Influenza viruses are RNA viruses in the Orthomyxoviridae family that cause seasonal flu epidemics and pandemics. They are spherical, 80-120nm in size, with segmented negative-sense RNA and replicate in the nucleus. Influenza A has different subtypes based on its hemagglutinin and neuraminidase proteins that determine its antigenicity and ability to cause pandemics through genetic reassortment. Seasonal flu is associated with upper respiratory illness but can lead to pneumonia. Diagnosis involves PCR, antigen detection, virus isolation and serology. Treatment focuses on antivirals while vaccination provides moderate protection against matched strains. High risk groups like the elderly are more susceptible to flu complications.

1. INFLUENZA VIRUS
KHOSIT PINMAI
Division of Microbiology & Immunology

2. TABLE 1 RNA Viruses with Examples of Diseases

3. Properties Orthomyxoviridae Paramyxoviridae
Size 80-120 nm 100-300 nm
Shape Spherical Pleomorphic
Nucleic acid Negative sense ssRNA
Segmental 8 pieces
Negative sense ssRNA
Unsegmental single
piece
Genetic recombination Seen Not seen
Antigenic variation Seen Not seen
Site for RNA
replication
Nucleus Cytoplasm
Important human
pathogens
Influenza virus Parainfluenza virus
Mumps virus
Measles virus
Respiratory syncytial
virus
Metapneumovirus
TABLE 1: Differences between Orthomyxoviridae
and Paramyxoviridae

4. ❑ They are one of the
major causes of
morbidity and mortality
and have been
responsible for several
epidemics and
pandemics of
respiratory diseases in
the last two centuries.
ORTOMYXOVIRIDAE
❑Influenza viruses are the
members of Orthomyxoviridae
family.

5. • Influenza viruses consist of
three genera-infuenza A, B, and C.
INFLUENZA VIRUSES
Morphology
Spherical: 80-120 nm in size.
Helical symmetry: a helical
nucleocapsid (9nm), surrounded
by an envelope.
Viral RNA: multiple segments of
(-ve) sense ss stranded RNA.
Site of replication: RNA
replication occurs typically in the
nucleus.
Viral proteins: 8 structural
proteins (PB1, PB2, PA, NP, HA,
NA, M1 and M2) and two non-
structural proteins (NS1 and NS2).

6. INFLUENZA VIRUSES
PB1, PB2, and PA are the polymerase proteins
responsible for RNA transcription and replication.
Nucleoprotein (NP) is the major capsid protein,
associated with viral RNA to form a ribonucleoprotein
(RNP) or nucleocapsid with a helical symmetry.
Matrix proteins: M1 protein is the major viral
protein ( 40%of total protein). It forms a shell (protein
layer) underneath the envelope. M2 proteins form
ion channels in the envelope, help in transport of
molecules.
Non-structural proteins: NS1 is an interferon
antagonist and inhibits pre-mRNA splicing. NS2 helps
in export of molecules across the nucleus.
Hemagglutinin (HA) and Neuraminidase (NA)
are the glycoproteins inserted into the lipid envelope.

7. INFLUENZA VIRUSES
Hemagglulinin (HA): It is triangular shaped
peplomer, binds to mucin or sialic acid receptors
on RBCs, resulting in clumping of RBCs to cause
hemagglutination. It also binds to the same
receptors on the respiratory epithelial cells, thus
facilitating viral entry.
Variable (classical Ag)
Envelope: Envelope is lipoprotein in nature.
Lipid part is derived from the host cell
membrane.
Proteins or the Peplomers are virus coded,
10 nm long glycoproteins that are inserted into
the lipid envelope. Two peplomers are present:

