Orthomyxoviruses

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565 
39Orthomyxoviruses (Influenza Viruses)
C H A P T E R
Respiratory illnesses are responsible for more than half of all 
acute illnesses each year in the United States. The Orthomyxo-
viridae (influenza viruses) are a major determinant of morbid-
ity and mortality caused by respiratory disease, and outbreaks 
of infection sometimes occur in worldwide epidemics. Influ-
enza 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 formidable challenges for control 
efforts. 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.
PROPERTIES OF ORTHOMYXOVIRUSES
Three immunologic types of influenza viruses are known, 
designated A, B, and C. Whereas antigenic changes continu-
ally occur within the type A group of influenza viruses and 
to a lesser degree in the type B group, type C appears to be 
antigenically stable. Influenza A strains are also known for 
aquatic birds, chickens, ducks, pigs, horses, and seals. Some 
of the strains isolated from animals are antigenically similar 
to strains circulating in the human population.
The following descriptions are based on influenza virus 
type A, the best-characterized type (Table 39-1).
Structure and Composition
Influenza virus particles are usually spherical and about 100 
nm in diameter (80–120 nm), although virions may display 
great variation in size (Figure 39-1).
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. Sizes and protein-coding assignments 
are known for all the segments (Table 39-2). Most of the seg-
ments code for a single protein. The first 12–13 nucleotides at 
each end of each genomic segment are conserved among all 
eight RNA segments; these sequences are important in viral 
transcription.
Influenza virus particles contain nine different struc-
tural proteins. The nucleoprotein (NP) associates with the 
viral RNA to form a ribonucleoprotein (RNP) structure 9 nm 
in diameter that assumes a helical configuration and forms 
the viral nucleocapsid. 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 impor-
tant in particle morphogenesis and is a major component of 
the virion (~40% of viral protein).
A lipid envelope derived from the cell surrounds the virus 
particle. Two virus-encoded glycoproteins, hemagglutinin 
(HA) and neuraminidase (NA), are inserted into the envelope 
and are exposed as spikes about 10 nm long on the surface of 
the particle. These two surface glycoproteins determine anti-
genic variation of influenza viruses and host immunity. The 
HA represents about 25% of viral protein and the NA about 
5%. The M2 ion channel protein and the NS2 protein are also 
present in the envelope but at only a few copies per particle.
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 reas-
sortment, may result in sudden changes in viral surface 
antigens—a property that explains the epidemiologic fea-
tures of influenza and poses significant problems for vaccine 
development.
Influenza viruses are relatively hardy in vitro and may 
be stored at 0–4°C for weeks without loss of viability. Lipid 
solvents, protein denaturants, formaldehyde, and irradiation 
destroy infectivity. Both infectivity and hemagglutination are 
more resistant to inactivation at alkaline pH than at acid pH.
Classification and 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.
Antigenic differences exhibited by two of the internal 
structural proteins, the nucleocapsid (NP) and matrix (M) 
proteins, are used to divide influenza viruses into types A, B, 
and C. These proteins possess no cross-reactivity among the 
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566 SECTION IV Virology
three types. Antigenic variations in the surface glycoproteins, 
HA and NA, are used to subtype type A viruses.
The standard nomenclature system for influenza virus 
isolates includes the following information: type, host of ori-
gin, geographic origin, strain number, and year of isolation. 
Antigenic descriptions of the HA and the NA are given in 
parentheses for type A. The host of origin is not indicated for 
human isolates, such as A/Hong Kong/03/68(H3N2), but it is 
indicated for others, such as A/swine/Iowa/15/30(H1N1).
So far, 18 subtypes of HA (H1–H18) and 11 subtypes of 
NA (N1–N11), in many different combinations, have been 
recovered from humans and animals.
The Orthomyxoviridae family also contains the genus 
Thogotovirus, members of which are not known to cause dis-
ease in humans.
Structure and Function of Hemagglutinin
The HA protein of influenza virus binds virus particles to 
susceptible cells and is the major antigen against which neu-
tralizing (protective) antibodies are directed. Variability in 
HA is primarily responsible for the continual evolution of 
new strains and subsequent influenza epidemics. HA derives 
its name from its ability to agglutinate erythrocytes under 
certain conditions.
The primary sequence of HA contains 566 amino acids 
(Figure 39-2A). A short signal sequence at the amino termi-
nal inserts the polypeptide into the endoplasmic reticulum; 
the signal is then removed. The HA protein is cleaved into 
two subunits, HA1 and HA2, that remain tightly associated 
by a disulfide bridge. A hydrophobic stretch near the carboxyl 
terminal of HA2 anchors the HA molecule in the membrane, 
with a short hydrophilic tail extending into the cytoplasm. 
Oligosaccharide residues are added at several sites.
TABLE 39-1 Important Properties of 
Orthomyxovirusesa
Virion: Spherical, pleomorphic, 80–120 nm in diameter (helical 
nucleocapsid, 9 nm)
Composition: RNA (1%), protein (73%), lipid (20%), carbohydrate 
(6%)
Genome: Single-stranded RNA, segmented (eight molecules), 
negative-sense, 13.6 kb overall size
Proteins: Nine structural proteins, one nonstructural
Envelope: Contains viral hemagglutinin and neuraminidase 
proteins
Replication: Nuclear transcription; capped 5′ termini of cellular RNA 
scavenged as primers; particles mature by budding from plasma 
membrane
Outstanding characteristics:
 Genetic reassortment common among members of the same 
 genus
 Influenza viruses cause worldwide epidemics
aDescription of influenza A virus, genus Influenzavirus A.
FIGURE 39-1 Influenza virus. A: Electron micrograph of influenza virus A/Hong Kong/1/68(H3N2). Note the pleomorphic shapes and 
glycoprotein projections covering particle surfaces (315,000×). (Courtesy of FA Murphy and EL Palmer.) B: Schematic view of influenza. Virus 
particles have segmented genomes consisting of seven or eight different RNA molecules, each coated by capsid proteins and forming helical 
nucleocapsids. Viral glycoproteins (hemagglutinin and neuraminidase) protrude as spikes through the lipid envelope. (Reproduced with 
permission from Willey JM, Sherwood LM, Woolverton CJ: Prescott, Harley, and Klein’s Microbiology, 7th ed. McGraw Hill, 2008. © The McGraw-
Hill Companies, Inc.)
