This document provides an overview of influenza viruses. It discusses that influenza viruses are a major cause of respiratory disease worldwide and have caused millions of deaths. It describes the three types of influenza viruses (A, B, C), their structures, proteins, replication cycles, mechanisms of antigenic drift and shift, and pathogenesis. The document also covers epidemiology, prevention strategies like vaccines and antiviral drugs, and treatment of influenza.

1. Introduction on influenza virus
The Orthomyxoviridae (influenza viruses) are a major cause of respiratory disease
worldwide.
Influenza has been responsible for millions of deaths worldwide.
Mutability and high frequency of genetic reassortment and resultant antigenic
changes in the viral surface glycoproteins make influenza viruses challenging to
control.
Influenza type A is antigenically highly variable and is responsible for most cases of
epidemic influenza.
Influenza type B may exhibit antigenic changes and sometimes causes epidemics.
Influenza type C is antigenically stable and causes only mild illness in
immunocompetent individuals.

2. Properties of Orthomyxoviruses
Three immunologic types of influenza viruses are known, designated A,
B, and C.
Antigenic changes continually occur within the type A group of influenza
viruses and to a lesser degree in the type B group, whereas type C
appears to be antigenically stable.
Influenza A strains are also known for aquatic birds, chickens, ducks,
pigs, horses, and seals besides human.

3. Structure & Composition
Influenza virus particles are usually spherical and about 100 nm in
diameter.
The single-stranded, negative-sense RNA genomes of influenza A and B
viruses occur as eight separate segments; influenza C viruses contain
seven segments of RNA, lacking a neuraminidase gene.
Most of the segments code for a single protein. The complete
nucleotide sequence is known for many influenza viruses.

5. Influenza virus particles contain different structural proteins.
The nucleoprotein (NP) associates with the viral RNA to form a
ribonucleoprotein (RNP).
Three large proteins (PB1, PB2, and PA) are bound to the viral RNP and
are responsible for RNA transcription and replication.
The matrix (M1) protein, which forms a shell underneath the viral lipid
envelope, is important in particle morphogenesis and is a major
component of the virion.
A lipid envelope derived from the cell surrounds the virus particle. Two
virus-encoded glycoproteins, the hemagglutinin (HA) and the
neuraminidase (NA), are inserted into the envelope and are exposed as
spikes.

6. These two surface glycoproteins are the important antigens that
determine antigenic variation of influenza viruses and host immunity.
Because of the segmented nature of the genome, when a cell is
coinfected by two different viruses of a given type, mixtures of
parental gene segments may be assembled into progeny virions.
This phenomenon, called genetic reassortment, may result in sudden
changes in viral surface antigens and poses significant problems for
vaccine development.
Influenza viruses may be stored at 0–4 °C for weeks without loss of
viability.
Lipid solvents, protein denaturants, formaldehyde, and irradiation
destroy infectivity.

7. Classification & Nomenclature
Genus Influenzavirus A contains human and animal strains of
influenza type A; Influenzavirus B contains human strains of type B;
and Influenzavirus C contains influenza type C viruses of humans
and swine.
The standard nomenclature system for influenza virus isolates
includes the following information: type, host of origin, geographic
origin, strain number, and year of isolation.
So far, 15 subtypes of HA (H1–H15) and nine subtypes of NA (N1–
N9), in many different combinations, have been recovered from
birds, animals, or humans.

8. Structure & Function of Hemagglutinin
The HA protein of influenza virus binds virus particles to susceptible cells and is
the major antigen against which neutralizing (protective) antibodies are
directed.
Variability in HA is primarily responsible for the continual evolution of new
strains and subsequent influenza epidemics. Hemagglutinin derives its name
from its ability to agglutinate erythrocytes under certain conditions.
The HA molecule is folded into a complex structure. The cleavage that
separates HA1 and HA2 is necessary for the virus particle to be infectious and
is mediated by cellular proteases.
Influenza viruses normally remain confined to the respiratory tract because the
protease enzymes that cleave HA are common only at those sites.