8. INFLUENZA VIRUSES
❑ It displaces HA from RBCs
resulting in reversal of
hemagglutination called elution.
❑ It facilitates release of virus
particles from infected cell
surfaces during budding
process by preventing self-
aggregation of virions to the
host cells.
❑ NA helps the virus to pass
through the mucin layer in the
respiratory tract to reach the
target epithelial cells.
Neuraminidase (NA): It is mushroom-shaped
peplomer, present in fewer number than HA. It is
a sialidase enzyme that degrades the sialic acid
receptors on RBCs; thus helps in:
Variable (classical Ag)

9. Influenza A virus life cycle

10. Antigenic Subtypes and Nomenclature
Three genera: Based on RNP and M proteins, influenza
viruses are divided into three genera: A, B and C.
Subtypes: Based on HA and NA antigens,
• Influenza A has distinct 16 H subtypes (H1 to H 16)
and 9 N subtypes (N1-N9).

11. The standard nomenclature system for
influenza virus
Type/ host (indicated
only for non-human
origin)/ geographic
origin/strain
number/year of
isolation (virus
subtype; HA NA
subtype).
Human strain:
Influenza A/Hong Kong/03/1968 (H3 N2).
Nonhuman strain:
lnfluenzaA/swine/Iowa/15/ 1930 (H1 N1).

12. Epidemiology: seasonal influenza
❑ Incidence: Influenza infects 5-15% of the world
population. It is estimated that annually about 3-5
million cases of severe illness and up to 1/2 million
deaths occur due to influenza epidemics worldwide
and is associated with significant economic impact.
❑ Seasonality: Influenza outbreaks are common
during timers. The most common seasonal flu strain
varies from season to season and from place to
place (e.g. H3N2 in Pondicherry in 2014).
❑ Epidemiological pattern: It depends upon the
nature of antigenic variation that occurs in the
influenza types
Influenza outbreaks occur worldwide almost every
year, however they differ widely in severity and the
extent of spread.

13. Antigenic Variation
Antigenic variation (‘drift’ and
‘shift’) is an important factor in global
epidemiology:
Antigenic drift: minor antigenic
changes in HA and NA as a result of
sequential point mutations (affects
types A, B and C).
: leads to frequent epidemics
Figure 1. Antigenic shift event. Where swine, birds
(ducks here), and humans live close together, the swine
can serve as a melting pot for creating “hybrid” influenza
viruses that are not rapidly neutralized by the human
immune system.
Antigenic shift: major antigenic
changes occur in HA and NA as a result of
genetic reassortment with animal viruses
(affects type A only).
: results in a change in
subtype and leads to
pandemics.

14. Pandemic
Name
Strain Source Suspected
Origin of
Outbreak
Year of
Emergence/App
Number of Deaths
Spanish flu H1N1 Birds The United
States and
China
1918/>50 million
(2-5% of the world
population died)
Asian flu H2N2 Birds China 1957/1–4 million
Hong Kong
flu
H3N2 Birds China 1968-1969/1–2
million
H5N1
(HPAI)
Birds China (Goose)
(HK:human)
2003
Swine flu H1N1 Swine,
birds
Mexico 2009/Up to 575,400
H7N9
(LPAI)
Birds China 2013
TABLE 2. Summary of the key characteristics of influenza
pandemics from the past one hundred years.

17. Pathogenesis and immune response
Spread by respiratory droplets and
aerosols; infects the upper respiratory
tract; incubation period of 18- 72 hours;
❑ Infection of cells in the respiratory tract
leads to the death of ciliated columnar
epithelial cells and causes inflammation
and irritation of the respiratory
epithelium.
❑ Immune system starts to hunt out and
clear the virus from the body.
❑ Innate immune responses hold the virus
at bay.
Habitat: Influenza virus infects humans, swine, and birds.
Virulence Factors: Hemagglutinin (H) and neuraminidase (N) spikes.
Ability to undergo antigenic shift.
❑ Antibody in serum (IgM) and secretions (IgA) appears about day 6.
❑ HA is an important virulence determinant.

18. Antibodies to HA prevent initiation of infection by inhibiting viral
entry; whereas antibodies to NA decrease the severity of the disease
and prevent the transmission of virus to contacts.