Nucleocapsid
Viral
glycoproteins
Envelope
BA
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CHAPTER39 Orthomyxoviruses (Influenza Viruses) 567
The three-dimensional structure of the HA protein has 
been revealed by x-ray crystallography. The HA molecule is 
folded into a complex structure (Figure 39-2B). Each linked 
HA1 and HA2 dimer forms an elongated stalk capped by a 
large globule. The base of the stalk anchors it in the mem-
brane. Five antigenic sites on the HA molecule exhibit exten-
sive mutations. These sites occur at regions exposed on the 
surface of the structure, are apparently not essential to the 
molecule’s stability, and are involved in viral neutralization. 
Other regions of the HA molecule are conserved in all iso-
lates, presumably because they are necessary for the molecule 
to retain its structure and function.
The HA spike on the virus particle is a trimer composed 
of three intertwined HA1 and HA2 dimers (Figure 39-2C). 
The trimerization imparts greater stability to the spike 
than could be achieved by a monomer. The cellular recep-
tor binding site (viral attachment site) is a pocket located at 
the top of each large globule. The pocket is inaccessible to 
antibody.
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 con-
fined to the respiratory tract because the protease enzymes 
that cleave HA are expressed only at those sites. Examples 
have been noted of more virulent viruses that have adapted 
to use a more ubiquitous enzyme, such as plasmin, to cleave 
HA and promote widespread infection of cells. The amino 
terminal of HA2, generated by the cleavage event, is neces-
sary for the viral envelope to fuse with the cell membrane, 
an essential step in the process of viral infection. Low pH 
triggers a conformational change that activates the fusion 
activity.
Structure and Function of Neuraminidase
The antigenicity of NA, the other glycoprotein on the surface 
of influenza virus particles, is also important in determining 
the subtype of influenza virus isolates.
TABLE 39-2 CODING ASSIGNMENTS OF INFLUENZA VIRUS A RNA SEGMENTS
Genome Segment Encoded Polypeptide
Numbera
Size (Number of 
Nucleotides) Designation
Predicted 
Molecular Weightb
Approximate 
Number of 
Molecules per 
Virion Function
1 2341 PB2 85,700 30–60 RNA transcriptase components
2 2341 PB1 86,500
3 2233 PA 84,200
4 1778 HA 61,500 500 Hemagglutinin; trimer; envelope glycoprotein; 
mediates virus attachment to cells; activated 
by cleavage; fusion activity at acid pH
5 1565 NP 56,100 1000 Associated with RNA and polymerase proteins; 
helical structure; nucleocapsid
6 1413 NA 50,000 100 Neuraminidase; tetramer; envelope 
glycoprotein; enzyme
7 1027 M
1
27,800 3000 Matrix protein; major component of virion; lines 
inside of envelope; involved in assembly; 
interacts with viral RNPs and NS
2
M
2
11,000 20–60 Integral membrane protein; ion channel; 
essential for virus uncoating; from spliced 
mRNA
8 890 NS
1
26,800 0 Nonstructural; high abundance; inhibits pre-
mRNA splicing; reduces interferon response
NS
2
14,200 130–200 Minor component of virions; nuclear export of 
viral RNPs; from spliced mRNA
aRNA segments are numbered in order of decreasing size.
bThe molecular weights of the two glycoproteins, HA and NA, appear larger (about 76,000 and 56,000, respectively) because of the added carbohydrate.
HA, hemagglutinin; M
1
, matrix protein; M
2
, integral membrane protein; NA, neuraminidase; NP, nucleoprotein; NS
1
 and NS
2
 are nonstructural proteins; PB2, PB1, and PA are 
polymerase proteins; RNP, ribonucleoprotein.
Adapted with permission from Lamb RA, Krug RM: Orthomyxoviridae: The viruses and their replication. In Fields BN, Knipe DM, Howley PM (editors-in-chief). Fields 
Virology, 3rd ed. Lippincott-Raven, 1996.
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568 SECTION IV Virology
The spike on the virus particle is a tetramer composed 
of four identical monomers (Figure 39-2D). A slender stalk 
is topped with a box-shaped head. There is a catalytic site for 
NA on the top of each head, so that each NA spike contains 
four active sites.
The NA functions at the end of the viral replica-
tion 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. It 
is possible that NA helps the virus negotiate through the 
mucin layer in the respiratory tract to reach the target 
epithelial cells.
FIGURE 39-2 Influenza virus hemagglutinin (HA) and neuraminidase (NA) surface glycoproteins. A: Primary structures of HA and NA 
polypeptides. The cleavage of HA into HA1 and HA2 is necessary for virus to be infectious. HA1 and HA2 remain linked by a disulfide bond 
(S–S). No posttranslational cleavage occurs with NA. Carbohydrate attachment sites • are shown. The hydrophobic amino acids that anchor 
the proteins in the viral membrane are located near the carboxyl terminal of HA and the amino terminal of NA. B: Folding of the HA1 and HA2 
polypeptides in an HA monomer. Five major antigenic sites (sites A–E) that undergo change are shown as shaded areas. The amino terminal 
of HA2 provides fusion activity (fusion peptide). The fusion particle is buried in the molecule until it is exposed by a conformational change 
induced by a low pH. C: Structure of the HA trimer as it occurs on a virus particle or the surface of infected cells. Some of the sites involved in 
antigenic variation are shown (A). Carboxyl terminal residues (C) protrude through the membrane. D: Structure of the NA tetramer. Each NA 
molecule has an active site on its upper surface. The amino terminal region (N) of the polypeptides anchors the complex in the membrane. 
(Redrawn with permission from [A, B] Murphy BR, Webster RG: Influenza viruses, pp. 1185 and 1186, and [C, D] Kingsbury DW: Orthomyxo-and 
paramyxoviruses and their replication, pp. 1163 and 1172. In Fields BN [editor-in-chief] Virology. Raven Press, 1985.)
S – S
NH2
Signal
peptide
Proteolytic
activation
cleavage
Hemagglutinin
Neuraminidase
Hydrophobic
membrane
domain
Hydrophobic
membrane
domain
Conserved
sequence
A
B
C
D
Hydrophilic
cytoplasmic
domain
COOH
COOH
Receptor site
Large globule
Protease cleavage
site
Small globule
Membrane
Active site
Stalk
C
N
13.5 nm
6 nm
Site B
Site D
Fusion peptide
Site A
Site E
Site C
NH2
HA2HA1
C
A A
A
A
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CHAPTER 39 Orthomyxoviruses (Influenza Viruses) 569
Antigenic Drift and Antigenic Shift
Influenza viruses are remarkable because of the frequent anti-
genic changes that occur in HA and NA. Antigenic variants 
of influenza virus have a selective advantage over the parental 
virus in the presence of antibody directed against the original 
strain. This phenomenon is responsible for the unique epide-
miologic features of influenza. Other respiratory tract agents 
do not display significant antigenic variation.
