Influenza Virus Research


Influenza (flu) is a respiratory infection in mammals and birds. It is caused by an RNA virus in the family Orthomyxoviridae. Influenza virus is divided into four main types (Influenza A, Influenza B, Influenza C, Influenza D), which are distinguished by differences in two major internal proteins (hemagglutinin (HA) and neuraminidase (NA)). Three of the four types of influenza viruses affect humans: Type A, Type B, and Type C. Type D has not been known to infect humans, but is believed to have the potential to do so. Influenza virus type A is found in a wide variety of bird and mammal species and can undergo major shifts in immunological properties. Influenza virus type B is largely confined to humans and is an important cause of morbidity. Little is known about Influenza virus type C, which is not an important source of morbidity. Influenza D was identified in 2016.

Influenza A virus is further divided into subtypes based on differences in the membrane proteins hemagglutinin (HA) and neuraminidase (NA), which are the most important targets for the immune system. The notation HhNn is used to refer to the subtype comprising the hth discovered Hemagglutinin (HA) protein and the nth discovered neuraminidase (NA) protein. The influenza viral Hemagglutinin (HA) protein is a homo trimer with a receptor binding pocket on the globular head of each monomer, and the influenza viral neuraminidase (NA) protein is a tetramer with an enzyme active site on the head of each monomer. Subtypes are further divided into strains; each genetically distinct virus isolate is usually considered to be a separate strain.

More information about influenza virus antigens

The influenza viral Hemagglutinin (HA) protein is a homo trimer with a receptor binding pocket on the globular head of each monomer. Hemagglutinin (HA) protein is translated in cells as a single protein, HA0, or hemagglutinin precursor protein. For viral activation, hemagglutinin precursor protein (HA0) must be cleaved by a trypsin-like serine endoprotease at a specific site, normally coded for by a single basic amino acid (usually arginine) between the HA1 and HA2 domains of the protein. After cleavage, the two disulfide-bonded protein domains produce the mature form of the protein subunits as a prerequisite for the conformational change necessary for fusion and hence viral infectivity.

Reagents of Hemagglutinin

Hemagglutinin ELISA Kits
H1N1 H3N2 H4N6 H5N1 H7N7
H7N9 H9N2 Influenza B

Influenza Hemagglutinin Structure

The hemagglutinin (HA) membrane glycoprotein of influenza virus is a trimer of identical subunits that are formed of two disulfide-linked polypeptides:
• Membrane-distal, HA1
• Membrane-proximal, HA2

The two domain are also called a triple-stranded coiled-coil of alpha-helices extends 76 A from the membrane and a globular region of antiparallel beta-sheet, which contains the receptor binding site and the variable antigenic determinants, is positioned on top of this stem. Each subunit has an unusual loop-like topology, starting at the membrane, extending 135 A distally and folding back to enter the membrane.
Influenza type A viruses into 16 HA (H1–H16) subtypes. Phylogenetically, there are two groups of HAs: group 1 contains H1, H2, H5, H6, H8, H9, H11, H12, H13, and H16, and group 2 contains H3, H4, H7, H10, H14, and H15

Hemagglutinin structure,Trimer

• Gold and silver: two of the monomers from each trimer
• The subunits that make up the third monomer are colored as follows:
blue: receptor binding
yellow: vestigial esterase
magenta and red: fusion subdomains

Hemagglutinin groups

• Phylogenetic tree:
16 subtypes of HA that fall into two distinct groups

Influenza Hemagglutinin Function

Hemagglutinin (HA) has two functions in virus infection:
• Receptor binding
• Membrane fusion

Hemagglutinin (HA) mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies.
Viruses are bound by HAs to cell-surface sialic acid receptors and are taken into cells by endocytosis. This activity is the target of antibodies that block infection. The HA1 domain of hemagglutinin binds to the monosaccharide sialic acid which is present on the surface of its target cells. Many strain-specific antibodies bind in or near the HA1, membrane-distal, receptor-binding site. By contrast, a number of cross-reactive anti-HA antibodies have been described that bind to the membrane proximal regions of HA and block membrane fusion.

Influenza Hemagglutinin Reference

• Donald J. Benton,Influenza hemagglutinin membrane anchor,PNAS,2018 115 (40):10112-10117
• Steven J. Gamblin,Influenza Hemagglutinin and Neuraminidase Membrane Glycoproteins,J Biol Chem. 2010 Sep 10; 285(37): 28403–28409
• Wilson IA.1981.Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution. Nature. 289 (5796): 366–73
• Boonstra S. 2018. Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective. Annual Review of Biophysics. 47 (1): 153–173.

Influenza neuraminidase is 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 and are required for influenza virus replication. In addition to the mutations that arise due to antigenic drift, the NA of influenza A viruses (IAVs) can exist in different forms.Based on HA and NA antigenicity using serologic tests with hyperimmune sera, there have been a total of 16 HA (H1-16) and 9 NA (N1-9) subtypes identified in birds.Nine subtypes of influenza A NA are divided into two phylogenic groups. The first group consists of the neuraminidases of N1, N4, N5 and N8 subtypes, and the second one consists of N2, N3, N6 N7 and N9 subtypes.These are expressed in numerous combinations of viruses isolated from aquatic avian species, and an additional two combinations, H17N10 and H18N11, have been identified in bats

Reagents of Neuraminidase

Neuraminidase Proteins
H1N1 H3N2 H4N6 H5N1 H7N7 H7N9
H9N2 H10N8 H12N5 Influenza B
Neuraminidase Antibodies
H1N1 H3N2 H4N6 H5N1 H7N7 H9N2
Neuraminidase cDNAs
H1N1 H3N2 H4N6 H5N1 H5N8 Influenza B

Influenza Neuraminidase Structure

The neuraminidase (NA) assembles as a tetramer of four identical polypeptides.The four monomers fold into four distinct structural domains:
• cytoplasmic tail
• transmembrane region
• stalk
• catalytic head

NA tetramer exists in local clusters on the virion surface or as isolated spikes surrounded by HA. Reduced stalk length may impact the ability of NA to contact sialic acids on mucins or cellular receptors as neighboring HA may sterically hinder its approach. Depending on the length of the stalk region, the NA may protrude slightly more or less above the viral envelope than the HA, which may influence the overall enzymatic activity of the virus.

