H5N1 genetic structure

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The genetic structure of H5N1, a highly pathogenic avian influenza virus (influenza A virus subtype H5N1), is characterized by a segmented RNA genome consisting of eight gene segments that encode for various viral proteins essential for replication, host adaptation, and immune evasion.

Contents

Virus

Influenza A virus subtype H5N1 (A/H5N1) is a subtype of the influenza A virus, which causes influenza (flu), predominantly in birds. It is enzootic (maintained in the population) in many bird populations, and also panzootic (affecting animals of many species over a wide area). [1] A/H5N1 virus can also infect mammals (including humans) that have been exposed to infected birds; in these cases, symptoms are frequently severe or fatal. All subtypes of the influenza A virus share the same genetic structure and are potentially able to exchange genetic material by means of reassortment [2] [3]

A/H5N1 virus is shed in the saliva, mucus, and feces of infected birds; other infected animals may shed bird flu viruses in respiratory secretions and other body fluids (such as milk). [4] The virus can spread rapidly through poultry flocks and among wild birds. [4] An estimated half a billion farmed birds have been slaughtered in efforts to contain the virus. [2]

Symptoms of A/H5N1 influenza vary according to both the strain of virus underlying the infection and on the species of bird or mammal affected. [5] [6] Classification as either Low Pathogenic Avian Influenza (LPAI) or High Pathogenic Avian Influenza (HPAI) is based on the severity of symptoms in domestic chickens and does not predict the severity of symptoms in other species. [7] Chickens infected with LPAI A/H5N1 virus display mild symptoms or are asymptomatic, whereas HPAI A/H5N1 causes serious breathing difficulties, a significant drop in egg production, and sudden death. [8]

In mammals, including humans, A/H5N1 influenza (whether LPAI or HPAI) is rare. Symptoms of infection vary from mild to severe, including fever, diarrhoea, and cough. [6] Human infections with A/H5N1 virus have been reported in 23 countries since 1997, resulting in severe pneumonia and death in about 50% of cases. [9] Between 2003 and November 2024, the World Health Organization has recorded 948 cases of confirmed H5N1 influenza, leading to 464 deaths. [10] The true fatality rate may be lower because some cases with mild symptoms may not have been identified as H5N1. [11]

A/H5N1 influenza virus was first identified in farmed birds in southern China in 1996. [12] Between 1996 and 2018, A/H5N1 coexisted in bird populations with other subtypes of the virus, but since then, the highly pathogenic subtype HPAI A(H5N1) has become the dominant strain in bird populations worldwide. [13] Some strains of A/H5N1 which are highly pathogenic to chickens have adapted to cause mild symptoms in ducks and geese, [14] [7] and are able to spread rapidly through bird migration. [15] Mammal species that have been recorded with H5N1 infection include cows, seals, goats, and skunks. [16]

Due to the high lethality and virulence of HPAI A(H5N1), its worldwide presence, its increasingly diverse host reservoir, and its significant ongoing mutations, the H5N1 virus is regarded as the world's largest pandemic threat. [17] Domestic poultry may potentially be protected from specific strains of the virus by vaccination. [18] In the event of a serious outbreak of H5N1 flu among humans, health agencies have prepared "candidate" vaccines that may be used to prevent infection and control the outbreak; however, it could take several months to ramp up mass production. [4] [19] [20]

Nomenclature

This section is an excerpt from Influenza A virus § Influenza virus nomenclature.[ edit ]

Due to the high variability of the virus, subtyping is not sufficient to uniquely identify a strain of influenza A virus. To unambiguously describe a specific isolate of virus, researchers use the Influenza virus nomenclature, [21] which describes, among other things, the subtype, year, and place of collection. Some examples include: [22]