The two surface antigens of influenza undergo antigenic 
variation independent of each other. Minor antigenic changes 
are termed antigenic drift; major antigenic changes in HA or 
NA, called antigenic shift, result in the appearance of a new 
subtype (Figure 39-3). Antigenic shift is most likely to result 
in an epidemic.
Antigenic drift is caused by the accumulation of point 
mutations in the gene, resulting in amino acid changes in 
the protein. Sequence changes can alter antigenic sites on 
the molecule such that a virion can escape recognition by the 
host’s immune system. The immune system does not cause 
the antigenic variation but rather functions as a selection 
force that allows new antigenic variants to expand. A variant 
must sustain two or more mutations before a new, epidemio-
logically significant strainemerges.
Antigenic shift reflects drastic changes in the sequence 
of a viral surface protein, caused by genetic reassortment 
between human, swine, and avian influenza viruses. Influ-
enza B and C viruses do not exhibit antigenic shift because 
few related viruses exist in animals.
Influenza Virus Replication
The replication cycle of influenza virus is summarized in 
Figure 39-4. The viral multiplication cycle proceeds rapidly. 
FIGURE 39-3 Antigenic drift and antigenic shift account for 
antigenic changes in the two surface glycoproteins (hemagglutinin 
[HA] and neuraminidase [NA]) of influenza virus. Antigenic drift is a 
gradual change in antigenicity caused by point mutations that affect 
major antigenic sites on the glycoprotein. Antigenic shift is an abrupt 
change caused by genetic reassortment with an unrelated strain. 
Changes in HA and NA occur independently. Internal proteins of 
the virus, such as the nucleoprotein (NP), do not undergo antigenic 
changes.
HA
or
NA
HA or NA
NP
One yearYears
D
ec
re
as
in
g 
se
ro
lo
gi
c 
re
la
te
dn
es
s
Antigenic drift Antigenic shift
FIGURE 39-4 Schematic diagram of the life cycle of 
influenza virus. After receptor-mediated endocytosis, the viral 
ribonucleoprotein complexes are released into the cytoplasm and 
transported to the nucleus, where replication and transcription 
take place (1). Messenger RNAs are exported to the cytoplasm 
for translation. (2) Early viral proteins required for replication and 
transcription, including nucleoprotein (NP) and a polymerase protein 
(PB1), are transported back to the nucleus. RNA polymerase activity 
of the PB1 protein synthesizes positive single-stranded RNA (ssRNA) 
from genomic negative single-stranded RNA (–ssRNA) molecules. 
(3) These +ssRNA templates are copied by the RNA polymerase 
activity of the PB1 protein. (4) Some of these new genome segments 
serve as templates for the synthesis of more viral mRNA. Later in the 
infection, they become progeny genomes. Viral mRNA molecules 
transcribed from some genome segments encode structural 
proteins such as hemagglutinin (HA) and neuraminidase (NA). These 
messages are translated by endoplasmic reticulum-associated 
ribosomes and delivered to the cell membrane (5). Viral genome 
segments are packaged as progeny virions bud from the host cell 
(6). ER, endoplasmic reticulum. (Reproduced with permission from 
Willey JM, Sherwood LM, Woolverton CJ (eds): Prescott, Harley, & 
Klein’s Microbiology. McGraw-Hill, 2008, p. 457. © The McGraw-Hill 
Companies, Inc.)
43
1
2
5
6
Coated
pit
Coated
vesicle
Endosome
pH
5-6
RNA
nucleocapsid
–ssRNAs+ssRNA
C5′ C
 5′ C
C
C
(+)
Host mRNA
Nucleus
PB1NP
3′
Viral mRNA
Cytoplasm
Rough ER
Golgi
apparatus
Insertion of
envelope proteins
Budding
HA NA
3′
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570 SECTION IV Virology
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.
A. Viral Attachment, Penetration, and Uncoating
The virus attaches to cell-surface sialic acid via the receptor site 
located on the top of the large globule of the HA. Virus parti-
cles are then internalized within endosomes through receptor-
mediated endocytosis. The next step involves fusion between 
the viral envelope and cell membrane, triggering uncoat-
ing. The low pH within the endosome is required for virus-
mediated membrane fusion that releases viral RNPs into the 
cytosol. Acid pH causes a conformational change in the HA 
structure to bring the HA2 “fusion peptide” in correct contact 
with the membrane. 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.
B. Transcription and Translation
Transcription mechanisms used by orthomyxoviruses differ 
markedly from those of other RNA viruses in that cellular 
functions are more intimately involved. Viral transcription 
occurs in the nucleus. The mRNAs are produced from viral 
nucleocapsids. The virus-encoded polymerase, consisting of 
a complex of the three P proteins, is primarily responsible for 
transcription. Its action must be primed by scavenged capped 
and methylated 5′ terminals from cellular transcripts that 
are newly synthesized by cellular RNA polymerase II. This 
explains why influenza virus replication is inhibited by dacti-
nomycin and α-amanitin, which block cellular transcription, 
but other RNA viruses are not affected because they do not 
use cellular transcripts in viral RNA synthesis.
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 pref-
erentially synthesized. At later times, the structural proteins 
are synthesized at high rates. The two glycoproteins, HA and 
NA, are modified using the secretory pathway.
The influenza virus nonstructural protein NS1 has a 
posttranscriptional role in regulating viral and cellular gene 
expression. The NS1 protein binds to poly(A) sequences, 
inhibits pre-mRNA splicing, and inhibits the nuclear export 
of spliced mRNAs, ensuring a pool of donor cellular mole-
cules to provide the capped primers needed for viral mRNA 
synthesis. The NS2 protein interacts with M1 protein and is 
involved in nuclear export of viral RNPs.
C. 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 abun-
dance of one or more of the viral nucleocapsid proteins.