Neuraminidase structure, trtramerPicture 1: NA structure

Neuraminidase stalk length

Picture 2: Stalk length of NA

Influenza Neuraminidase Function

Neuraminidase (NA) has several functions in virus replication and infection:
• Virus Entry
• Receptor Binding
• Virus Internalization
• Catalytic Activity
• NA Substrate Specificity

Rather than just a sialidase that facilitates virus release from infected cells, the NA is a complicated multifunctional protein with an important role at many stages of the infectious process. While the NA is the main target for current antiviral therapies, recent approaches to new influenza therapy include targeting the HA with monoclonal antibodies. However, given the NA also has the capacity to bind receptors, there needs to be caution in this approach, as it is possible that compensating mutations in the NA may allow escape from inhibition of the HA.

Influenza Neuraminidase Reference

• Y.A. Shtyrya.Influenza Virus Neuraminidase: Structure and Function.Acta Naturae. 2009 Jul; 1(2): 26–32.
• Russell R.J.. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature. 2006;44:45–49
• Julie L. McAuley.Influenza Virus Neuraminidase Structure and Functions.Front. Microbiol., 29 January 2019
• Feng Wen.Influenza Neuraminidase: Underrated Role in Receptor Binding.VOLUME 27, ISSUE 6, P477-479, JUNE 01, 2019

Influenza virus NP is a major structural protein in Influenza virus particles and has multiple functions in the viral infectious cycle. Nucleoprotein (NP) is major component of the ribonucleoprotein complex and a critical factor in the viral infectious cycle in switching influenza virus RNA synthesis from transcription mode to replication mode. NP binds RNA with high affinity in a sequence-independent manner. Isolated influenza A virus nucleoprotein exists in an equilibrium between monomers and trimers while the wild type (wt) nucleoprotein is trimers. The trimers bind RNA with high affinity but remain trimmers, whereas the monomers polymerise onto RNA forming nucleoprotein-RNA complexes.

Reagents of Nucleoprotein

Nucleoprotein Proteins
H1N1 H2N2 H3N2 H7N9 Influenza B
Nucleoprotein Antibodies
H3N2 H7N9 Influenza B
Nucleoprotein cDNAs
H1N1 H3N2 H5N8 H7N7 H7N9
H9N2 H10N8 Influenza B

Influenza Nucleoprotein Structure

In Influenza A, Nucleoprotein is composed of a head and a body domain and a tail loop/ linker region. The head domain is more conserved than the body domain. NP proteins assume the overall shape of a crescent with a head and a body domain. In between the two domains is a deep groove enriched for basic amino acid residues and thus may function as the RNA-binding site.
Structure of Influenza D NP is a tetramer.

Neuraminidase structure, trtramer

Influenza A/NP: timer

Neuraminidase stalk length

Influenza D/NP: tetramer

Here is the illustration of functional domains of NP.

Sub-fragments of NP identified as capable of binding RNA (blue), NP (green) or PB2 (yellow) are indicated on a linear representation of the NP molecule. Numbers refer to the amino acid co-ordinates. Also indicated is a C-terminal acidic region (red), which acts as a repressor of PB2 and NP binding. Black bars indicate regions shown to be important for binding the cellular polypeptides actin, BAT1/UAP56, importin α (NLS I) and/or function as nuclear localization signals (NLS I and II) or as a cytoplasmic accumulation signal (CAS).

Influenza Neuraminidase Function

Neuraminidase (NA) has several functions in virus replication and infection:
• Virus Entry
• Receptor Binding
• Virus Internalization
• Catalytic Activity
• NA Substrate Specificity

Rather than just a sialidase that facilitates virus release from infected cells, the NA is a complicated multifunctional protein with an important role at many stages of the infectious process. While the NA is the main target for current antiviral therapies, recent approaches to new influenza therapy include targeting the HA with monoclonal antibodies. However, given the NA also has the capacity to bind receptors, there needs to be caution in this approach, as it is possible that compensating mutations in the NA may allow escape from inhibition of the HA.

Influenza Neuraminidase Reference

• Y.A. Shtyrya.Influenza Virus Neuraminidase: Structure and Function.Acta Naturae. 2009 Jul; 1(2): 26–32.
• Russell R.J.. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature. 2006;44:45–49
• Julie L. McAuley.Influenza Virus Neuraminidase Structure and Functions.Front. Microbiol., 29 January 2019
• Feng Wen.Influenza Neuraminidase: Underrated Role in Receptor Binding.VOLUME 27, ISSUE 6, P477-479, JUNE 01, 2019

The non-structural (NS1) protein of influenza A viruses is a non-essential virulence factor that has multiple accessory functions during viral infection. In recent years, the major role ascribed to NS1 has been its inhibition of host immune responses, especially the limitation of both interferon (IFN) production and the antiviral effects of IFN-induced proteins. The various roles NS1 has in regulating viral replication mechanisms, host innate/adaptive immune responses, and cellular signalling pathways.

Reagents of Nonstructural protein 1 / NS1

Nonstructural protein 1 Proteins
Nonstructural protein 1 cDNAs

Influenza Nonstructural protein 1 / NS1 Structure

NS1 is notionally divided into two distinct functional domains: an N-terminal RNA-binding domain (residues 1–73), which in vitro binds with low affinity to several RNA species in a sequence independent manner, and a C-terminal ‘effector’ domain (residues 74–230), which predominantly mediates interactions with host-cell proteins, but also functionally stabilizes the RNA-binding domain. Full-length NS1 likely exists as a homodimer, with both the RNA binding and effector domains contributing to multimerization.

NS1 has a strain-specific length of 230–237 aa, and an approximate molecular mass of 26 kDa. The N-terminal 73 amino acids form a functional RNA-binding domain, whilst the effector domain predominantly mediates interactions with host-cell proteins. The final C-terminal ~20 amino acids may be natively unstructured. NS1 contains two nuclear localization sequences (NLS1 and NLS2), and a nuclear export sequence (NES). A nucleolar localization sequence (NoLS) has been reported for some strains, and is concomitant with NLS2.

