The influenza virus has been a focus of intensive investigation in many disciplines of modern biology. All influenza viruses are characterized by a segmented negative-sense RNA core surrounded by a lipid envelope. The most effective way to control influenza infection is vaccination and designing of a successful vaccine needs a proper understanding of the virus morphology and its host interaction.

The influenza virus particles are pleomorphic with spherical or filamentous morphology, or both. The spherical or filamentous morphology varies with the different number of passages. Like in clinical isolates filamentous particles outnumber the spherical particles as they undergo a limited number of passages in eggs or cell culture, whereas laboratory strains consist almost exclusively of spherical virions (80–120 nm in diameter) as they are extensively passaged. It is an enveloped virus with the following –

— An outer layer is a lipid membrane which is taken from the host cell in which the virus multiplies.

—- Inserted into the lipid membrane are ‘spikes,’ which are proteins – precisely glycoproteins, because they consist of the protein linked to sugars – known as HA (hemagglutinin) and NA (neuraminidase). These are the proteins that determine the subtype of influenza virus (A/H1N1, for example). The HA spikes are rod-shaped, whereas the NA spikes resemble mushrooms with slender stalks. The HA and NA are essential in the immune response against the virus; antibodies (proteins made by us to combat infection) against these spikes may protect against infection. The NA protein is the target of the antiviral drugs Relenza and Tamiflu. HA has a propensity to bind and aggregate red blood cells, as its name implies. This property of HA is exploited for the detection of influenza virus. Importantly, HA, which is a trimer, is the viral protein that recognizes the cellular receptor for the entry.

—-Also embedded in the lipid membrane is the M2 protein, which acts as an ion channel. The integral homo-tetrameric M2 membrane protein, although abundantly expressed at the surface of virus-infected cells, is nonetheless a relatively minor component of virions. It is the target of the antiviral adamantanes – amantadine and rimantadine.

—- Beneath the lipid membrane is a viral protein called M1, or matrix protein. This protein, which forms a shell, gives strength and rigidity to the lipid envelope. Cryoelectron microscopic studies suggest that the M1 can modify the lipid bilayer, causing the viral envelope to thicken. M1 is the primary determinant of virus budding.

Within the interior of the virion are the eight RNA segments. It is also called a “segmented genome” or “split genome,” because the genome is split into eight segments. The multiplicity of the genome is attributable to the emergence of viral variants through genetic recombination. Each RNA segment is a single-strand RNA 0.9 – 2.3 kb in length. It is also called “vRNA.” Being a negative-strand RNA, it is neither capped at the 5 end or polyadenylated at the 3 end. Instead, it has a triphosphate group at the 5 end (i.e., pppAp—) and a hydroxyl group at the 3 end (i.e., CUUUUGCU-OH-30 ). These are the genetic material of the virus; they code for one or two proteins.

Each RNA segment consists of RNA joined with several proteins – PB1, PB2, PA, NP. The interior of the virion also contains another protein called NEP. Unlike other RNA viruses, influenza viral genome replication occurs in the nucleus. Hence, the viral proteins essential for viral genome replication needs to be imported into the nucleus. For instance, NP (nucleocapsid protein), RdRp (PB1, PB2, PA subunit), NS1, and NEP are imported to the nucleus. The nucleocapsids are constituted by vRNA, NP, and RdRp (i.e., PB1, PB2, PA). This RNP complex now enters the nucleus via the nuclear pore. Most RNA polymerases do not need an RNA primer for transcription initiation (i.e., de novo initiation). However, influenza viral RdRp needs a primer for transcription initiation.

Moreover, influenza virus RdRp steals a capped RNA fragment from the cellular mRNAs and utilizes them as primers. Viral RdRp is composed of 3 subunits: PB1 acts as an RNA polymerase, PB2 exhibits cap-binding ability, and PA exhibits endonuclease activity. In particular, the endonuclease activity of PA cleaves a capped RNA fragment from the 5 end of cellular mRNAs, which is then used as a primer for viral mRNA transcription. This process is referred to as “cap-snatching.” Unlike cellular mRNA, the poly (A) tail is copied from the template during transcription. A short run of U residues (i.e., U6 7) at the 50 end of vRNA are repeatedly copied to make the tail (see Fig. 15.2B). In other words, poly (A) tail at the 3 end of viral mRNA is added via template-dependent manner. The mechanism is called “stuttering.” Viral mRNA sequences are not complementary to the 5 end of vRNA because the viral transcription is terminated after polyadenylation. Resulting viral mRNAs are exported to the cytoplasm and used as mRNA for the viral protein synthesis.

Influenza virus enters the cell via recognition of the cellular receptor, a sialic acid. The engagement of the HA timer to a sialic acid moiety of glycan on the cell membrane triggers endocytosis. The sialic acids are linked to galactose via either an α-2,3 linkage or an α-2,6 linkage. The HA of human influenza virus prefers to bind to an α-2,6 linkage, while HA of avian influenza virus prefers to bind to an α-2,3 linkage. Glycans in human upper respiratory tracts are largely composed of α-2,6 linkage. This is the reason why human infection of avian influenza virus is restricted. Upon endocytosis, the virus particles are located inside the endosome.

The acidic pH in the endosome triggers membrane fusion between the two membranes. Via the M2 ion channels, protons are imported inside of the viral envelope, and the resulting lower pH induces a conformational change of HA trimer such that an embedded fusion peptide domain becomes unfolded and activated. This activated fusion peptide triggers membrane fusion between two membranes, and as a result, the nucleocapsids inside the envelope are released to the cytoplasm.

Nowadays the focus of the influenza study has shifted to understand the interplay between influenza viruses and their host cells. Earlier studies, however, focused on the essential functions of viral proteins in the viral life cycle. In genome-wide RNA interference (RNAi) studies, double-stranded RNA molecules are used for the homology-dependent suppression of cellular gene activity to identify genes that are critical for the influenza viral life cycle 1-4.

In other studies, yeast two-hybrid analyses, proteomics approaches, gene-expression profiling studies, and mass spectrometry analyses have been used to identify cellular factors that interact with influenza virus proteins 5-10. These studies have identified a significant number of cellular factors that may interact with influenza virus proteins; however, follow-up studies are largely missing that assess the biological significance of the respective cellular protein for the viral life cycle.


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