As with all other negative-strand viruses, templates 
for viral RNA synthesis remain coated with NPs. The only 
completely free RNAs are mRNAs. The first step in genome 
replication is production of positive-strand copies of each 
segment. These antigenome copies differ from mRNAs at 
both terminals; the 5′ ends are not capped, and the 3′ ends 
are neither truncated nor polyadenylated. These copies serve 
as templates for synthesis of faithful copies of genomic RNAs.
Because there are common sequences at both ends of 
all viral RNA segments, they can be recognized efficiently by 
the RNA-synthesizing machinery. 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.
D. Maturation
The virus matures by budding from the surface of the cell. 
Individual viral components arrive at the budding site by 
 different routes. Nucleocapsids are assembled in the nucleus 
and move out to the cell surface. The glycoproteins, HA and 
NA, are synthesized in the endoplasmic reticulum; are modi-
fied and assembled into trimers and tetramers, respectively; 
and are inserted into the plasma membrane. The M1 protein 
serves as a bridge, linking the nucleocapsid to the cytoplas-
mic ends of the glycoproteins. Progeny virions bud off the 
cell. During this sequence of events, the HA is cleaved into 
HA1 and HA2 if the host cell possesses the appropriate pro-
teolytic enzyme. The NA removes terminal sialic acids from 
cellular and viral surface glycoproteins, facilitating release of 
virus particles from the cell and preventing their aggregation.
Many of the particles are not infectious. Particles some-
times fail to encapsidate the complete set of genome segments; 
frequently, one of the large RNA segments is missing. These 
noninfectious particles are capable of causing hemagglutina-
tionand can interfere with the replication of intact virus.
Reverse-genetics systems that allow the generation of 
infectious influenza viruses from cloned cDNAs of viral RNA 
segments are available and allow for mutagenesis and func-
tional studies.
INFLUENZA VIRUS INFECTIONS 
IN HUMANS
A comparison of influenza A virus with other viruses that 
infect the human respiratory tract is shown in Table 39-3. 
Influenza virus is considered here.
Pathogenesis and Pathology
Influenza virus spreads from person to person by airborne 
droplets or by contact with contaminated hands or surfaces. 
A few cells of respiratory epithelium are infected if deposited 
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CHAPTER 39 Orthomyxoviruses (Influenza Viruses) 571
virus particles avoid removal by the cough reflex and escape 
neutralization by preexisting specific immunoglobulin A 
(IgA) antibodies or inactivation by nonspecific inhibitors in 
the mucous secretions. Progeny virions are soon produced 
and spread to adjacent cells, where the replicative cycle is 
repeated. Viral NA lowers the viscosity of the mucous film in 
the respiratory tract, laying bare the cellular surface receptors 
and promoting the spread of virus-containing fluid to lower 
portions of the tract. Within a short time, many cells in the 
respiratory tract are infected and eventually killed.
The incubation period from exposure to virus and the 
onset of illness varies from 1 day to 4 days, depending on the 
size of the viral dose and the immune status of the host. Viral 
shedding starts the day preceding onset of symptoms, peaks 
within 24 hours, remains elevated for 1–2 days, and then 
declines over the next 5 days. Infectious virus is very rarely 
recovered from blood.
Interferon is detectable in respiratory secretions about 1 
day after viral shedding begins. Influenza viruses are sensitive 
to the antiviral effects of interferon, and it is believed that the 
innate immunity response contributes to host recovery from 
infection. Specific antibody and cell-mediated responses can-
not be detected for another 1–2 weeks.
Influenza infections cause cellular destruction of the 
superficial mucosa of the respiratory tract but do not affect 
the basal layer of epithelium. Complete reparation of cellular 
damage probably takes up to 1 month. Viral damage to the 
respiratory tract epithelium lowers its resistance to secondary 
bacterial pathogens, especially staphylococci, streptococci, 
and Haemophilus influenzae.
Edema and mononuclear infiltrations in response to 
cytokine release and cell death caused by viral replication 
probably account for local symptoms. The fever and systemic 
symptoms associated with influenza reflect the action of 
cytokines.
Clinical Findings
Influenza attacks mainly the upper respiratory tract. It poses 
a serious risk for elderly adults, very young children, and peo-
ple with underlying medical conditions such as lung, kidney, 
or heart problems, diabetes, cancer, or immunosuppression.
TABLE 39-3 Comparison of Viruses That Infect the Human Respiratory Tract
Virus Disease Number of Serotypes
Lifelong Immunity to 
Disease Vaccine Available Viral Latency
RNA viruses
 Influenza A virus Influenza Many No + −
 Metapneumovirus Croup, bronchiolitis Several No − −
 Parainfluenza virus Croup Many No − −
 Respiratory syncytial 
 virus
Bronchiolitis, 
pneumonia
Two No − −
 Rubella virus Rubella One Yes + −
 Measles virus Measles One Yes + −
 Mumps virus Parotitis, meningitis One Yes + −
 Rhinovirus Common cold Many No − −
 Coronavirus Common cold Many No − −
 Coxsackievirus Herpangina, 
pleurodynia
Many No − −
DNA viruses
 Herpes simplex virus 
 type 1
Gingivostomatitis One No − +
 Epstein-Barr virus Infectious 
mononucleosis
One Yes − +
 Varicella-zoster virus Chickenpox, 
shingles
One Yesa + +
 Adenovirus Pharyngitis, 
pneumonia
Many No − +
aLifelong immunity to reinfections with varicella (chickenpox) but not to reactivation of zoster (shingles).
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572 SECTION IV Virology
A. 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. 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. 
Coryza and cough may last for several weeks.
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 seizures can occur. Influenza A viruses are 
an important cause of croup, which may be severe, in children 
younger than 1 year of age. Finally, otitis media may develop.
When influenza appears in epidemic form, clinical 
findings are consistent enough that the disease can be diag-
nosed presumptively. Sporadic cases cannot be diagnosed on 
clinical grounds because disease manifestations cannot be 
distinguished from those caused by other respiratory tract 
pathogens. However, those other agents rarely cause severe 
viral pneumonia, which can be a complication of influenza A 
virus infection.
B. Pneumonia
Serious complications usually occur only in elderly adults 
and debilitated individuals, especially those with underly-
ing chronic disease. Pregnancy appears to be a risk factor 
for lethal pulmonary complications in some epidemics. The 
lethal impact of an influenza epidemic is reflected in the 
excess deaths caused by pneumonia and cardiopulmonary 
diseases.
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.