NS1 is composed of N-terminal RNA-binding domain (RBD, amino acids 1–73) and C-terminal effector domain (ED, amino acids 74–207).

Schematic ribbon diagrams of the RNA-binding domain (PDB ID,2N74) and effector domain (PDB ID, 3EE8).

Influenza Nonstructural protein 1 / NS1 Function

The influenza A virus NS1 protein interacts with a variety of proteins to inhibit host cell immune responses and promote viral replication. The NS1 protein is known to bind to double-stranded RNA via N-terminal RNA-binding domain and it specifically binds to the region of the RNA containing either 5′- or 3′-terminal common genomic sequence. The binding of influenza A virus NS1 protein to dsRNA protects the virus against the antiviral state induced by interferon-α/β.

NS1 is important for multiple viral functions, including:
• Temporal adjustment of viral RNA synthesis;
• Control of viral mRNA splicing;
• Adjustment of virus particle morphogenesis;
• Suppression of host apoptotic response through the activation of phosphoinositide 3-kinase (PI3K);
• Interact with replication intermediates of viral RNA to block molecules from recognition by cellular pattern recognition receptors (PRRs)

Influenza Nonstructural protein 1 / NS1 Reference

• Chang Woo Han.Structure and Function of the Influenza A Virus Non-Structural Protein 1.J. Microbiol. Biotechnol. 2019
• Benjamin G. Hale.The multifunctional NS1 protein of influenza A viruses.Journal of General Virology.2008
• Robert M. Krug.Functions of the Influenza A Virus NS1 Protein In Antiviral Defense.Curr Opin Virol. 2015
• Daniel Marc.Influenza virus non-structural protein NS1:interferon antagonism and beyond.Journal of General Virology.2014

NS2 is also described as nuclear export protein (NEP). In Influenza A virus and Influenza B virus, the NS2 protein (nuclear export protein) is proposed to mediate the nucleocytoplasmic trafficking of viral ribonucleoprotein (vRNP) by forming NS2-vRNP complexes. NS2 protein is a structural component of the viral particle and it associates with the viral matrix M1 protein. New and unexpected roles for NEP during the influenza virus life cycle have started to emerge. These recent studies have shown NEP to be involved in regulating the accumulation of viral genomic vRNA and antigenomic cRNA as well as viral mRNA synthesized by the viral RNA-dependent RNA polymerase.

Reagents of Nonstructural protein 2 / NS2

Influenza Nonstructural protein 2 / NS2 Structure

NS2/NEP can be divided into a protease-sensitive N-terminal domain (amino acids 1–53) and a protease-resistant C-terminal domain (amino acids 54–121). The NES is proposed to interact with the cellular nuclear export protein Crm1 and is unusual in the sense that three of the five critical hydrophobic residues are methionines rather than the canonical leucine.NEP is phosphorylated during the influenza replication cycle. The phosphorylation of a highly conserved serine-rich motif (S23, S24, and S25) proximal to the NES has recently been demonstrated in virion-associated NEP.
The highly structured C-terminal domain consists of two ahelices C1 (amino acids 64–85) and C2 (amino acids 94–115) that are connected by a short interhelical turn. The two a-helices are comparable in length and interact extensively, forming an almost perfectly antiparallel hairpin. N-terminal domain effectively buries the hydrophobic face of the C-terminal hairpin.

Organisation and structure of influenza virus A NEP

Influenza Nonstructural protein 2 / NS2 Function

NS2/NEP is proposed to play multiple biologically important roles during the influenza virus life cycle. NS2 is involved in nuclear export of viral ribonucleoprotein complexes. NEP was first thought to be nonstructural in function, however it is now recognised that NEP is resident within influenza virions where it may interact with M1. NS2 mediates the export of vRNPs from the nucleus to the cytoplasm through export signal via its interaction with XPO1, ensuring that the viral genomic segments are available for packaging into daughter virions on the cellular periphery.

Recent studies have suggested that NEP may have more than one function during the influenza virus replication cycle. NEP contributes to the viral budding process through interaction with a cellular ATPase. NEP is capable of regulating the accumulation of viral RNA species, potentially leading to a switch from viral transcription during early viral replication to favour the production of genomic vRNPs.

However, many functions of NS2, in particular its transit through the cytoplasm and its incorporation into the viral particle, are not understood.

Influenza Nonstructural protein 2 / NS2 Reference

• Duncan Paterson.Emerging Roles for the Influenza A Virus Nuclear Export Protein (NEP).PLOS Pathogens.2012
• M. Imai.Influenza B virus NS2, a nuclear export protein, directly associates with the viral ribonucleoprotein complex.Archives of Virology.2013
• Yong Hu.CHD3 facilitates vRNP nuclear export by interacting with NES1 of influenza A virus NS2.Cell. Mol. Life Sci.2015
• Benoıˆt de Chassey.The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication.PLOS Pathogens.2013

Influenza A virus matrix protein M1 is one of the most important and abundant proteins in the virus particles broadly involved in essential processes of the viral life cycle. The matrix protein M1 protein is membrane associates and forms a rigid matrix layer under the viral envelope utilizing multiple protein-lipid and protein-protein interactions. M1 protein is a candidate antigen for a broad-spectrum influenza virus vaccine and the adjuvant chitosan significantly improved the efficacy of the M1 vaccine.

Reagents of Matrix 1

Matrix 1 Proteins
H1N1 H3N2 H7N9
Matrix 1 Antibodies
Matrix 1 cDNAs
H1N1 H2N2 H3N2
H7N7 H7N9

Influenza Matrix 1 Structure

M1 is a structurally polarized molecule with a highly-ordered NM-fragment and a potentially unstructured C-terminal domain. The M1 protein consists of 252 amino acid residues with a calculated molecular mass (MM) based on the amino acid sequence of ,28 kDa. Numerous attempts to crystallize and solve the structure of full length M1 have been unsuccessful and consequently no high resolution model exists for the entire protein. The crystal structure of the 18 kDa NM domain (amino acids 1-164) has been determined at pH 4. Unfortunately, crystallographic studies have not yet provided structural information about the C-terminal domain of M1.