  • A/Rio de Janeiro/62434/2021 (H3N2). [22]
    • The starting A indicates that the virus is an influenza A virus.
    • Rio de Janeiro indicates the place of collection. 62434 is a laboratory sequence number. 2021 (or just 21) indicates that the sample was collected in 2021. No species is mentioned so by default, the sample was collected from a human.
    • (H3N2) indicates the subtype of the virus.
  • A/swine/South Dakota/152B/2009 (H1N2). [22]
    • This example shows an additional field before the place: swine. It indicates that the sample was collected from a pig.
  • A/California/04/2009 A(H1N1)pdm09. [22]
    • This example carries an unusual designation in the last part: instead of a usual (H1N1), it uses A(H1N1)pdm09. This was in order to distinguish the Pandemic H1N1/09 virus lineage from older H1N1 viruses. [22]
This section is an excerpt from Avian influenza § Highly pathogenic avian influenza.[ edit ]

Because of the impact of avian influenza on economically important chicken farms, a classification system was devised in 1981 which divided avian virus strains as either highly pathogenic (and therefore potentially requiring vigorous control measures) or low pathogenic. The test for this is based solely on the effect on chickens – a virus strain is highly pathogenic avian influenza (HPAI) if 75% or more of chickens die after being deliberately infected with it. The alternative classification is low pathogenic avian influenza (LPAI). [23] This classification system has since been modified to take into account the structure of the virus' haemagglutinin protein. [24] Other species of birds, especially water birds, can become infected with HPAI virus without experiencing severe symptoms and can spread the infection over large distances; the exact symptoms depend on the species of bird and the strain of virus. [23] Classification of an avian virus strain as HPAI or LPAI does not predict how serious the disease might be if it infects humans or other mammals. [23] [25]

Since 2006, the World Organization for Animal Health requires all LPAI H5 and H7 detections to be reported because of their potential to mutate into highly pathogenic strains. [26]

Structure and genome

Influenza A virus structure Viruses-10-00497-g001.png
Influenza A virus structure

Structure

The influenza A virus has a negative-sense, single-stranded, segmented RNA genome, enclosed in a lipid envelope. The virus particle (also called the virion) is 80–120 nanometers in diameter such that the smallest virions adopt an elliptical shape; larger virions have a filamentous shape. [27]

Core - The central core of the virion contains the viral RNA genome, which is made of eight separate segments. [28] The nucleoprotein (NP) coats the viral RNA to form a ribonucleoprotein that assumes a helical (spiral) configuration. Three large proteins (PB1, PB2, and PA), which are responsible for RNA transcription and replication, are bound to each segment of viral RNP. [28] [29] [30]

Capsid - The matrix protein M1 forms a layer between the nucleoprotein and the envelope, called the capsid. [28] [29] [30]

Envelope - The viral envelope consists of a lipid bilayer derived from the host cell. Two viral proteins; hemagglutinin (HA) and neuraminidase (NA), are inserted into the envelope and are exposed as spikes on the surface of the virion. Both proteins are antigenic; a host's immune system can react to them and produce antibodies in response. The M2 protein forms an ion channel in the envelope and is responsible for uncoating the virion once it has bound to a host cell. [28] [29] [30]

Genome

The table below presents a concise summary of the influenza genome and the principal functions of the proteins which are encoded. Segments are conventionally numbered from 1 to 8 in descending order of length. [31] [32] [33] [34]

RNA SegmentLengthProteinFunction
1- PB22341PB2 (Polymerase Basic 2)A component of the viral RNA polymerase.

PB2 also inhibits JAK1/STAT signaling to inhibit host innate immune response

2- PB12341PB1 (Polymerase Basic 1)A component of the viral RNA polymerase.

It also degrades the host cell’s mitochondrial antiviral signaling protein

PB1-F2 (Polymerase Basic 1-Frame 2)An accessory protein of most IAVs. Not needed for virus replication and growth, it interferes with the host immune response.
3- PA2233PA (Polymerase Acid)A component of the viral RNA polymerase
PA-XArises from a ribosomal frameshift in the PA segment. Inhibits innate host immune responses, such as cytokine and interferon production.
4- HA1775 HA (Hemagglutinin) Part of the viral envelope, a protein that binds the virion to host cells, enabling the virus’s RNA genetic material to invade it
5- NP1565 NP (Nucleoprotein) The nucleoprotein associates with the viral RNA to form a ribonucleoprotein (RNP).