Combined viral–bacterial pneumonia is approximately 
three times more common than primary influenza pneumo-
nia. A molecular basis for a synergistic effect between virus 
and bacteria may be that some S aureus strains secrete a pro-
tease able to cleave the influenza HA, thereby allowing pro-
duction of much higher titers of infectious virus in the lungs.
C. Reye Syndrome
Reye syndrome is an acute encephalopathy of children and 
adolescents, usually between 2 and 16 years of age. The mor-
tality rate is high (10–40%). The cause of Reye syndrome is 
unknown, but it is a recognized rare complication of influ-
enza B, influenza A, and herpesvirus varicella-zoster infec-
tions. There is a possible relationship between salicylate use 
and subsequent development of Reye syndrome. The inci-
dence of the syndrome has decreased with the reduced use of 
salicylates in children with flulike symptoms.
Immunity
Immunity to influenza is long lived and subtype specific. 
Whereas antibodies against HA and NA are important in 
immunity to influenza, antibodies against the other virus-
encoded proteins are not protective. Resistance to initiation of 
infection is related to antibody against the HA, but decreased 
severity of disease and decreased ability to transmit virus to 
contacts are related to antibody directed against the NA.
Protection correlates with both serum antibodies and 
secretory IgA antibodies in nasal secretions. The local secre-
tory antibody is probably importantin preventing infection. 
Serum antibodies persist for many months to years; secre-
tory antibodies are of shorter duration (usually only several 
months). Antibody also modifies the course of illness. A per-
son with low titers of antibody may be infected but will expe-
rience a mild form of disease. Immunity can be incomplete; 
reinfection with the same virus can occur.
The three types of influenza viruses are antigenically 
unrelated and therefore induce no cross-protection. When a 
viral type undergoes antigenic drift, a person with preexisting 
antibody to the original strain may have only mild infection 
with the new strain. Subsequent infections or immunizations 
reinforce the antibody response to the first subtype of influ-
enza experienced years earlier, a phenomenon called “origi-
nal antigenic sin.”
The primary role of cell-mediated immune responses in 
influenza is believed to be clearance of an established infec-
tion; cytotoxic T cells lyse infected cells. The cytotoxic T lym-
phocyte response is cross-reactive (able to lyse cells infected 
with any subtype of virus) and appears to be directed against 
both internal proteins (NP, M) and the surface glycoproteins.
Laboratory Diagnosis
Clinical characteristics of viral respiratory infections can be 
produced by many different viruses. Consequently, diagnosis 
of influenza relies on identification of viral antigens or viral 
nucleic acid in specimens, isolation of the virus, or demon-
stration of a specific immunologic response by the patient.
Nasopharyngeal swabs and nasal aspirate or lavage fluid 
are the best specimens for diagnostic testing and should be 
obtained within 3 days after the onset of symptoms.
A. Polymerase Chain Reaction
Rapid tests based on detection of influenza RNA in clinical 
specimens using reverse transcription polymerase chain 
reaction (RT-PCR) are preferred for diagnosis of influenza. 
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CHAPTER 39 Orthomyxoviruses (Influenza Viruses) 573
RT-PCR is rapid (<1 day), sensitive, and specific. Multiplex 
molecular technologies are available that allow for the rapid 
detection of multiple pathogens in a single test.
B. Isolation and Identification of Virus
The sample to be tested for virus isolation should be held at 
4°C until inoculation into cell culture because freezing and 
thawing reduce the ability to recover virus. However, if storage 
time will exceed 5 days, the sample should be frozen at –70°C.
Viral culture procedures take 3–10 days. Classically, 
embryonated eggs and primary monkey kidney cells have 
been the isolation methods of choice for influenza viruses, 
although other cell lines may be used. Inoculated cell cultures 
are incubated in the absence of serum, which may contain 
nonspecific viral inhibitory factors, and in the presence of 
trypsin, which cleaves and activates the HA so that replicat-
ing virus will spread throughout the culture.
Cell cultures can be tested for the presence of virus by 
hemadsorption 3–5 days after inoculation, or the culture fluid 
can be examined for virus after 5–7 days by hemagglutination 
or immunofluorescence. If the results are negative, a passage is 
made into fresh cultures. This passage may be necessary because 
primary viral isolates are often fastidious and grow slowly.
Viral isolates can be identified by hemagglutination inhi-
bition (HI), a procedure that permits rapid determination of 
the influenza type and subtype. To do this, reference sera to 
currently prevalent strains must be used. Hemagglutination 
by the isolate will be inhibited by specific antiserum to the 
homologous subtype.
For rapid diagnosis, cell cultures on coverslips in shell 
vials may be inoculated and stained 1–4 days later with mono-
clonal antibodies to respiratory agents. Rapid viral cultures 
can also be tested by RT-PCR to identify a cultured agent.
It is possible to identify viral antigen directly in exfoli-
ated cells in nasal aspirates using fluorescent antibodies. This 
test is rapid (taking only a few hours) but is not as sensitive as 
PCR or viral isolation, does not provide full details about the 
viral strain, and does not yield an isolate that can be charac-
terized. Rapid influenza antigen detection tests are commer-
cially available that take less than 15 minutes. However, these 
tests vary in sensitivity and specificity, and a negative result 
does not rule out influenza infection.
C. Serology
Antibodies to several viral proteins (HA, NA, NP, and 
matrix) are produced during infection with influenza virus. 
The immune response against the HA glycoprotein is associ-
ated with resistance to infection.
Routine serodiagnostic tests in use are based on HI and 
enzyme-linked immunosorbent assay. Paired acute and con-
valescent sera are necessary because normal individuals usu-
ally have influenza antibodies. A fourfold or greater increase 
in titer must occur to indicate influenza infection. Human 
sera often contain nonspecific mucoprotein inhibitors that 
must be destroyed before testing by HI.
The HI test reveals the strain of virus responsible for 
infection only if the correct antigen is available for use. Neu-
tralization tests are the most specific and the best predic-
tor of susceptibility to infection but are more unwieldy and 
more time consuming to perform than the other tests. The 
enzyme-linked immunosorbent assay is more sensitive than 
other assays.
Complications may be encountered in attempting to 
identify the strain of infecting influenza virus by the patient’s 
antibody response because anamnestic responses frequently 
occur.