9. Function of Neuraminidase
The NA functions at the end of the viral replication cycle. It is
a sialidase enzyme that removes sialic acid from
glycoconjugates.
It facilitates release of virus particles from infected cell
surfaces during the budding process and helps prevent self-
aggregation of virions by removing sialic acid residues from
viral glycoproteins.

10. Antigenic Drift
Antigenic drift occurs as a result of point mutations in influenza A and
B viruses and refers to minor, gradual, antigenic changes in the HA or
NA proteins.
These variants can then no longer be neutralized by antibodies to the
parental strains. Antigenic drift has also been observed among
influenza viruses in land-based poultry, although to a lesser extent
than in humans.
Mutations in the human virus HA or NA amino acid sequence occur at
a frequency of less than 1% per year. Nevertheless, antigenic drift
variants can cause epidemics and typically prevail for 2 to 5 years
before being replaced by a different variant.

12. Antigenic Shift
Antigenic shift involves major antigenic changes in which a new HA or
NA subtype is introduced into the human population.
The newly introduced proteins are immunologically distinct from the
previously circulating strains and result in high infection rates in the
immunologically naive population, leading to pandemics.
An antigenic shift is caused by reassortment, typically between human
and avian viruses.

13. Influenza Virus Replication
The replication cycle of influenza virus is summarized in Figure .
Influenza is unusual among nononcogenic RNA viruses because all of
its RNA transcription and replication occur in the nucleus of infected
cells.
The viral multiplication cycle proceeds rapidly. There is the shut-off of
host cell protein synthesis by about 3 hours postinfection, permitting
selective translation of viral mRNAs.
New progeny viruses are produced within 8–10 hours.

15. Viral Attachment, Penetration, and Uncoating
The virus attaches to cell-surface sialic acid via the receptor site
located on the HA. Virus particles are then internalized within
endosomes by a process called receptor-mediated endocytosis.
The next step involves fusion between the viral envelope and cell
membrane, triggering uncoating. The low pH within the endosome
is required for virus-mediated membrane fusion that releases viral
RNPs into the cytosol.
The M2 ion channel protein present in the virion permits the entry
of ions from the endosome into the virus particle, triggering the
conformational change in HA.
Viral nucleocapsids are then released into the cell cytoplasm.

16. Transcription and Translation
Viral transcription occurs in the nucleus.
The mRNAs are produced from viral nucleocapsids.
The virus-encoded polymerase, is primarily responsible for transcription.
Six of the genome segments yield monocistronic mRNAs that are translated in
the cytoplasm into six viral proteins.
The other two transcripts undergo splicing, each yielding two mRNAs that are
translated in different reading frames.
At early times after infection, the NS1 and NP proteins are preferentially
synthesized. At later times, the structural proteins are synthesized at high
rates.
The two glycoproteins, HA and NA, are modified using the secretory pathway.

17. Viral RNA Replication
Viral genome replication is accomplished by the same virus-encoded
polymerase proteins involved in transcription.
The mechanisms that regulate the alternative transcription and replication
roles of the same proteins are related to the abundance of one or more of
the viral nucleocapsid proteins.
Intermingling of genome segments derived from different parents in
coinfected cells is presumably responsible for the high frequency of genetic
reassortment typical of influenza viruses within a genus.
Frequencies of reassortment as high as 40% have been observed.

18. Maturation
The virus matures by budding from the surface of the cell.
Many of the particles are not infectious. Particles sometimes fail to
encapsidate the complete complement of genome segments;
frequently, one of the large RNA segments is missing.
These noninfectious particles are capable of causing hemagglutination
and can interfere with the replication of intact virus.