At the early stage of infection, the RNP binds to the host cell’s importin-α which transports it into the host cell nucleus, where the viral RNA is transcribed and replicated.

At a later stage of infection, newly manufactured viral RNA segments assemble with the NP protein and polymerase (PB1, PB2 and PA) to form the core of a progeny virion

6- NA1409 NA (Neuraminidase) Part of the viral envelope. NA enables the newly assembled virions to escape the host cell and go on to propagate the infection.

NA also facilitates the movement of infective virus particles through mucus, enabling them to reach host epithelial cells.

7- M1027 M1 (Matrix Protein 1) Forms the capsid, which coats the viral nucleoproteins and supports the structure of the viral envelope.

M1 also assists with the function of the NEP protein.

M2 (Matrix Protein 2) Forms a proton channel in the viral envelope, which is activated once a virion has bound to a host cell. This uncoats the virus, exposing its infective contents to the cytoplasm of the host cell
8- NS890 NS1 (non-structural protein 1) Counteracts the host’s natural immune response and inhibits interferon production.
NEP (Nuclear Export Protein, formerly NS2 non-structural protein 2)Cooperates with the M1 protein to mediate the export of viral RNA copies from nucleus into cytoplasm in the late stage of viral replication

Three viral proteins - PB1, PB2, and PA - associate to form the RNA-dependent RNA polymerase (RdRp) which functions to transcribe and replicate the viral RNA.

Viral messenger RNA Transcription - The RdRp complex transcribes viral mRNAs by using a mechanism called cap-snatching. It consists in the hijacking and cleavage of host capped pre-mRNAs. Host cell mRNA is cleaved near the cap to yield a primer for the transcription of positive-sense viral mRNA using the negative-sense viral RNA as a template. [35] The host cell then transports the viral mRNA into the cytoplasm where ribosomes manufacture the viral proteins. [31] [32] [33] [34]

Replication of the viral RNA -The replication of the influenza genome involves two steps. The RdRp first of all transcribes the negative-sense viral genome into a positive-sense complimentary RNA (cRNA), then the cRNAs are used as templates to transcribe new negative-sense vRNA copies. These are exported from the nucleus and assemble near the cell membrane to form the core of new virions. [31] [32] [33] [34]

Surface encoding gene segments

All influenza A viruses have two gene segments titled HA and NA which code for the antigenic proteins hemagglutin and neuraminidase which are located on the external envelope of the virus.

HA

HA codes for hemagglutinin, which is an antigenic glycoprotein found on the surface of the influenza viruses and is responsible for binding the virus to the cell that is being infected. Hemagglutinin forms spikes at the surface of flu viruses that function to attach viruses to cells. This attachment is required for efficient transfer of flu virus genes into cells, a process that can be blocked by antibodies that bind to the hemagglutinin proteins. One genetic factor in distinguishing between human flu viruses and avian flu viruses is that avian influenza HA bind to alpha 2-3 sialic acid receptors while human influenza HA bind alpha 2-6 sialic acid receptors. [36]

NA

NA codes for neuraminidase which is an antigenic glycoprotein enzyme found on the surface of the influenza viruses. It helps the release of progeny viruses from infected cells. The antiviral drugs Tamiflu and Relenza work by inhibiting some strains of neuraminidase. [37]

Matrix encoding gene segments

M

M codes for the matrix proteins (M1 and M2) that, along with the two surface proteins (hemagglutinin and neuraminidase), make up the capsid (protective coat) of the virus. It encodes by using different reading frames from the same RNA segment.

Nucleoprotein encoding gene segments.

NP

NP codes for a structural protein which encapsidates the negative strand viral RNA. [39]

NS

NS codes for two nonstructural proteins (NS1 and Nuclear Export Protein NEP - formerly called NS2).