Influenza Matrix 1 Function

Influenza A virus matrix protein M1 plays essential structural and functional roles in the virus life cycle. Influenza virions M1 protein forms a well ordered helical layer adjacent to the viral envelope, and the close interaction of M1 with the surrounding envelope determines the virion morphology.The rigid matrix layer of M1 maintains the integrity and shape of the intact influenza virus and structurally organises the virus membrane. M1 provides the basement and an anchor point for the HA fusion machinery.

Influenza Matrix 1 Reference

• Eleonora V. Shtykova.Structural Analysis of Influenza A Virus Matrix Protein M1 and Its Self-Assemblies at Low pH.PLOS ONE.2013
• Nancy Hom.Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance.Journal of Virology.2019
• David Saletti.The Matrix protein M1 from influenza C virus induces tubular membrane invaginations in an in vitro cell membrane model.Scientific Reports.2017
• Ismail Dahmani.Influenza A matrix protein M1 induces lipid membrane deformation via protein multimerization.Bioscience Reports.2019.

The matrix 2 M2 protein is a proton-selective ion channel protein, integral in the viral envelope of the influenza A virus. The channel itself is a homotetramer (consists of four identical M2 units), where the units are helices stabilized by two disulfide bonds. It is activated by low pH. M2 protein is encoded on the seventh RNA segment together with the matrix protein M1. Proton conductance by the M2 protein in influenza A is essential for viral replication

Reagents of Matrix 2

Influenza Matrix 2 Structure

The influenza virus M2 protein is a 97-amino-acid integral membrane protein that forms disulfide-linked tetramers. M2 is predominantly associated with its wellcharacterized proton channel activity. During the virus entry process, this activity allows for the acidification of the virion interior, which permits vRNP release from M1.

• The C-terminal 54 amino acids of M2: Form the highly conserved cytoplasmic tail, which is important for both the assembly and budding processes but has little effect on the M2 proton channel activity. The membrane-distal region of the cytoplasmic tail has been shown to be critical for the incorporation of vRNPs into budding particles.
• The membrane-proximal region of M2 : Induce membrane curvature and has been implicated in ESCRT-independent membrane scission and budding of IAV particles.

Influenza Matrix 2 Function

The influenza A virus (IAV) M2 protein is a multifunctional protein with critical roles in virion entry, assembly, and budding. M2 is targeted to the apical plasma membrane of polarized epithelial cells, and the interaction of the viral proteins M2, M1, HA, and NA near glycolipid rafts in the apical plasma membrane is hypothesized to coordinate the assembly of infectious virus particles.

Influenza Matrix 2 Reference

• Nicholas Wohlgemuth. Influenza A Virus M2 Protein Apical Targeting Is Required for Efficient Virus Replication.Journal of Virology.2018
• Kolpe A.M2-based influenza vaccines: recent advances and clinical potential.Expert Rev Vaccines. 2017

PA is a key protein in the influenza virus polymerase complex, although its role was only partly outlined until recently. PA contains an N-terminal endonuclease domain (PAN) that interacts with PB26 and a C-terminal domain (PA-CTD) that interacts with PB1. There have been reports of peptide inhibitors and small molecule inhibitors that bind to PA and disrupt the PA-PB1 interaction.

Reagents of polymerase acidic / PA

Influenza polymerase acidic / PA Structure

PA can be cleaved by limited tryptic digestion into two domains: a smaller N-terminal domain of ~25 kD and a larger C-terminal of ~55 kD. The two domains are separated by a long linker peptide. Neither the N-terminal nor C-terminal domains of PA could ensure a stable interaction with PB1 without the presence of the linker.

The crystal structure of the N-terminal domain of PA, which has been implicated in a diverse range of functions, such as endonuclease and protease activities.The PAN structure has an α/β architecture with five mixed β-strands (β1-5) forming a twisted plane surrounded by seven α-helices (α1-7). A strongly negatively charged cavity, formed by a concentration of acidic residues, is surrounded by helices α2−α5 and strand β3 and houses a metal binding site. Structural comparison of PAN revealed a close match with other endonucleases, pointing towards PAN as a new member of the (P)DXN(D/E)XK endonuclease superfamily.

Organisation and structure of influenza virus A NEP

Influenza polymerase acidic / PA Function

The role of PA in the polymerase heterotrimer has only been partly outlined. It has been reported to be required for replication and for transcription of vRNA as well as endonuclease cleavage of the cap RNA primer.
Among its various putative functions, PA was reported to harbour proteolytic activity that can induce generalized proteolysis of both viral and host proteins. PA can lead to degradation of the large subunit of RNA polymerase II complex in host cells, and has also been implicated as a novel serine protease with Ser624 at the active site.

Influenza polymerase acidic / PA Reference

• Spencer O. Moen.Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1.SCIENTIFIC REPORTS.2014
• LIU YingFang.Structure-function studies of the influenza virus RNA polymerase PA subunit.SCIENCE IN CHINA PRESS.2009
• Chu-Wen Yang.A Comparative Study of Short Linear Motif Compositions of the Influenza A Virus Ribonucleoproteins.PLoS ONE.2012
• Benjamin Ma¨nz. Disruption of the Viral Polymerase Complex Assembly as a Novel Approach to Attenuate Influenza A Virus.THE JOURNAL OF BIOLOGICAL CHEMISTRY.2011

PB1 is the RNA-dependent RNA polymerase (RdRP) subunit, which carries out viral mRNA and genomic RNA synthesis in reactions with the cap-binding subunit PB2 and the endonuclease subunit PA. The influenza virus PB1 protein is the core subunit of the heterotrimeric polymerase complex (PA, PB1 and PB2) in which PB1 is responsible for catalyzing RNA polymerization and binding to the viral RNA promoter.

Reagents of Polymerase basic 1/ PB1

Influenza Polymerase basic 1/ PB1 Structure

There is no crystal structure available for PB1 protein except its N terminal 25 amino acids and C terminal about 80 amino acids. This is mainly due to its low solubility when expressed alone in bacteria or the low productivity of the active heterotrimeric polymerase complex when expressed in insect cells and mammalian cells.