Epidemiology
Influenza viruses occur worldwide and cause annual out-
breaks of variable intensity. It is estimated that annual epi-
demics of seasonal influenza cause 3–5 million cases of severe 
illness and 250,000–500,000 deaths worldwide. The eco-
nomic 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 popula-
tion in industrialized countries, depending on the size of the 
epidemic.
The three types of influenza vary markedly in their epi-
demiologic patterns. Influenza C is least significant; it causes 
mild, sporadic respiratory disease but not epidemic influ-
enza. Influenza B sometimes causes epidemics, but influenza 
type A can sweep across continents and around the world in 
massive epidemics called pandemics.
The incidence of influenza peaks during the winter. In the 
United States, influenza epidemics usually occur from Janu-
ary through April (and from May to August in the Southern 
Hemisphere). A continuous person-to-person chain of trans-
mission must exist for maintenance of the agent between 
epidemics. Some viral activity can be detected in large popu-
lation centers throughout each year, indicating that the virus 
remains endemic in the population and causes a few subclini-
cal or minor infections.
A. Antigenic Change
Periodic outbreaks appear because of antigenic changes in 
one or both surface glycoproteins of the virus. When the 
number of susceptible persons in a population reaches a suf-
ficient level, the new strain of virus causes an epidemic. The 
change may be gradual (hence the term “antigenic drift”) 
because of point mutations reflected in alterations at major 
antigenic sites on the glycoprotein (see Figure 39-3) or drastic 
and abrupt (hence the term “antigenic shift”) owing to genetic 
reassortment during coinfection with an unrelated strain.
All three types of influenza virus exhibit antigenic 
drift. However, only influenza A undergoes antigenic shift, 
 presumably because types B and C are restricted to humans, 
but related influenza A viruses circulate in animal and bird 
populations. These animal strains account for antigenic shift 
by genetic reassortment of the glycoprotein genes. Influenza 
A viruses have been recovered from many aquatic birds, 
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574 SECTION IV Virology
 especially ducks; from domestic poultry, such as turkeys, 
chickens, geese, and ducks; from pigs and horses; and even 
from seals and whales. Serologic surveys indicate a high prev-
alence of influenza virus infection in domestic cats.
Influenza outbreaks occur in waves, although there is no 
regular periodicity in the occurrence of epidemics. The expe-
rience in any given year will reflect the interplay between 
extent of antigenic drift of the predominant virus and waning 
immunity in the population. The period between epidemic 
waves of influenza A tends to be 2–3 years; the interepi-
demic period for type B is longer (3–6 years). Every 10–40 
years, when a new subtype of influenza A appears, a pan-
demic results. Seroepidemiology studies suggest the cause 
of epidemics in 1890 (H2N8) and 1900 (H3N8), with known 
virologic confirmation of epidemics in 1918 (H1N1), 1957 
(H2N2), and 1968 (H3N2). The H1N1 subtype reemerged in 
1977, although no epidemic materialized.
In early 2009, a novel swine-origin H1N1 virus appeared 
and reached pandemic spread by mid-year. It was a quadru-
ple reassortant, containing genes from both North Ameri-
can and Eurasian swine viruses, as well as from avian and 
human influenza viruses. The virus was readily transmis-
sible among humans and spread globally, causing more than 
18,000 deaths. The severity of illness was comparable to that 
of seasonal flu. The pandemic virus, designated A(H1N1)
pdm09, has become a seasonal influenza virus, continuing to 
circulate with other seasonal viruses, and appears to have dis-
placed the previously circulating H1N1 strain virus.
Surveillance for influenza outbreaks is necessary to iden-
tify the early appearance of new strains, with the aim of pre-
paring vaccines against them before an epidemic occurs. That 
surveillance may extend into animal populations, especially 
birds, pigs, and horses. Isolation of a virus with an altered HA 
in the late spring during a mini-epidemic signals a possible 
epidemic the following winter. This warning sign, termed a 
“herald wave,” has been observed to precede influenza A and 
B epidemics.
B. Avian Influenza
Sequence analyses of influenza A viruses isolated from many 
hosts in different regions of the world support the theory that all 
mammalian influenza viruses derive from the avian influenza 
reservoir. Of the 18 HA subtypes found in birds, only a few have 
been transferred to mammals (H1, H2, H3, H5, H7 and H9 in 
humans; H1, H2 and H3 in swine; and H3 and H7 in horses). 
The same pattern holds for NA; 11 NA subtypes are known for 
birds, only 2 of which are found in humans (N1, N2).
Avian influenza ranges from inapparent infections to 
highly lethal infections in chickens and turkeys. Most influ-
enza infections in ducks are avirulent. Influenza viruses of 
ducks multiply in cells lining the intestinal tract and are shed 
in high concentrations in fecal material into water, where 
they remain viable for days or weeks, especially at low tem-
peratures. It is likely that avian influenza is a waterborne 
infection, moving from wild to domestic birds and pigs.
To date, all human pandemic strains have been reassor-
tants between animal and human influenza viruses. Evidence 
supports the model that pigs serve as mixing vessels for reas-
sortants because their cells contain receptors recognized by 
both human and avian viruses (Figure 39-5). The pandemic 
strain of 2009 was a novel reassortant that contained swine-
origin viral genes as well as those from avian and human 
influenza viruses. School-age children are the predominant 
vectors of influenza transmission. Crowding in schools favors 
the aerosol transmission of virus, and children take the virus 
home to their families.
In 1997, in Hong Kong, the first documented infection 
of humans by avian influenza A virus (H5N1) occurred. The 
source was domestic poultry. By 2006, the geographic pres-
ence of this highly pathogenic H5N1 avian influenza virus in 
both wild and domestic birds had expanded to include many 
countries in Asia, Africa, Europe, and the Middle East. Out-
breaks were the largest and most severe on record. Of about 
425 laboratory-confirmed human cases by May 2009, more 
than half were fatal. So far, isolates from human cases have 
contained all RNA gene segments from avian viruses, indi-
cating that, in those infections, the avian virus had jumped 
directly from bird to human. All evidence to date indicates 
that close contact with diseased birds has been the source of 
human H5N1 infection. The concern is that, given enough 
opportunities, the highly pathogenic H5N1 avian influenza 
virus will acquire the ability to spread efficiently and be sus-
tained among humans, either by reassortment or by adap-
tive mutation. This would result in a devastating influenza 
pandemic. Other avian influenza strains have been found in 
human infections following close bird exposure, including 
H7N9 H9N2 viruses.