19. Pathogenesis & Pathology
Influenza virus spreads from person to person by airborne droplets or by
contact with contaminated hands or surfaces.
The incubation period from exposure to virus and the onset of illness varies
from 1 day to 4 days, depending upon the size of the viral dose and the
immune status of the host.
Interferon is detectable in respiratory secretions about 1 day after viral
shedding begins. Influenza viruses are sensitive to the antiviral effects of
interferon.
Influenza infections cause cellular destruction and desquamation of
superficial mucosa of the respiratory tract but do not affect the basal layer of
epithelium.
Viral damage to the respiratory tract epithelium lowers its resistance to
secondary bacterial invaders, especially staphylococci, streptococci, and
Haemophilus influenzae.

20. Epidemiology
Influenza viruses occur worldwide and cause annual outbreaks of variable
intensity. It is estimated that annual epidemics cause 3–5 million cases of
severe illness and 250,000–500,000 deaths worldwide.
The economic impact of influenza A outbreaks is significant because of the
morbidity associated with infections. Economic costs have been estimated at
$10–60 million per million population in industrialized countries, depending
on the size of the epidemic.
The three types of influenza vary markedly in their epidemiologic patterns.
Influenza C is least significant; it causes mild, sporadic respiratory disease but
not epidemic influenza. Influenza B sometimes causes epidemics, but
influenza type A can sweep across continents and around the world in
massive epidemics called pandemics.
A continuous person-to-person chain of transmission must exist for
maintenance of the agent between epidemics.

21. Prevention & Treatment by Drugs
Amantadine hydrochloride and an analog, rimantadine, are M2 ion
channel inhibitors for systemic use in the treatment and prophylaxis of
influenza A.
The NA inhibitors zanamivir and oseltamivir were approved in 1999 for
treatment of both influenza A and influenza B. To be maximally
effective, the drugs must be administered very early in the disease.

22. Prevention & Control by Vaccines
Inactivated viral vaccines are the primary means of prevention of
influenza in the United States.
However, certain characteristics of influenza viruses make prevention
and control of the disease by immunization especially difficult. Existing
vaccines are continually being rendered obsolete as the viruses undergo
antigenic drift and shift.
Surveillance programs by government agencies and the World Health
Organization constantly monitor subtypes of influenza circulating
around the world to promptly detect the appearance and spread of new
strains.

23. Reassortment
Reassortment is the rearrangement of viral gene segments in cells infected
with two different influenza viruses . Reassortment can theoretically result in
256 (28) different gene variations for influenzae virus (i.e., the two parental
genotypes and 254 new gene combinations). Reassortment occurs for
influenza A, B, and C viruses, but has not been observed among the different
types of influenza viruses.
Recombination
Recombination has been detected in influenza virus segments that contain
genetic material from more than one origin. For negative-sense RNA viruses,
homologous recombination is not a common event; however, recombination
by template switching can take place and lead to increased biological fitness of
the virus

24. Reassortment

25. Recombination

26. Clinical Findings
Influenza attacks mainly the upper respiratory tract. It poses a serious risk for
the elderly, the very young, and people with underlying medical conditions
such as lung, kidney, or heart problems, diabetes, or cancer.
Uncomplicated Influenza
Symptoms of classic influenza usually appear abruptly and include chills,
headache, and dry cough, followed closely by high fever, generalized
muscular aches, malaise, and anorexia.
The fever usually lasts 3–5 days, as do the systemic symptoms. Respiratory
symptoms typically last another 3–4 days.
The cough and weakness may persist for 2–4 weeks after major symptoms
subside. Mild or asymptomatic infections may occur.

27. These symptoms may be induced by any strain of influenza A or B. In contrast,
influenza C rarely causes the influenza syndrome, causing instead a common
cold illness.
Clinical symptoms of influenza in children are similar to those in adults,
although children may have higher fever and a higher incidence of
gastrointestinal manifestations such as vomiting.
Febrile convulsions can occur. Influenza A viruses are an important cause of
croup in children under 1 year of age, which may be severe. Finally, otitis
media may develop.