PB1, the catalytic core and structural backbone of the polymerase, possesses four highly conserved amino acid motifs that are present among all viral RNA-dependent RNA polymerases. These four conserved motifs form a large functional domain with at least one ‘invariant’ amino acid per motif.

Influenza Polymerase basic 1/ PB1 Function

PB1 plays a central role in synthesis of influenza virus RNA genome, it has also become a promising target for developing new anti-influenza drugs. Mutations in the PB1 subunit of RNA-dependent RNA polymerase (RdRp) of influenza A virus can affect replication fidelity. Before the influenza A/H1N1 pandemic in 2009, most human influenza A/H1N1 viruses contained the avian-associated residue, serine, at position 216 in PB1. However, near the onset of the 2009 pandemic, human viruses began to acquire the mammalian-associated residue, glycine, at PB1–216, and PB1–216G became predominant in human viruses thereafter.

Influenza Polymerase basic 1/ PB1 Reference

• Chunfeng Li.Integrating computational modeling and functional assays to decipher the structure-function relationship of influenza virus PB1 protein.SCIENTIFIC REPORTS.2014
• Giorgi Metrevelia.The origin of the PB1 segment of swine influenza A virus subtype H1N2 determines viral pathogenicity in mice.Virus Res. 2014
• Ruey-Wen Lin.Naturally occurring mutations in PB1 affect influenza A virus replication fidelity, virulence, and adaptability.Journal of Biomedical Science.2019
• Caroline Chu.Functional Analysis of Conserved Motifs in Influenza .Virus PB1 Protein.PLoS ONE.2012

The PB2 subunit of the influenza virus RNA polymerase is a major determinant of viral pathogenicity. The molecular mechanisms of how PB2 determines pathogenicity remain poorly understood. PB2 is responsible for binding to the 5΄ cap of nascent host pre-mRNAs to facilitate cleavage by PA into short capped RNA fragments, which are used as primers for viral transcription. Meanwhile, PB2 has been implicated in virulence and host adaptation. PB2 associates with mitochondria and inhibits the function of the mitochondrial antiviral signaling protein MAVS, implicating PB2 in the regulation of innate immune responses.

Reagents of polymerase basic 2/ PB2

Influenza polymerase basic 2/ PB2 Structure

PB2 is an 87-kDa basic cap-binding protein involved in the initiation of viral transcription as well as viral replication. The N- and C-terminal egions of PB2 contain independent NP binding sites, located between residues 1–269 and 580–683, respectively. The interaction of PB2 with NP affected the activity of RNPs, and may be involved in regulating the switch from viral transcription to replication. Two regions of PB2 (aa 448–496 and aa 736–739) were required for the nuclear localization of influenza virus PB2.

An N-terminal mitochondrial targeting sequence (MTS) was found to be responsible for the mitochondrial localization of PB2. Despite high sequence conservation in this region, position 9 shows variations in influenza A viruses of different hosts and is a determinant of the mitochondrial localization of PB2. Most human seasonal influenza virus pre-2009 H1N1, H2N2, and H3N2 strains encode mitochondrial PB2 with asparagine at position 9 (N9-PB2).

Influenza polymerase basic 2/ PB2 Function

Polymerase basic 2 (PB2) protein is a component of the influenza A virus RNA-dependent RNA polymerase complex alongside the polymerase basic 1 (PB1) and polymerase acidic (PA) protein subunits. PB2 associates with mitochondria and inhibits the function of the mitochondrial antiviral signaling protein MAVS. PB2 of some influenza virus strains has also been found to localize to the mitochondria, independentlyf PB1 and PA.

PB2 has been implicated in virulence and host adaptation. Several residues in PB2 have been found to be important for host adaptation.

Influenza polymerase basic 2/ PB2 Reference

• YQ Shirleen Soh.Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans.eLife. 2019
• Joshua C. D. Long.The PB2 Subunit of the Influenza A Virus RNA Polymerase Is Imported into the Mitochondrial Matrix.Journal of Virology.2016
• Tinghong Zhang.NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus.Scientific Reports.2017
• Amelia Nieto.Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza.Frontiers in Microbiology.2017
• Adriana Forero.The 1918 Influenza Virus PB2 Protein Enhances Virulence through the Disruption of Inflammatory and Wnt-Mediated Signaling in Mice.Journal of Virology.2016
• Shufang Fan.Novel residues in avian influenza virus PB2 protein affect virulence in mammalian hosts.Nat Commun.2018

More information about influenza virus antigens

Influenza H1N1 (also called “swine flu”) is a influenza virus causing illness in people. Influenza H1N1 was first detected in people in the United States in April 2009. Influenza H1N1 is spreading from person-to-person worldwide. In 2009, H1N1 was spreading fast around the world, so the World Health Organization called it a pandemic.
Influenza A (H1N1) is similar to seasonal influenza but has been characterized by higher activity during the northern summer season, higher fatality rates among healthy young adults and higher incidence of viral pneumonia.Symptoms of swine flu in people are similar to the symptoms of regular human flu and include fever, cough, sore throat, body aches, headache, chills and fatigue.

Why is H1N1 called Swine Flu?
Many of Influenza H1N1 genes were tested to be similar to influenza virus that in swine in North America. But, it’s wrong when study goes further. 2009 H1N1 is different from influenza virus which is found in swine. It has genes from flu viruses and avian virused and human genes. Scientists call 2009 Influenza H1N1 a “quadruple reassortant” virus.

