1. ORTHOMYXOVIRUSES

2. Introduction
Influenza virus infections have become such a common and integral part of our lives that any respiratory infection that causes discomfort is typically referred to as an episode of ’flu.
In reality, most of these infections are probably not caused by influenza viruses but by more benign agents.
True influenza virus infections can pose a serious threat.
Influenza virus infection in humans occurs in seasonal epidemics and is estimated to result in up to 5 million cases of serious disease with 250,000–500,000 deaths

3. Introduction
The family Orthomyxoviridae contains three genera (or types):
Influenzavirus A, B, and C.
They are distinguished by their antigenically distinct nucleoprotein (NP) and matrix (M) proteins.
Ortho
True or regular, distinguishes these from the Paramyxoviruses.
Myxo
Mucus, refers to the ability of these viruses to attach to mucoproteins on the cell surface.

4. Influenza Viruses
Most human infections are caused by influenza A and B.
Type C viruses cause only minor upper respiratory illness.
Influenza A viruses have been designated on the basis of the antigenic relationships of the hemagglutinin “HA or H”, and neuraminidase “NA or N” proteins.
There are 16 types of H (H1-16) and 9 types of N (N 1-9).
Only viruses with H1, 2, 3 and N1, 2 are known to infect humans
Type B strains are designated without H, N numbers since antigenic shift in these viruses has so far not been observed.

6. Morphology
Virions are spherical, nm in diameter, helical symmetry, enveloped with spikes.
About 80% of the spikes are hemagglutinin antigen and the remainder are neuraminidase.

7. Morphology
There is a layer of matrix protein which encloses the (-) ss-RNA genome of the virus.
RNA is associated with nucleoprotein.
The genome is composed of eight fragments complexed with protein to form ribonucleoprotein arranged in helix.
Hemagglutinin “HA” is a rod-shaped glycoprotein with triangular cross section.
It agglutinates erythrocytes, and plays an important role in the attachment and entry of the virus to host cells and in determining virulence.
Host cell protease cleaves HA into two molecules; HA1 and HA2; a necessary step for infection.

8. Morphology
The neuraminidase “NA” is an enzyme which destroys neuraminic acid “sialic acid”, a component of the specific cell receptors for the virus.
Its main function is in the release of new virus from cells.
NA is a glycoprotein, its spikes look like mushrooms.
Inside the matrix shell are the nucleoprotein and an RNA transcriptase, that is essential for replication.

9. Replication Attachment to specific receptors on the cell membrane.
Endocytosis: engulfment of virion into vacuoles (endosomes), acidic pH induces a change in the configuration of the HA.
Uncoating.
Virus RNA is transported to the cell nucleus
Transcription by virus RNA transcriptase to complementary (+) strand that can function as mRNA
It also serves as template for the Synthesis of negative RNA strands for new virions.
Translation, in host cell cytoplasm, to produce viral proteins.
The new virions are assembled at the host cell surface membrane.
Budding and release

10. The virion binds to a sialic acid
Releasing the eight viral nucleocapsids into the cytoplasm
The viral nucleocapsids are transported into the nucleus.
The (-) strand RNAs are copied by RNA polymerase
Some of the mRNA encoding NS2/NEP and M2 is spliced, and (6) the mRNAs are transported to the cytoplasm
Translation of the viral membrane proteins (HA, NA, and M2)
These proteins enter the host cell’s secretory pathway, where HA and NA are glycosylated.
& 9 All other mRNAs are translated by ribosomes in cytoplasm
,11 & 12 Some proteins are imported to nucleus for synthesis of + strand RNA & then – strand RNA
newly synthesized (-) strand RNAs enter the pathway for mRNA synthesis.
Shutting down of synthesis and export of progeny nucleocapsids to the cytoplasm.
The HA, NA, and M2 proteins are transported to the cell surface
17, 18 & 19 Incorporation of envelope proteins, packaging of genome in capsid and into envelope and then release.

11. Pathogenesis
Infection is acquired by the respiratory route causing upper respiratory tract infection.
Virus multiplies in the epithelium and destroys the cilia, followed by transient viremia.
Complications may include secondary bacterial infection, Reye’s syndrome
Reye’s syndrome
A rare but potentially fatal disease of the liver), children with fever due to influenza especially type B should avoid taking aspirin as this may lead to Reye's syndrome.

12. Pathogenesis Incubation period 2-3 days. Symptoms may include:
shivering,
headache,
malaise
and aching in the limbs and back.
The temperature rises rapidly to around 39 ºC.
The severity of influenza is proportional to age.