C. Reconstruction of 1918 Influenza Virus
PCR technology has yielded gene fragments of influenza 
virus from archival lung tissue specimens from victims 
of the 1918 Spanish flu epidemic. The complete coding 
FIGURE 39-5 Pigs may act as an intermediate host for the 
generation of human–avian reassortant influenza viruses with 
pandemic potential. (Reprinted by permission from Macmillan 
Publishers Ltd: Claas ECJ, Osterhaus ADME: New clues to the 
emergence of flu pandemics. Nat Med 1998;4:1122. Copyright © 1998).
Human
virus
Reassortant virus
Avian virus
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CHAPTER 39 Orthomyxoviruses (Influenza Viruses) 575
sequences of all eight viral RNA segments have been deter-
mined, and the sequences document that it was an H1N1 
influenza A virus. It appears that the 1918 virus was not a 
reassortant but was derived entirely from an avian source 
that adapted to humans. Using reverse genetics, an infec-
tious virus containing all the gene segments from the 1918 
pandemic virus was constructed. In contrast to ordinary 
influenza viruses, the 1918 virus was highly pathogenic, 
including being able to kill mice rapidly. The 1918 HA and 
polymerase genes appeared to be responsible for the high 
virulence.
Prevention and Treatment by Drugs
Amantadine hydrochloride and an analog, rimantadine, 
classed as adamantane drugs, are M2 ion channel inhibi-
tors for systemic use in the treatment and prophylaxis of 
influenza A. The NA inhibitors zanamivir and oseltami-
vir (approved in 1999), and peramivir (approved in 2014) 
are useful for treatment of both influenza A and influenza 
B. To be maximally effective, the drugs must be adminis-
tered very early in the disease. Resistant viruses emerge 
more frequently during therapy with M2 inhibitors than 
with NA inhibitors and more frequently in children than 
adults. Resistance to oseltamivir has been associated with 
the H275Y mutation in NA gene. During 2013–2014, all cir-
culating influenza viruses were resistant to M2 inhibitors, 
but most were sensitive to NA inhibitors. Depending on the 
susceptibility of the predominantly circulating strains, sub-
typing may be useful to determine optimal therapy.
Prevention and Control by Vaccines
Inactivated viral vaccines are the primary means of preven-
tion of influenza in the United States. However, certain char-
acteristics of influenza viruses make prevention and control 
of the disease by immunization especially difficult. Exist-
ing vaccines are continually being rendered obsolete as the 
viruses undergo antigenic drift and shift. Surveillance pro-
grams by government agencies and the World Health Orga-
nization constantly monitor subtypes of influenza circulating 
around the world to promptly detect the appearance and 
spread of new strains.
A major advance would be the ability to design a vaccine 
that stimulates production of a broadly neutralizing antibody 
response effectiveagainst many influenza subtypes.
Several other problems are worthy of mention. 
Although protection can reach from 70% to 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.
A. 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 one type B virus of the strains isolated in the pre-
vious winter’s outbreaks.
Selected seed strains are grown in embryonated eggs, the 
substrate used for vaccine production. Sometimes the natural 
isolates grow too poorly in eggs to permit vaccine produc-
tion, in which case a reassortant virus is made in the labora-
tory. The reassortant virus, which carries the genes for the 
surface antigens of the desired vaccine with the replication 
genes from an egg-adapted laboratory virus, is then used for 
vaccine production. A cell-based vaccine using animal cell 
cultures became available in 2012, which overcomes some 
limitations of egg-based production.
Virus is harvested, purified, concentrated by zonal cen-
trifugation, and inactivated with formalin or β-propiolactone. 
The quantity of HA is standardized in each vaccine dose 
(~15 μg of antigen), but the quantity of NA is not standard-
ized because it is more labile under purification and storage 
conditions. Each dose of vaccine contains the equivalent of 
about 10 billion virus particles.
Vaccines are either whole virus (WV), subvirion (SV), or 
surface antigen preparations. The WV vaccine contains intact, 
inactivated virus; the SV vaccine contains purified virus dis-
rupted with detergents; and the surface antigen vaccines con-
tain purified HA and NA glycoproteins. All are efficacious.
B. Live-Virus Vaccines
A live-virus vaccine must be attenuated so as not to induce 
the disease it is designed to prevent. In view of the constantly 
changing face of influenza viruses in nature and the extensive 
laboratory efforts required to attenuate a virulent virus, the 
only feasible strategy is to devise a way to transfer defined 
attenuating genes from an attenuated master donor virus to 
each new epidemic or pandemic isolate.
A cold-adapted donor virus, able to grow at 25°C but not at 
37°C—the temperature of the lower respiratory tract—should 
replicate in the nasopharynx, which has a cooler temperature 
(33°C). 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.
C. Use of Influenza Vaccines
The only contraindication to vaccination is a history of 
allergy to egg protein, although the cell-based vaccine over-
comes this limitation. When the vaccine strains are grown 
in eggs, some egg protein antigens are present in the vaccine.
Annual influenza vaccination is recommended for all 
children ages 6 months to 18 years and for high-risk groups. 
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576 SECTION IV Virology
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 met-
abolic or renal disorders; residents of nursing homes; persons 
infected with the human immunodeficiency virus; 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 individ-
uals in the high-risk groups.
Prevention by Hand Hygiene
Although transmission of influenza virus occurs primar-
ily by aerosol spread, hand transmission also is potentially 
important. Studies have shown that handwashing with 
soap and water or the use of alcohol-based hand rubs is 
highly effective at reducing the amount of virus on human 
hands.
CHAPTER SUMMARY
•	 Influenza viruses are major respiratory pathogens.
•	 Influenza type A is highly variable antigenically and 
causes most epidemics and all global pandemics.
•	 Influenza type B sometimes undergoes antigenic changes 
and can cause epidemics.
•	 Influenza type C is antigenically stable.
•	 Influenza A strains are also found in aquatic birds, ducks, 
domestic poultry, pigs, and horses.
•	 The viral genome is single-stranded, negative-sense RNA 
consisting of eight separate segments.
•	 Surface glycoproteins, HA and NA, determine influenza 
virus antigenicity and host immunity.
•	 Minor antigenic changes in HA and NA, termed anti-
genic drift, occur independently and are caused by accu-
mulation of point mutations.
•	 A major antigenic change in HA or NA, called anti-
genic shift, results in a new influenza virus subtype and 
is caused by genetic reassortment of genome segments 
between human and animal viruses.