28. Pneumonia
Serious complications usually occur only in the elderly and debilitated,
especially those with underlying chronic disease.
Pregnancy appears to be a risk factor for lethal pulmonary complications in
some epidemics.
Pneumonia complicating influenza infections can be viral, secondary
bacterial, or a combination of the two. Increased mucous secretion helps
carry agents into the lower respiratory tract.
Influenza infection enhances susceptibility of patients to bacterial
superinfection. This is attributed to loss of ciliary clearance, dysfunction of
phagocytic cells, and provision of a rich bacterial growth medium by the
alveolar exudate. Bacterial pathogens are most often Staphylococcus aureus,
Streptococcus pneumoniae, and H influenzae.

29. Reye's Syndrome
Reye's syndrome is an acute encephalopathy of children and adolescents,
usually between 2 and 16 years of age.
The mortality rate is high (10–40%). The cause of Reye's syndrome is unknown,
but it is a recognized rare complication of influenza B, influenza A, and
herpesvirus varicella-zoster infections.
There is a possible relationship between salicylate use and subsequent
development of Reye's syndrome. The incidence of the syndrome has
decreased with the reduced use of salicylates in children with flu-like
symptoms.

30. Prevention & Control by Vaccines
Inactivated viral vaccines are the primary means of prevention of influenza in
the United States.
However, certain characteristics of influenza viruses make prevention and
control of the disease by immunization especially difficult.
Existing vaccines are continually being rendered obsolete as the viruses
undergo antigenic drift and shift.
Surveillance programs by government agencies and the World Health
Organization constantly monitor subtypes of influenza circulating around the
world to promptly detect the appearance and spread of new strains.

31. Several other problems are worthy of mention. Although protection can
reach 70–100% in healthy adults, frequency of protection is lower (30–60%)
among the elderly and among young children.
Inactivated viral vaccines usually do not generate good local IgA or cell-
mediated immune responses. The immune response is influenced by
whether the person is "primed" by having had prior antigenic experience
with an influenza A virus of the same subtype.

32. Preparation of Inactivated Viral Vaccines
Inactivated influenza A and B virus vaccines are licensed for parenteral use
in humans. Federal bodies and the World Health Organization make
recommendations each year about which strains should be included in the
vaccine.
The vaccine is usually a cocktail containing one or two type A viruses and a
type B virus of the strains isolated in the previous winter's outbreaks.

33. Live-Virus Vaccines
A live-virus vaccine must be attenuated so as not to induce the disease it is
designed to prevent.
A live attenuated, cold-adapted, temperature-sensitive, trivalent influenza
virus vaccine administered by nasal spray was licensed in the United States in
2003.
It was the first live-virus influenza vaccine approved in the United States, as
well as the first nasally administered vaccine in the United States.

34. Use of Influenza Vaccines
The only contraindication to vaccination is a history of allergy to egg protein.
Since vaccine strains are grown in eggs, some egg protein antigens are
present in the vaccine.
Annual influenza vaccination is recommended for high-risk groups.
These include individuals at increased risk of complications associated with
influenza infection (those with either chronic heart or lung disease, including
children with asthma, or metabolic or renal disorders; residents of nursing
homes; persons infected with the human immunodeficiency virus [HIV]; and
those 65 years of age and older) and persons who might transmit influenza
to high-risk groups (medical personnel, employees in chronic care facilities,
household members).
The live-virus intranasal vaccine is not currently recommended for
individuals in the high-risk groups.

35. Anti-influenza Agents
Amantadine and Rimantadine
a. Primary use: respiratory infections caused by influenza A
b. Mechanism of action: inhibits viral uncoating – interacts with viral M2
protein (ion channel). Blocks entry of protons into virions, prevents
uncoating.
c. Good oral absorption; excreted by kidney unmetabolized
d. Side effects: Minor dose-related CNS effects (less with Rimantadine)
and GI effects
Zanamivir & Oseltamivir
a. Primary use: Treatment of uncomplicated influenza infection; types A & B
b. Mechanism of action: Inhibit neuraminidase which is required for viral
replication and release
c. Side effects: Well tolerated