Polymerase encoding gene segments

PA

PA codes for the PA protein which is a component of the viral polymerase.

PB1

PB1 codes for the PB1 protein and the PB1-F2 protein.

PB2

PB2 codes for the PB2 protein which is a component of the viral polymerase.

Mutation

This section is an excerpt from Influenza A virus § Pandemic potential.[ edit ]
Influenza viruses have a relatively high mutation rate that is characteristic of RNA viruses. [41] The segmentation of the influenza A virus genome facilitates genetic recombination by segment reassortment in hosts who become infected with two different strains of influenza viruses at the same time. [42] [43] With reassortment between strains, an avian strain which does not affect humans may acquire characteristics from a different strain which enable it to infect and pass between humans - a zoonotic event. [44] It is thought that all influenza A viruses causing outbreaks or pandemics among humans since the 1900s originated from strains circulating in wild aquatic birds through reassortment with other influenza strains. [45] [46] It is possible (though not certain) that pigs may act as an intermediate host for reassortment. [47]
This section is an excerpt from Influenza A virus § Surveillance.[ edit ]
The Global Influenza Surveillance and Response System (GISRS) is a global network of laboratories that monitor the spread of influenza with the aim to provide the World Health Organization with influenza control information and to inform vaccine development. [48] Several millions of specimens are tested by the GISRS network annually through a network of laboratories in 127 countries. [49] As well as human viruses, GISRS also monitors avian, swine, and other potentially zoonotic influenza viruses.

See also

Related Research Articles

<i>Influenza A virus</i> Species of virus

Influenza A virus (IAV) is the only species of the genus Alphainfluenzavirus of the virus family Orthomyxoviridae. It is a pathogen with strains that infect birds and some mammals, as well as causing seasonal flu in humans. Mammals in which different strains of IAV circulate with sustained transmission are bats, pigs, horses and dogs; other mammals can occasionally become infected.

<span class="mw-page-title-main">Avian influenza</span> Influenza caused by viruses adapted to birds

Avian influenza, also known as avian flu or bird flu, is a disease caused by the influenza A virus, which primarily affects birds but can sometimes affect mammals including humans. Wild aquatic birds are the primary host of the influenza A virus, which is enzootic in many bird populations.

<span class="mw-page-title-main">Antigenic shift</span> Process by which two or more different strains of a virus combine to form a new subtype

Antigenic shift is the process by which two or more different strains of a virus, or strains of two or more different viruses, combine to form a new subtype having a mixture of the surface antigens of the two or more original strains. The term is often applied specifically to influenza, as that is the best-known example, but the process is also known to occur with other viruses, such as visna virus in sheep. Antigenic shift is a specific case of reassortment or viral shift that confers a phenotypic change.

<span class="mw-page-title-main">Hemagglutinin (influenza)</span> Hemagglutinin of influenza virus

Influenza hemagglutinin (HA) or haemagglutinin[p] is a homotrimeric glycoprotein found on the surface of influenza viruses and is integral to its infectivity.

<i>Orthomyxoviridae</i> Family of RNA viruses including the influenza viruses

Orthomyxoviridae is a family of negative-sense RNA viruses. It includes seven genera: Alphainfluenzavirus, Betainfluenzavirus, Gammainfluenzavirus, Deltainfluenzavirus, Isavirus, Thogotovirus, and Quaranjavirus. The first four genera contain viruses that cause influenza in birds and mammals, including humans. Isaviruses infect salmon; the thogotoviruses are arboviruses, infecting vertebrates and invertebrates. The Quaranjaviruses are also arboviruses, infecting vertebrates (birds) and invertebrates (arthropods).

<span class="mw-page-title-main">Influenza A virus subtype H5N1</span> Subtype of influenza A virus

Influenza A virus subtype H5N1 (A/H5N1) is a subtype of the influenza A virus, which causes influenza (flu), predominantly in birds. It is enzootic in many bird populations, and also panzootic. A/H5N1 virus can also infect mammals that have been exposed to infected birds; in these cases, symptoms are frequently severe or fatal.

