Influenza virus genome

A virus is a parasitic microorganism, measuring approximately from 20-400 nm, which encases its RNA or DNA genome, in a capsid, which is composed of protein subunits called capsomers.

The capsid carries out the role to protect the virus genome, in order to avoid genome inactivation. Moreover, the capsid proteins of numerous viruses allow the binding of the virion to specific receptors on host cells, thus allowing their genome to be released within the host cell. Furthermore, some viruses consist of a lipid-protein envelope, which encloses the nucleic acids and the capsids (nucleocapsid). This envelope consists of mainly integral proteins, of more then one form, which allow the binding of the virion to the host cell membrane and thus entrance via fusion and endocytosis [1].

The influenza virus is one of the virion's that consists of an envelope enclosing the nucleocapsid. Two of the integral proteins that it contains on its envelope are glycoproteins, these antigens are called Haemagglutinin and Neuraminidase, and there is a third protein, which is non-glycosylated, called M2.

Orthomyxovirus is the family to which influenza virus belongs. Moreover, there are three types of influenza virus, type A, B and C, from which the influenza A virus possesses the capability to infect other mammals, such as pigs and birds as well as humans. Conversely, the presence of influenza B and C is only in humans [2].

Influenza A virus has further subtypes, with the subtypes H1N1 and H3N2 being responsible for the seasonal flu [3].

The seasonal flu affects mainly the respiratory pathway, that is to say the throat, nose and bronchi; moreover, the lungs are also infected in some cases [3].

Influenza can be cured with vaccines or antiviral drugs. However, it still possesses the potential to lead to mortality in cases of immunocompromised patients, the elderly, that is to say people 65 years of age and over, the very young, that is to say children under the age of 2 years and individuals with medical conditions such as CHD's and diabetes. Consequently, annually 250 000 to 500 000 deaths result worldwide [3].

Nevertheless, despite the existence of vaccines against influenza A and B, every so often the influenza virus excels from an epidemic to a global pandemic.

The occurrence of a global pandemic with regard to influenza is high, as there have been many incidents in time when a new genome variant, a reassortant of the influenza virus surpassed its parental genome [1]. This is due to the capability of the reassortant, of enhancing its survival in the host cell, or decreasing its chances of it being removed from its host cell, being greater than that of its parental genome.

Consequently, ones immune system can no longer eliminate this new strain of influenza, that is to say ones body does not possibly produce the antibodies that recognise the new antigens present on this new strain, as they have never encountered this strain of influenza.

Moreover, influenza is vastly contagious, that is to say, one can transmit influenza when they cough and sneeze, as droplets dispensed from their mouth are carried and passed via air molecules, and therefore infect the surrounding people. Moreover, the dispensed droplets containing influenza are transmitted by one touching other surfaces with infected hands [3], or coughing and sneezing on surfaces, which other people then touch and further pass on the infection if not contract it.

Thus, the new strain of influenza, like, the previous strains is effectively transmitted from one individual to another. Moreover, the presence of the new strain occurring in more then one geographic region due to intermixing of people, materials and such from one region to another, gives rise to a global pandemic of the influenza virus.

Incidents of these pandemic strains of influenza have occurred since the year of 1918, at which point it resulted in approximately 50 million deaths globally. This was the ‘Spanish flu' epidemic, caused by a virus which resulted from an adaptation of an avian influenza virus in the human host, resulting in a H1N1 virus, which is still accumulating within the human population today and has evolved in many ways [4].

Such an evolution of the influenza virus has, after more than 40 years resulted in a global pandemic. The pandemic alert level of the H1N1 virus, ‘Swine flu' had been raised to phase 6 on the 11th of June 2009, with its severity categorised as moderate [5].

Swine flu has been existent even in the earlier years; however, as flu in pigs only. Nevertheless, the swine flu referred to today, that is to say the H1N1 virus strain of 2009, has somehow jumped the species barrier and infected humans, becoming a swine-avian-human virus.