19. ADCC

20. Associated disease
Upper respiratory tract: Influenza C causes mild
respiratory illness mainly in children, otitis media;
Lower respiratory tract: primary
viral pneumonia, secondary bacterial
pneumonia (Influenza A & B);
Symptoms:
➢ High grade fever, headache, myalgia,
pharyngeal pain, coughing, anorexia, and
shortness of breath.
➢ As the epithelium is replaced by healthy
cells, usually over a week or two,
symptoms abate.
Central nervous system: Reye’s syndrome; fatty
degeneration of liver with acute encephalopathy

21. Secondary
bacterial
pneumonia

22. Diagnosis
Nasopharyngeal swab: kept at 4°
1. Molecular methods:
1.1 reverse transcription PCR (RT-PCR): gold standard
1.2 Real time-RT PCR - quantifies viral RNA
2. Antigen detection by
2.1 Immunofluorescence (requires NPA)
2.2 EIA; point-of-care tests utilizing immunochromatography
3. Isolation of virus:
Inoculation in embryonated eggs and primary monkey
kidney cell lines.
Growth is detected by hemadsorption, hemagglutination
test.
Clotted blood: Serology
1. Complement fixation Test
2. Haemagglutination inhibition test
3. ELISA

23. Hemagglutinatlon Inhibition (HAI)
test
RBCs
Virus Antibody to virus
+
Neutralized virus
+
Button
Haemagglutination
+
RBCs Virus
No
Antibody
to virus
Matt

24. Figs 2 A Hemagglutination inhibition test

25. ➢ Vaccines since the 1940’s target the serum
neutralizing antibody response to HA
➢ This specific response can be measured by a
serum hemagglutination inhibition assay
➢ This is an established correlate of protective
immunity
➢ A 4-fold increase in HAI titer (or >1:40) is
indicative of protection from influenza virus
infection by a matched strain.
25
Advantage of the potent anti-HA neutralizing
antibody response for vaccines

26. The following are at increased risk of
complications associated with influenza virus
infection.
❑Age: children ( <2 years) and old age(> 65 years).
❑Pregnancy
❑Underlying chronic lung. cardiac, renal, hepatic, and
CNS conditions.
❑Low immunity (HIV infected people).
❑Older children are at high risk of developing croup,
sinusitis, otitis media, high-grade fever, and
diarrhoea.
High risk groups

27. Specific Treatment
For patients at risk of severe influenza
infection: Three prescription drugs are currently
recommended for the treatment of influenza
Interferes with viral
entry into the cell
Amantadine and
rimantadine
are not currently
recommended because of
high levels of resistance.
Zanamivir (Relenza)
Oseltamivir (Tamiflu)
Peramivir (Rapivab)
Decrease
the duration of the disease,
the severity of
symptoms and
slowed virus transmission.

28. Non-specific Treatment
Mainly to control symptoms, include
1. Fluids rehydration
2. Bed rest
3. Nonaspirin pain relievers and anti-
inflammatory drugs eg. paracetamol
Aspirin is not indicated because it significantly
increases the risk for Reye’s syndrome, a rare
disease that strikes the brain, liver, and kidney
and is characterized by the fatty degeneration of
those organs.

29. Prevention Inactivated trivalent vaccines
have an efficacy of 60–80%, provided that
vaccine components and current wild-type
viruses are sufficiently similar.
2018
2019
January: three or four virus
variants are selected according
to evidence that predicts the
most prominent strains to
circulate that Year
Four component vaccines add
an additional virus, B/
Phuket/3073/2013-like virus
(B/Yamagata lineage)
January
CDC delivers the correct
virus seed stock to
manufacturers.
February March April May
The viruses are harvested,
processed, and inactivated by
chemical
treatment to create the vaccine.
June July
In June/July, the
vaccine is tested
for purity, safety,
and sterility.
August September
In August/September, the
vaccine is dispensed,
prepared for
injection, and shipped to
medical centers and
pharmacies.
October November
October/November,
the vaccination
programs begin.