<span class="mw-page-title-main">Influenza pandemic</span> Pandemic involving influenza

An influenza pandemic is an epidemic of an influenza virus that spreads across a large region and infects a large proportion of the population. There have been five major influenza pandemics in the last 140 years, with the 1918 flu pandemic being the most severe; this is estimated to have been responsible for the deaths of 50–100 million people. The 2009 swine flu pandemic resulted in under 300,000 deaths and is considered relatively mild. These pandemics occur irregularly.

<span class="mw-page-title-main">Influenza A virus subtype H3N2</span> Virus subtype

Influenza A virus subtype H3N2 (A/H3N2) is a subtype of influenza A virus (IAV). Some human-adapted strains of A/H3N2 are endemic in humans and are one cause of seasonal influenza (flu). Other strains of H1N1 are endemic in pigs and in birds. Subtypes of IAV are defined by the combination of the antigenic H and N proteins in the viral envelope; for example, "H1N1" designates an IAV subtype that has a type-1 hemagglutinin (H) protein and a type-1 neuraminidase (N) protein.

<span class="mw-page-title-main">Transmission and infection of H5N1</span> Spread of an influenza virus

Transmission and infection of H5N1 from infected avian sources to humans has been a concern since the first documented case of human infection in 1997, due to the global spread of H5N1 that constitutes a pandemic threat.

<span class="mw-page-title-main">Influenza A virus subtype H5N2</span> Virus subtype

H5 N2 is a subtype of the species Influenzavirus A. The subtype infects a wide variety of birds, including chickens, ducks, turkeys, falcons, and ostriches. Affected birds usually do not appear ill, and the disease is often mild as avian influenza viral subtypes go. Some variants of the subtype are much more pathogenic than others, and outbreaks of "high-path" H5N2 result in the culling of thousands of birds in poultry farms from time to time. It appears that people who work with birds can be infected by the virus, but suffer hardly any noticeable health effects. Even people exposed to the highly pathogenic H5N2 variety that killed ostrich chicks in South Africa only seem to have developed conjunctivitis, or a perhaps a mild respiratory illness. There is no evidence of human-to-human spread of H5N2. On November 12, 2005 it was reported that a falcon was found to have H5N2. On June 5, 2024, the first confirmed human case of H5N2 was reported in Mexico.

<span class="mw-page-title-main">Spanish flu research</span> Scientific research of the 1918 influenza pandemic

Spanish flu research concerns studies regarding the causes and characteristics of the Spanish flu, a variety of influenza that in 1918 was responsible for the worst influenza pandemic in modern history. Many theories about the origins and progress of the Spanish flu persisted in the literature, but it was not until 2005, when various samples of lung tissue were recovered from American World War I soldiers and from an Inupiat woman buried in permafrost in a mass grave in Brevig Mission, Alaska, that significant genetic research was made possible.

<span class="mw-page-title-main">Fujian flu</span> Strains of influenza

Fujian flu refers to flu caused by either a Fujian human flu strain of the H3N2 subtype of the Influenza A virus or a Fujian bird flu strain of the H5N1 subtype of the Influenza A virus. These strains are named after Fujian, a coastal province in Southeast China.

<span class="mw-page-title-main">Goose Guangdong virus</span> Strain of H5N1 influenza virus

The Goose Guangdong virus refers to the strain A/Goose/Guangdong/1/96 (Gs/Gd)-like H5N1 HPAI viruses. It is a strain of the Influenzavirus A subtype H5N1 virus that was first detected in a goose in Guangdong in 1996. It is an HPAI virus, meaning that it can kill a very high percentage of chickens in a flock in mere days. It is believed to be the immediate precursor of the current dominant strain of HPAI A(H5N1) that evolved from 1999 to 2002 creating the Z genotype that is spreading globally and is epizootic and panzootic, killing tens of millions of birds and spurring the culling of hundreds of millions of others to stem its spread.