H1N1 Proteins

  • • H1N1 Hemagglutinin / HA protein
  • • H1N1 Neuraminidase / NA protein
  • • H1N1 Nucleoprotein / NP protein
  • • H1N1 Matrix protein 1 / M1 protein
  • • H1N1 Nonstructural protein 1 / NS1 protein
  • • H1N1 Nonstructural protein 2 / NS2 protein

H1N1 Antibodies

  • • H1N1 Hemagglutinin / HA antibody
  • • H1N1 Neuraminidase / NA antibody
  • • H1N1 Matrix protein 1 / M1 antibody

H1N1 cDNAs/Genes

  • • H1N1 Hemagglutinin / HA cDNA
  • • H1N1 Neuraminidase / NA cDNA
  • • H1N1 Nucleoprotein / NP cDNA
  • • H1N1 Matrix protein 1 / M1 cDNA
  • • H1N1 Nonstructural protein 1 / NS1 cDNA

H1N2 is a subtype of the influenza A virus, which is also referred to as bird flu. Influenza H1N2 can infect both human and pig. H1N2 reassortant viruses between H1N1 and H3N2 human viruses appeared in 2001 and became established, circulating viruses until 2004. Lately, H1N2 has been reported that infected human in Netherlands in 2018 and in Sweden in 2019. It is a reassortant of human seasonal flu viruses containing the same hemagglutinin “H1” gene as circulating seasonal A (H1N1) pdm09 viruses and the same neuraminidase “N2” gene as circulating seasonal A(H3N2) viruses.

Inactivated Influenza Vaccines. Joseph S.Bresee, Alicia M.Fry, Suryaprakash Sambhara, Nancy J.Cox. Plotkin’s Vaccines.2018

Reagents of H1N2 by Influenza Antigens

H1N2 Proteins

  • • H1N2 Hemagglutinin / HA protein

H1N2 Antibodies

  • • H1N2 Hemagglutinin / HA antibody

H1N2 cDNAs/Genes

  • • H1N1 Hemagglutinin / HA cDNA

H2N2 is also called Asian Flu which has emerged in East Asia, triggering a pandemic in 1957. H2N2 virus is originated from an avian influenza A virus, including the H2 hemagglutinin and the N2 neuraminidase genes. It was first reported in Singapore in February 1957, Hong Kong in April 1957, and in coastal cities in the United States in summer 1957. The 1957 A/H2N2 influenza virus caused an estimated 2 million fatalities during the pandemic.

Reagents of H2N2 by Influenza Antigens

H2N2 Proteins

  • • H2N2 Hemagglutinin / HA protein
  • • H2N2 Nucleoprotein / NP protein

H2N2 Antibodies

  • • H2N2 Hemagglutinin / HA antibody

H2N2 cDNAs/Genes

  • • H2N2 Hemagglutinin / HA cDNA
  • • H2N2 Matrix protein 1 / M1 cDNA

Influenza H3N2 is one of the three major influenza pandemics that occurred in the last century. In 1968, H3N2 virus emerged in Hong Kong, China and led to a global epidemic which cause more than one million deaths world-wide. Before 1968, there was no case of H3N2 virus circulating in human. This viral strain of H3N2 combines with the HA and PB1 fragments of avian H3N2, and the NA from the H2N2 pandemic strain of 1957 that led to the ability to infect and transmit between humans.

James D. Allen. H3N2 influenza viruses in humans: Viral mechanisms, evolution, and evaluation. Hum Vaccin Immunother. 2018.

Reagents of H3N2 by Influenza Antigens

H3N2 Proteins

  • • H3N2 Hemagglutinin / HA protein
  • • H3N2 Neuraminidase / NA protein
  • • H3N2 Nucleoprotein / NP protein
  • • H3N2 Matrix protein 1 / M1 protein

H3N2 Antibodies

  • • H3N2 Hemagglutinin / HA antibody
  • • H3N2 Neuraminidase / NA antibody
  • • H3N2 Nucleoprotein / NP antibody

H3N2 cDNAs/Genes

  • • H3N2 Hemagglutinin / HA cDNA
  • • H3N2 Neuraminidase / NA cDNA
  • • H3N2 Nucleoprotein / NP cDNA
  • • H3N2 Matrix protein 1 / M1 cDNA

H5N1 is called avian influenza or bird flu that causes a highly infectious, severe respiratory disease in birds. H5N1 is hard to transmit form people to people. But, the mortality of people infected by H5N1 is about 60%. H5N1 infection in humans can cause severe disease. It would be horrible if H5N1 could transmit among humans easily.
H5N1 is a type of highly pathogenic avian influenza (HPAI). In 1966, H5N1 was first found in geese in China. In 1997, H5N1 was first found in humans in HongKong, China. Since then, H5N1 are found in poultry and wild birds in more than 50 countries.

WHO, FAQs: H5N1 influenza;
CDC, Highly Pathogenic Asian Avian Influenza A(H5N1) Virus

Reagents of H5N1 by Influenza Antigens

H5N1 Proteins

  • • H5N1 Hemagglutinin / HA protein
  • • H5N1 Neuraminidase / NA protein

H5N1 Antibodies

  • • H5N1 Hemagglutinin / HA antibody
  • • H5N1 Neuraminidase / NA antibody

H5N1 cDNAs/Genes

  • • H5N1 Hemagglutinin / HA cDNA
  • • H5N1 Neuraminidase / NA cDNA

H7N7 was firstly detected in chickens in Italy in 1902. Since then, H7N7 viruses have been widely detected in wild birds and domestic poultry around the world. There are highly pathogenic strains and low pathogenic strains of influenza H7N7. H7N7 avian influenza viruses can cross-species (birds, pigs, seals, and horses) and transmit to humans.
The first reported human infection of H7N7 virus occurred in England in1996, when a woman exposed to ducks developed conjunctivitis. In 2003, an outbreak of highly pathogenic H7N7 virus occurred in the Netherlands, resulting in the culling of more than 30 million birds. During this outbreak, 86 humans involved in the culling operation and three of their family members who did
not have direct contact with infected poultry were confirmed to have H7N7 virus infections, suggesting that limited human-to- human transmission of the H7N7 virus occurred. In 2013 in Italy, three poultry workers with conjunctivitis were diagnosed with highly pathogenic H7N7 avian influenza virus infections. This represents a pandemic threat.