13. Immune Response Antibodies Interferon Cell-mediated immunity
Anti-hemagglutinin, the most important, it prevents virus from attaching to cells.
Anti-neuraminidase, prevents the release from host cells.
IgA antibodies prevent infection, they act at the mucus surfaces of the respiratory tract “local antibodies”
Interferon
Non-specific inhibitors of influenza
Cell-mediated immunity
Cytotoxic T cells
Alveolar macrophages

14. Genetic variation in influenza viruses Antigenic shift “gene reassortment”
Occurs in influenza A virus.
In a cell infected with two different viruses, the progeny virions may contain mixtures of each parent’s genes.
Influenza A viruses of human and animal origin may recombine to form a new subtype.
New reassortment subtypes will have different HA or NA or both.
New subtypes cause devastating epidemics in non-immune population.

15. Antigenic drift
Caused by minor changes in HA, NA or both due to mutations
It occurs in both influenza A and B.

16. Difference between Antigenic Shift & Drift
Antigenic Shift
Antigenic Drift 1
Major Antigenic Change
Minor Antigenic Change 2
Forming new sub-type
Forming new strain of virus 3
Large change in nucleotides of RNA
Small mutation of RNA 4
Occurs as a results of genome reassortment between difference subtypes.
Occurs as a result of the accumulation of point mutations in the gene. 5
An antigenic change which results in severe alternation in HA (hemagglutinin) or NA (neuraminidase) subtypes.
An antigenic change can alter antigenic sites on the molecule such that a virion can escape recognition by the host’s immune system. 6
Large and sudden mutation
Random and Spontaneous Mutation

17. Influenza Epidemics
New epidemics of influenza are caused by a virus antigenically different from that which was present in earlier epidemics.
The pandemic of was especially terrible in its effects in Europe.
Worldwide, it killed about million people.
Since 1977 the H3N2 and H1N1 strains have circulated side by side.
H1N1, H1N2, H3N2 are the only known Flu A virus subtypes currently Circulating among humans.
Epidemic refers to an increase, often sudden, in the number of cases of a disease above what is normally expected in that population in that area.
Pandemic refers to an epidemic that has spread over several countries or continents, usually affecting a large number of people.

18. Laboratory Diagnosis
Immunofluorescence staining of cells in nasopharyngeal aspirates.
Virus isolation from throat or nasal swabs, using chick embryo or cell culture.
Hemagglutination test or hemagglutination inhibition.

19. Prophylaxis- Chemoprophylaxis
Amantadine
Inhibits virus replication by blocking a viral ion channel (M2 protein) and prevents the virus from infecting cells.
Resistant strains have developed against amantadine.
If amantadine is given during the first day of illness, it shortens the average duration of pyrexia.
Oseltamivir (Tamiflue) and Zanamivir (Relenza)
They are neuraminidase inhibitors

20. Prophylaxis- Vaccination
Types:
Live attenuated vaccine (in chick embryo)
Inactivated vaccine- in chick embryo, harvested, purified by ultracentrifugation, inactivated with formalin or β-propiolactone.
Split vaccines: Whole virus extracted with ether to reduce side effects of whole virus vaccines.
Subunit or surface antigen: Purified HA and NA extracted with detergent.

21. Prophylaxis- Vaccination
Who should be immunized?
Individuals at special risk, e.g., old people and those with chronic diseases, infants.
People in closed institutions
Groups in community service, e.g., healthcare Staff.

22. Avian Influenza Virus (Bird flu), H5N1
Avian influenza virus occurs naturally among birds.
Wild birds carry viruses in their intestine but usually do not get sick of them.
The virus is very contagious among birds and can make some domesticated birds including chickens, ducks and turkeys very sick and kill them.
Infected birds shed the virus in their saliva, nasal secretions and feces.

23. Avian Influenza Virus (Bird flu), H5N1
The highly pathogenic form of the virus spreads more rapidly through flocks of poultry, it may affect multiple internal organs and has a mortality rate that can reach % often within 48 hours.
Infection with H5N1 influenza can occur in humans.
Infection results from contact with infected poultry e.g domesticated chickens, ducks and turkey.
Infection from one ill person to another is rare.

24. Avian Influenza Virus (Bird flu), H5N1
Symptoms in humans have ranged:
influenza-like symptoms (fever, cough, sore throat and muscle aches)
eye infections,
pneumonia and severe respiratory diseases
and other life threatening complications
e.g respiratory failure.
Some virulent influenza strains can escape innate and adaptive immunity via NS1 protein (nonstructural protein).

25. Control Elimination of infected birds. Careful dealing with birds.
Restriction of poultry and egg import.
Administration of antiviral drugs.
Vaccine is available.

26. Swine Flu (H1N1) The causative agent of 2009 pandemic.
This strain is a reassortment of several strains of H1N1 that are usually found separately in humans, birds and pigs.
The virus can spread from person to person

28. Control Personal hygiene. Aeration of living and work places.
Sneezing and coughing using tissue paper and disposing it immediately.
Bed rest of infected persons
Avoid contact with infected persons.
Antiviral drugs (e.g Neuraminidase inhibitors)
Vaccine is available.

29. Laboratory diagnosis RT-PCR
Serological testing for specific antibodies.