30. Prevention
Traditional vaccination, approved for the
majority of individuals 6 months or older, is
an inactivated trivalent or quadrivalent
vaccine (containing antigens from 3 viral
strains) injected intramuscularly, 0.5 ml.
Serious complication of influenza vaccines:
Guillain-Barré syndrome
❑ It is a neurological condition that can arise in approximately
1 in 100,000 vaccine recipients.
❑ This syndrome appears to be an autoimmunity induced by
viral proteins and marked by varying degrees of
demyelination of the peripheral nervous system, leading to
weakness and sensory loss.
❑ Most patients recover function, but the disease can also be
debilitating and fatal.

31. Vaccine/age Type Substrate
Fluzone
(Sanofi)/≥3 yrs
Formalin inactivated, split, and
purified
Embryonated chicken
eggs
Flucelvax
(Seqirus)/≥4 yrs
β-propiolactone (BPL)
inactivated, split, and purified
Madin-Darby canine
kidney (MDCK) cells
FluBlok (Protein
Sciences)/≥18
yrs
rHA protein subunit, detergent
extracted, purified
SF9 (insect) cells
Flumist
(AstraZeneca)/2
through 49 yrs
Live-attenuated, purified, and
filtered
Embryonated chicken
eggs
31
Inactivated (subunit) vaccines (IIV): 0.5 mL prefilled syringe
• Target the HA eliciting neutralizing serum antibody responses
• Most have “contaminating” antigens, including NA, but these are
not quantitated or considered in immunogenicity or efficacy
Live-attenuated influenza vaccine (LAIV)
• Elicits mucosal and serum antibody, as well as cellular immune
responses: 0.2 prefilled intranasal sprayer (2 through 49 yrs)
Flavors of licensed influenza vaccines
https://www.cdc.gov/flu/protect/vaccine/vaccines.htm

32. Trivalent vaccines for use in the 2018-2019
influenza season (southern hemisphere winter)
– an A/Michigan/45/2015 (H1N1)pdm09- like
virus
– an A/Singapore/ INFIMH-16-0019/2016 (H3N2)-
like virus
– a B/Phuket/3073/2013-like virus
It is recommended that quadrivalent vaccines
containing two influenza B viruses contain the above
three viruses and a B/Brisbane/60/2008-like virus.

33. Influenza infection animation
by medical media

34. Avian Flu
❑ Birds are the primary reservoir for influenza viruses.
❑ All influenza subtypes (16H types and 9N types) are
found in birds and some of the subtypes can be
transmitted to mammals (e.g; H1, H2, H3, and H5 to
Humans; H 1 and H3 to swine)
❑ Infection of humans with avian influenza does not mean a
pandemic will occur.
❑ Usually the avian flu strains are highly virulent as they possess
PB1F2 protein, which targets host mitochondria and induces
apoptosis.
❑ A/H5N1 is the most common avian flu strain that has been
endemic in the world for the past 15 years.
❑ Other avian flu strains that can cause human infections are:
❑ A/H7N7(Netherlands)
❑ A/H9N2 (Hong Kong)
❑ A/H7N9 (caused an outbreak in China, 2013)

35. Avian Flu
❑ Transmission to man occurs only from birds,
and requires close respiratory contact.
❑ Less morbidity: As there is no human-human
transmission, morbidity is less.
❑ More mortality: The avian flu strains are
highly virulent (due to presence of PB1F2
protein) and mortality rate is >60%.
❑ Clinical feature: H5N1 avian flu strains are
associated with higher rates of pneumonia
(>50%) and extra pulmonary manifestations
such as diarrhoea and CNS involvement.
❑ Treatment: Drug of choice is oseltamivir
(Tamiflu)
Avian Flu Infection in Humans
❑ Avian influenza has spilled over into human repeatedly