Pengfei Cui. New influenza A (H7N7) viruses detected in live poultry markets in China. Virology.2016

Reagents of H7N7 by Influenza Antigens

H7N7 Proteins

  • • H7N7 Hemagglutinin / HA protein
  • • H7N7 Neuraminidase / NA protein

H7N7 Antibodies

  • • H7N7 Hemagglutinin / HA antibody
  • • H7N7 Neuraminidase / NA antibody

H7N7 cDNAs/Genes

  • • H7N7 Hemagglutinin / HA cDNA
  • • H7N7 Neuraminidase / NA cDNA
  • • H7N7 Nucleoprotein / NP cDNA
  • • H7N7 Matrix protein 1 / M1 cDNA

H7N9 has caused 5 epidemic waves of infection among humans in China, resulting in 1307 laboratory-confirmed clinical cases and 489 deaths among 2013 to 2017 since its first documentation. According to reports of H7N9 virus outbreaks among humans in China, the virus clustered into the Yangtze River Delta lineage and the Pearl River Delta lineage. Infections of H7N9 are associated with considerable morbidity and mortality, particularly within certain demographic groups. This rapid increase in cases over a brief time period is alarming and has raised concerns about the pandemic potential of the H7N9 virus.

• Nianchen Wang. Avian Influenza A (H7N9) Viruses Co-circulating among Chickens, Southern China. Emerging Infectious Diseases.2017
• W. D. TANNER. REVIEW ARTICLE The pandemic potential of avian influenza A (H7N9) virus: a review. Epidemiol. Infect. 2015

Reagents of H7N9 by Influenza Antigens

H7N9 Proteins

  • • H7N9 Hemagglutinin / HA protein
  • • H7N9 Neuraminidase / NA protein
  • • H7N9 Nucleoprotein / NP protein
  • • H7N9 Matrix protein 1 / M1 protein

H7N9 Antibodies

  • • H7N9 Hemagglutinin / HA antibody
  • • H7N9 Nucleoprotein / NP antibody

H7N9 cDNAs/Genes

  • • H7N9 Hemagglutinin / HA cDNA
  • • H7N9 Neuraminidase / NA cDNA
  • • H7N9 Nucleoprotein / NP cDNA
  • • H7N9 Matrix protein 1 / M1 cDNA
  • • H7N9 Nonstructural protein 1 / NS1 cDNA

H9N2 subtype influenza viruses have become endemic in various types of terrestrial poultry in Eurasian and African countries and have caused sporadic infections in humans and mammals. China is regarded as the epidemic center of H9N2 viruses.
In China, H9N2 subtype avian influenza outbreak is firstly reported in Guangdong province in 1992. Subsequently, the disease spreads into vast majority regions nationwide and has currently become endemic there. Over vicennial genetic evolution, the viral pathogenicity and transmissibility have showed an increasing trend as year goes by, posing serious threat to poultry industry.
H9N2 has demonstrated significance to public health as it could not only directly infect mankind, but also donate partial or even whole cassette of internal genes to generate novel human-lethal reassortants like H5N1, H7N9, H10N8 and H5N6 viruses.

Min Gu. Current situation of H9N2 subtype avian influenza in China. Gu et al. Vet Res.2017
Chong Li. Genetic evolution of influenza H9N2 viruses isolated from various hosts in China from 1994 to 2013. Emerging Microbes & Infections .2017
Trushar Jeevan. A(H9N2) influenza viruses associated with chicken mortality in outbreaks in Algeria 2017. Influenza Other Respi Viruses. 2019

Reagents of H9N2 by Influenza Antigens

H9N2 Proteins

  • • H9N2 Hemagglutinin / HA protein
  • • H9N2 Neuraminidase / NA protein

H9N2 Antibodies

  • • H9N2 Hemagglutinin / HA antibody
  • • H9N2 Neuraminidase / NA antibody

H9N2 cDNAs/Genes

  • • H9N2 Hemagglutinin / HA cDNA
  • • H9N2 Neuraminidase / NA cDNA
  • • H9N2 Nucleoprotein / NP cDNA
  • • H9N2 Polymerase PA cDNA
  • • H9N2 Polymerase PB1 cDNA
  • • H9N2 Polymerase PB2 cDNA

Since 2004, the H10N7 subtype avian influenza virus (AIV) has caused sporadic human infections with variable clinical symptoms world-wide. Three H10N7 subtype avian influenza viruses were isolated from chickens in live poultry markets in Eastern China in 2014. In spring 2014, increased mortality of harbor seals (Phoca vitulina), associated with infection with an influenza A(H10N7) virus, was reported in Sweden and Denmark. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals.

Bodewes R. Spatiotemporal Analysis of the Genetic Diversity of Seal Influenza A(H10N7) Virus, Northwestern Europe. J Virol. 2016
van den Brand JM. Influenza A (H10N7) Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets. PLoS One. 2016

Reagents of H10N7 by Influenza Antigens

H10N7 Proteins

  • • H10N7 Hemagglutinin / HA protein

H10N7 cDNAs/Genes

  • • H10N7 Hemagglutinin / HA cDNA

Influenza B viruses (IBVs) circulate annually along with influenza A (IAV) strains during seasonal epidemics. Influenza B viruses can dominate influenza seasons and cause severe disease, particularly in children and adolescents. Influenza B virus is only known to infect humans and seals with influenza.

Symptoms of Influenza B
• Fever, sometimes as high as 106 degrees F; children tend to experience higher fevers than adults
• Fatigue
• Body aches
• Respiratory ailments such as cough, runny nose, and sore throat; these become more pronounced as the fever subsides
• Stomach irritation, including loss of appetite, vomiting, and nausea.