<span class="mw-page-title-main">Human mortality from H5N1</span>

H5N1 influenza virus is a type of influenza A virus which mostly infects birds. H5N1 flu is a concern due to the fact that its global spread that may constitute a pandemic threat. The yardstick for human mortality from H5N1 is the case-fatality rate (CFR); the ratio of the number of confirmed human deaths resulting from infection of H5N1 to the number of those confirmed cases of infection with the virus. For example, if there are 100 confirmed cases of a disease and 50 die as a consequence, then the CFR is 50%. The case fatality rate does not take into account cases of a disease which are unconfirmed or undiagnosed, perhaps because symptoms were mild and unremarkable or because of a lack of diagnostic facilities. The Infection Fatality Rate (IFR) is adjusted to allow for undiagnosed cases.

<span class="mw-page-title-main">Influenza</span> Infectious disease

Influenza, commonly known as the flu, is an infectious disease caused by influenza viruses. Symptoms range from mild to severe and often include fever, runny nose, sore throat, muscle pain, headache, coughing, and fatigue. These symptoms begin one to four days after exposure to the virus and last for about two to eight days. Diarrhea and vomiting can occur, particularly in children. Influenza may progress to pneumonia from the virus or a subsequent bacterial infection. Other complications include acute respiratory distress syndrome, meningitis, encephalitis, and worsening of pre-existing health problems such as asthma and cardiovascular disease.

<span class="mw-page-title-main">Viral neuraminidase</span> InterPro Family

Viral neuraminidase is a type of neuraminidase found on the surface of influenza viruses that enables the virus to be released from the host cell. Neuraminidases are enzymes that cleave sialic acid groups from glycoproteins. Viral neuraminidase was discovered by Alfred Gottschalk at the Walter and Eliza Hall Institute in 1957. Neuraminidase inhibitors are antiviral agents that inhibit influenza viral neuraminidase activity and are of major importance in the control of influenza.

<span class="mw-page-title-main">H5N1 vaccine</span> Vaccine designed to provide immunity against H5N1 influenza

A H5N1 vaccine is an influenza vaccine intended to provide immunization to influenza A virus subtype H5N1.

<span class="mw-page-title-main">Influenza A virus subtype H7N9</span> Subtype of the influenza A virus

Influenza A virus subtype H7N9 (A/H7N9) is a subtype of the influenza A virus, which causes influenza (flu), predominantly in birds. It is enzootic in many bird populations. The virus can spread rapidly through poultry flocks and among wild birds; it can also infect humans that have been exposed to infected birds.

<span class="mw-page-title-main">Host switch</span> Evolutionary change of the host specificity of a parasite or pathogen

In parasitology and epidemiology, a host switch is an evolutionary change of the host specificity of a parasite or pathogen. For example, the human immunodeficiency virus used to infect and circulate in non-human primates in West-central Africa, but switched to humans in the early 20th century.

<span class="mw-page-title-main">2020–2024 H5N1 outbreak</span> Global outbreak of avian flu H5N1 in 2020–2024

Since 2020, outbreaks of avian influenza subtype H5N1 have been occurring, with cases reported from every continent except Australia as of December 2024. Some species of wild aquatic birds act as natural asymptomatic carriers of a large variety of influenza A viruses, which can infect poultry, other bird species, mammals and humans if they come into close contact with infected feces or contaminated material, or by eating infected birds. In late 2023, H5N1 was discovered in the Antarctic for the first time, raising fears of imminent spread throughout the region, potentially leading to a "catastrophic breeding failure" among animals that had not previously been exposed to avian influenza viruses. The main virus involved in the global outbreak is classified as H5N1 clade 2.3.4.4b, however genetic diversification with other clades such as 2.3.2.1c has seen the virus evolve in ability to cause significant outbreaks in a broader range of species including mammals.

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