infected host cell giving rise to novel genotypes.


Cleavage of the HA by host tryptases is required for infectivity, and the amino acid sequence of the cleavage site is a major determinant of pathogenicity for AI. LPAI viruses carry a monobasic cleavage site and replication is restricted to sites that express proteases that recognise this sequence i.e. in the respiratory or intestinal tract of birds. Poultry infected with LPAI typically exhibit mild clinical signs and limited cases of mortality, although increases in mortality can be seen in some instances such as co-infection with other pathogens 24. HPAI H5 and H7 HA proteins carry a multi-basic cleavage site (MBCS) and may be cleaved by ubiquitous intracellular furin-like serine proteases such as furin and PC6 25–30. Restriction to the respiratory or intestinal tract no longer applies and a systemic infection ensues, leading to increased pathogenesis 31. These viruses cause high levels of morbidity and mortality in chickens and other poultry but are often less severe in wild birds.

The pathobiology of HPAI has been well described: severe damage of endothelial cells and parenchymal organs is typical, although pathobiology may vary and include: swelling of the head, haemorrhages, cyanosis, edema, congestion and organ necrosis and inflammation. Interestingly, infections in waterfowl (i.e. ducks and geese) demonstrate more neurologically associated pathobiology revealed by clinical signs such as ruffled feathers (inability to groom), torticollis (twisted neck) and loss of balance. The overall mortality for waterfowl such as domestic ducks is generally lower than for chickens 32–34.

The pathogenicity of influenza A viruses is determined by their genotype (H5 and H7 subtypes with a MBCS) and officially defined by a standard test in chickens described by the World Organisation for Animal Health (OIE) as the intravenous pathogenicity index (IVPI), carried out in ten 4 to 8 week old chickens intravenously injected with virus and scored for disease over 10 days 35.

Contributed by: Jason Long (Imperial College London)

Copyright © 2016 Jason Long

First posted: 2-Nov-2016


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