Virus evolution occurs as a result of either mutations in the genome of the virus, recombination of RNA or DNA segments of the virus, and reassortment of RNA or DNA segments of two different strains of segmented viruses. Moreover, acquisition of cell genes also occurs, which causes the immune system to recognise the virus as one of the host's cell instead of a foreign cell [1].

The evolution of a virus enclosing RNA genome is more frequent and probable, compared to the evolution of a virus enclosing DNA genome. This is due to the possibilities of the occurrence of errors during replication of the RNA genome is higher that that of the DNA genome, as it undergoes proofreading by its DNA polymerases in order to avoid and eliminate any errors made. Conversely, RNA genome does not have such polymerases carrying out proofreading; resulting in more frequent and rapid evolution of the RNA genome viruses, compared to that of the DNA genome viruses. Thus, numerous new genome variants are produced of viruses with a RNA genome [1].

Influenza is a RNA genome virus; therefore, many variants emerge due to frequent evolution, forming new strains of influenza.

Moreover, influenza undergoes evolution due to reassortment of its RNA genome [1].

Influenza consists of a segmented genome, that is to say its minus-strand RNA has 8 segments, with two of the 8 segments responsible for encoding the antigen proteins haemagglutinin and neuraminidase. Reassortment of the RNA sequence leads to a difference in the production of these integral, glycoprotein antigens, Haemagglutinin (H) and Neuraminidase (H). Thus, this antigenic variation means that the virus is able to avoid the immune system, as antibodies present in ones immune system can no longer recognise the newly formed antigens on the influenza's envelope.

When the host cell is infected with two different strains of the same virus, replication of the RNA of both strains occurs. Thereafter, reassortment of the two different genomes occurs in the infected host cell, producing reassortants, that is to say genome variants. These assortants contain genes of both parent strains, therefore, the reassortants have both antigens, that is to say, haemagglutinin and neuraminidase of both parent strains present on their envelope. The reassortant that then dominates and surpasses the previous strains is the reassortant that is more efficient and possesses an advantage over the other reassortants and strains in that particular niche, such as having a better tolerance towards antiviral drugs. This reassortant then infects another host cell, allowing replication of its variant genome, resulting in virion's with this new variant genome. Thus, a new strain of influenza is formed, which will then deceive the immune system, and therefore be able to infect more host cells within the individual and other individuals as well, causing an epidemic, which can then excel to a global pandemic. [1]

In usual cases of viral infections, such as the influenza seasonal flu, the symptoms go away in 1 to 2 weeks time due to the effective immune system.

The immune system produces antibodies, which are immunoglobulin glycoproteins. Antibodies recognise specific antigens on specific virus surfaces that have been encountered by the host before. These antibodies then bind to the virion and eradicate the ability of the virus to infect. Moreover, antibodies binding to the antigens on the virion allow phagocytises of the virion, via phagocytes, that is to say neutrophils and macrophages. [1]

Moreover, interferons are part of ones immune system that come into action when the host cell is infected with a virus. They exist in alpha beta and gamma forms, and induce anti-viral mechanisms. This is due to the release of these protein molecules, which then bind to their receptors cites on host cells, blocking any further replication of the virus or destroying the cell.

Globally mortality rates increase due to individuals that are immunocompromised, very elderly, very young, or diagnosed with particular medical conditions, as they are highly incapable of tolerating the new strains, as their body's immune system is not as good as the average individual. Nevertheless, successful vaccines and viral drugs, Tami-flu tablets and H1N1 vaccine have been prepared, since swine flu has become a global pandemic. Moreover, the patients mentioned above are being vaccinated before others, such as diabetics.

Nevertheless, it is not probable for one to develop immunity to influenza, as influenza frequently undergoes genetic changes; it evolves into new strains, resulting in mortality on occasions, especially if the host is immunocompromised, very old, very young or diagnosed with particular medical conditions.


[1] John Carter, Venetia Saunders, Virology, Principles and Applications Carter, J, Saunders, V (2008). Virology. Italy: John Wiley & Sons Ltd. Pg 39, 105-108, 261-268





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