36. Sialic Acid Receptors
Sialic acid receptors found on the host cell
surfaces are specific for HA antigens of
influenza which in turn determines the
different host specificities of influenza virus.
 2,3 sialic acid receptors are
specific for avian influenza strains
and are found abundantly on bird's
intestinal epithelium.
In humans, they are present in
very few numbers on upper
respiratory tract, and also on some
epithelial cells in the lower tract.
2,6 sialic acid receptors are specific
for human influenza strains and are
found abundantly on human upper
respiratory tract epithelium, but not
on lower respiratory tract.
2,6 2,3

37. American Journal of Pathology. 2007;171:1215-1223
Attachment of influenza viruses to human
respiratory tissues
H5N1 virus
attachment to
type II
pneumocytes
in human
alveoli

38. Attachment of H3N2 virus and H5N1 virus to the
submucosal glands in human trachea.
Tracheal submucosal glands produce a different
sialosaccharide (α-2,3-SA) from that predominantly
expressed by tracheal epithelial cells (α-2,6-SA).

39. Sialic Acid Receptors

40. A/H1N1 2009 Flu
❑ Origin: H1N1 2009 flu originated by
genetic reassortment of four strains
(1 human strain+ 2 swine strains+ 1
avian strain) and the mixing had
occurred in pigs (Fig. 44.3).
❑ Swine flu: a reassortant of four strains.
❑ Transmission: It can be transmitted from human to human,
which has accounted for its rapid spread.
❑ However, it is less virulent (as it lacks the PB1 F2 protein)
❑ The H1N1 2009 flu Has caused more morbidity but less mortality.
❑ It has caused the most recent pandemic of influenza,
emerged in California in March 2009 and rapidly
spread to the entire world.
❑ WHO declared the pandemics in 11th June2009
❑ It is believed that all human pandemic strains have
originated by reassortment between avian and
human influenza viruses and the mixing has occurred
in pigs.

41. A/H1N1 2009 Flu
❑ Complicated/severe influenza can occur very
rarely in high risk groups, is characterized by features
such as pneumonia or acute respiratory distress
syndrome (ARDS), secondary bacterial pneumonia,
dehydration, CNS involvement, and multi organ failure.
❑ Treatment: Drug of choice is neuraminidase inhibitors
❑ Oseltamivir (Tamiflu) tablet- 75 mg twice a day for
5 days
❑ Zanamivir (inhalational forms)
❑ H1N1 flu is resistant to amantadine
Clinical Features
❑ Uncomplicated Influenza: Most of the
cases present with mild upper respiratory
tract illness and diarrhoea.

42. A/H1N1 2009 Flu: Prevention
General preventive measures include
❑ Avoid contact with infected people
❑ Stay at home if you are sick
❑ Contain your coughs and sneezes-by using mask
(special N95 mask for health care workers)
❑ Wash your hands thoroughly and frequently
Vaccine
❑ Vaccine: Both killed injectable and live nasal spray
vaccines are available for A/H1N1 2009 flu.

43. ➢ Multiple types and subtypes of
influenza are circulating (and changing)
in humans
➢ Zoonotic influenzas are all around us
posing potential threats
➢ Not all influenzas are equal
➢ Outcomes of infection are varied
➢ Immunity to infection is potent,
although potentially not long-lived
43
To sum up

44. REFERENCES
https://www.nucleusmedicalmedia.com/nmm1_7

46. Sialic Acid Receptors
Sialic acid receptors found on the host cell
surfaces are specific for HA antigens of
influenza which in turn determines the
different host specificities of influenza virus.
 2-3 sialic acid receptors are
specific for avian influenza strains
and are found abundantly on bird's
intestinal epithelium.
In humans, they are present in
very few numbers on upper
respiratory tract, and also on some
epithelial cells in the lower tract.
2-6 sialic acid receptors are specific
for human influenza strains and are
found abundantly on human upper
respiratory tract epithelium, but not
on lower respiratory tract.