Koutsakos M. Knowns and unknowns of influenza B viruses. Future Microbiol. 2016

Reagents of Influenza B by Influenza Antigens

Influenza B Proteins

  • • Influenza B Hemagglutinin / HA protein
  • • Influenza B Neuraminidase / NA protein
  • • Influenza B Nucleoprotein / NP protein

Influenza B Antibodies

  • • Influenza B Hemagglutinin / HA antibody
  • • Influenza B Nucleoprotein / NP antibody

Influenza B cDNAs/Genes

  • • Influenza B Hemagglutinin / HA cDNA
  • • Influenza B Neuraminidase / NA cDNA
  • • Influenza B Nucleoprotein / NP cDNA

Influenza Virus Genome

The genome of influenza virus consists of segmented negative-sense single-strand RNA segments. Influenza viruses are members of the family Orthomyxoviridae. There are four genera of this family: types A, B, C and Thogotovirus, of which, however, only genera A and B are clinically relevant for humans. The eight genome segments of influenza A and B viruses are loosely encapsidated by the nucleoprotein (NP). The influenza genome contains eight genes encoding 11 proteins.The polymerase complexes consisting of the three polymerase proteins PB1, PB2, and PA are located at the ends of the nucleocapsids. These helical capsids are encircled by the M1 matrix protein and by a host-derived lipid bilayer envelope in which the virus surface glycoproteins haemagglutinin (HA) and neuraminidase (NA) as well as the M2 matrix protein are embedded. The HA is synthesized as precursor protein and cleaved by cellular serine proteases into the functional proteins HA1 and HA2.The proteins NS1 (nonstructural protein 1) and NS2/nuclear export protein (NEP), whose roles are still being investigated.

Influenza virus genome illustration

Influenza Virus Types / Classification

In virus classification, influenza viruses are RNA viruses that make up four of the seven genera of the family Orthomyxoviridae. Influenza virus can identified as Influenza A, Influenza B, Influenza C and Influenza D. Influenza A viruses infect humans and a variety of other wildlife, including pigs and birds, which perpetuate the virus in nature throughout the world. Human influenza A viruses are thought to have originated from strains that infected wild aquatic birds. Influenza B viruses infect humans (and seals, interestingly) and primarily affect children. Infection with influenza C generally results in mild or subclinical infections. Influenza A and B cause seasonal epidemics, but only influenza A has caused worldwide pandemics. Generally, influenza A infections account for about 2/3 of human infections each year.

Classification / types of Influenza virus

Influenza AInfluenza BInfluenza C
HostsHumans, waterfowl, poultry, pigs, horses, sea mammals, batsHumans, sealsHumans, pigs, dogs
Gene segments887
HA/NA antigenic subtypes18 HA, 11 NANoneNone
Clinical featuresModerate to severe illnessMilder disease than Influenza ALargely subclinical
Epidemiological featuresCauses pandemicsLess severe epidemics than Influenza A; no pandemicsDoes not cause epidemics or pandemics

Influenza Virus Structure

Influenza viruses possess segmented genomes: Influenza A viruses (IAVs) and type B viruses (IBVs) contain 8, negative-sense, single-stranded viral RNA (vRNA) gene segments, which encode transcripts for 10 essential viral proteins, as well as several strain-dependent accessory proteins. In comparison, influenza type C and D viruses only possess seven vRNA gene segments, as the hemagglutinin–esterase fusion protein vRNA replaces the hemagglutinin (HA or H) and the neuraminidase (NA or N) vRNAsInfluenza A, the predominant pathogen in seasonal influenza and the cause of pandemic influenza, provides the main focus for the remainder of this section. The influenza A genome encodes 11 viral proteins:

• Hemagglutinin (HA), which is divided into two subunits (HA1 and HA2);
• Neuraminidase (NA);
• two matrix proteins (M1 and M2);
• Heterotrimeric RNA-dependent RNA polymerase, composed of one polymerase acidic (PA) and two polymerase basic (PB1 and PB2) subunits and the alternatively transcribed proapoptotic peptide, PB1-F2;
• Nucleoprotein (NP);
• Two nonstructural proteins (NS1 and NS2; NS2 is also known as NEP, or nuclear export protein).
The virus particle (virion) has an irregular spherical shape with a lipid envelope, approximately 80–120 nm in diameter.

Influenza virus a-d structure

Influenza Virus Replication

Influenza virus replicates within the nucleus of the host cell. Here is the influenza virus replication cycle.


Cell Binding and Fusion

HA bind with SA residue


Genome Trafficking to the Host Cell Nucleus

vRNP trafficking to the nucleus,the viral proteins that make up the vRNP are NP, PA, PB1, and PB2.


Transcription and replication of the viral genome

The replication of the influenza genome involves two steps: transcription of complimentary RNA (cRNA), followed by transcription of new vRNA copies using the cRNAs as templates

Assembly and Trafficking of vRNPs

Export of vRNPs from the nucleus

vRNPs appear to be exported out of the nucleus via the CRM1 dependent pathway through the nuclear pores


Assembly and budding at the host cell’s plasma membrane

Virus particles bud from the apical side of polarized cells

Influenza Virus Symptoms

A clinical characteristic of human influenza virus symptoms is a sudden rise in body temperature to >38.5 °C 1–3 days following infection. Other symptoms include headache, limb ache, tiredness, general faintness and dry cough. Infectivity can start already shortly (<24 h) before the onset of the clinical symptoms and usually persists 3–5 days. Small children can excrete the viruses earlier and over a longer period of time than adults. The most serious outcomes are peracute death within only few hours and primary influenza pneumonia. Encephalitis or myocarditis can also occur.

Symptoms of influenza virus:
• Fever
• Headache
• Limb ache
• Tiredness
• General faintness
• Dry cough
• Encephalitis
• Myocarfitis
• Complications: chronic heart or lung disease, metabolic disorders

Influenza Virus Treatment

Some antiviral products for the treatment of influenza virus infections are authorised. The two classes of antiviral drugs used against influenza are neuraminidase inhibitors (oseltamivir, zanamivir, laninamivir and peramivir) and M2 protein inhibitors (adamantane derivatives).
• Due to adverse reactions, the M2 ion channel blocker amantadine is hardly used. Rimantadine has fewer side-effects.
• Neuraminidase inhibitors oseltamivir and zanamivir can help shorten the phase of the disease and reduce the symptoms if administered in time.
• In different country, there are different policy on those drugs.

Influenza Virus Research Reference

Arbeitskreis Blut.Influenza Virus.Transfus Med Hemother. 2009 Feb; 36(1): 32–39.
• Dan Dou.Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement.Front Immunol. 2018; 9: 1581.
• Tasleem Samji.Influenza A: Understanding the Viral Life Cycle.Yale J Biol Med. 2009 Dec; 82(4): 153–159.
• Scott H. James, Richard J. Whitley, in Infectious Diseases (Fourth Edition), 2017


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