•	 Because many different viruses can cause respiratory 
infections, diagnosis of influenza infection cannot reli-
ably be made clinically and relies on laboratory assays.
•	 Immunity to influenza is long lived and subtype specific. 
Only antibodies to HA and NA are protective.
•	 Both inactivated and live-virus vaccines exist but are 
continually being rendered obsolete as new antigenic 
variants of influenza viruses arise.
•	 Antiviral drugs exist, but resistant viruses emerge fre-
quently, especially to M2 ion channel inhibitors.
•	 Avian influenza A viruses, H5N1, H7N9, and H9N2 
cause sporadic human infections but have not acquired 
the ability for sustained human-to-human transmission.
REVIEW QUESTIONS
1. Which of the following statements regarding the prevention 
and treatment of influenza is correct?
(A) Booster doses of vaccine are not recommended.
(B) Drugs that inhibit neuraminidase are active only against 
influenza A.
(C) As with some other live vaccines, the attenuated influenza 
vaccine should not be given to pregnant women.
(D) The influenza vaccine contains several serotypes of virus.
(E) The virus strains in the influenza vaccine do not vary from 
year to year.
2. Which of the following statements about the neuraminidase of 
influenza virus is not correct?
(A) Is embedded in the outer surface of the viral envelope
(B) Forms a spike structure composed of four identical mono-
mers, each with enzyme activity
(C) Facilitates release of virus particles from infected cells
(D) Lowers the viscosity of the mucous film in the respiratory 
tract
(E) Is antigenically similar among all mammalian influenza 
viruses
3. Which of the following statements reflects the pathogenesis of 
influenza?
(A) The virus enters the host in airborne droplets.
(B) Viremia is common.
(C) The virus frequently establishes persistent infections in the 
lung.
(D) Pneumonia is not associated with secondary bacterial 
infections.
(E) Viral infection does not kill cells in the respiratory tract.
4. Which of the following symptoms is not typical of influenza?
(A) Fever
(B) Muscular aches
(C) Malaise
(D) Dry cough
(E) Rash
5. The type-specific antigen (A, B, or C) of influenza viruses is 
found on which viral constituent?
(A) Hemagglutinin
(B) Neuraminidase
(C) Nucleocapsid
(D) Polymerase complex
(E) Major nonstructural protein
(F) Lipid in the viral envelope
6. A 70-year-old nursing home patient refused the influenza vaccine 
and subsequently developed influenza. She died of acute pneu-monia 1 week after contracting the flu. The most common cause 
of acute postinfluenza pneumonia is which of the following?
(A) Legionella
(B) Staphylococcus aureus
(C) Measles
(D) Cytomegalovirus
(E) Listeria
7. Which of the following statements concerning antigenic drift in 
influenza viruses is correct?
(A) It results in major antigenic changes.
(B) It is exhibited only by influenza A viruses.
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CHAPTER 39 Orthomyxoviruses (Influenza Viruses) 577
(C) It is caused by frameshift mutations in viral genes.
(D) It results in new subtypes over time.
(E) It affects predominantly the matrix protein.
8. A 32-year-old male physician developed a “flulike” syndrome 
with fever, sore throat, headache, and myalgia. To provide 
 laboratory confirmation of influenza, a culture for the virus was 
ordered. Which of the following would be the best specimen for 
isolating the virus responsible for this infection?
(A) Stool
(B) Nasopharyngeal swab
(C) Vesicle fluid
(D) Blood
(E) Saliva
9. Which of the following statements about isolation of influenza 
viruses is correct?
(A) Diagnosis of an influenza virus infection can only be made 
by isolating the virus.
(B) Isolation of influenza virus is done using newborn mice.
(C) Isolation of virus can help determine the epidemiology of 
the disease.
(D) Primary influenza virus isolates grow readily in cell 
culture.
10. The principal reservoir for the antigenic shift variants of influ-
enza virus appears to be which of the following?
(A) Chronic human carriers of the virus
(B) Sewage
(C) Pigs, horses, and fowl
(D) Mosquitoes
(E) Rodents
11. Highly pathogenic H5N1 avian influenza (HPAI) can infect 
humans with a high mortality rate, but it has not yet resulted in 
a pandemic. The following are characteristics of HPAI, except 
for one. Which one is not?
(A) Efficient human-to-human transmission
(B) Presence of avian influenza genes
(C) Efficient infection of domestic poultry
(D) Contains segmented RNA genome
12. Which of the following statements about diagnostic testing for 
influenza is true?
(A) Clinical symptoms reliably distinguish influenza from 
other respiratory illnesses.
(B) Viral culture is the “gold standard” diagnostic test because 
it is the most rapid assay.
(C) Patient antibody responses are highly specific for the strain 
of infecting influenza virus.
(D) Reverse transcription polymerase chain reaction is 
 preferred for its speed, sensitivity, and specificity.
13. The mechanism of “antigenic drift” in influenza viruses includes 
all but one of the following
(A) Can involve either hemagglutinin or neuraminidase 
antigens
(B) Mutations caused by viral RNA polymerase
(C) Can predominate under selective host population immune 
pressures
(D) Reassortment between human and animal or avian 
reservoirs
(E) Can involve genes encoding structural or nonstructural 
proteins
14. Each of the following statements concerning the prevention and 
treatment of influenza is correct except
(A) The inactivated influenza vaccine contains H1N1 virus but 
the live, attenuated influenza vaccine contains H3N2 virus.
(B) The vaccine is recommended to be given each year because 
the antigenicity of the virus drifts.
(C) Oseltamivir is effective against both influenza A and influ-
enza B viruses.
(D) The main antigen in the vaccine that induces protective 
antibody is the hemagglutinin.
15. Each of the following statements concerning the antigenicity of 
influenza A virus is correct except
(A) Antigenic shifts, which represent major changes in antige-
nicity, occur infrequently and are caused by the reassort-
ment of segments of the viral genome.
(B) Antigenic shifts affect both the hemagglutinin and the 
neuraminidase.
(C) The worldwide epidemics caused by influenza A virus are 
caused by antigenic shifts.
(D) The protein involved in antigenic drift is primarily the 
internal ribonucleoprotein.
16. Which of the following infectious agents is most likely to cause 
a pandemic?
(A) Influenza A virus
(B) Streptococcus pyogenes
(C) Influenza B virus
(D) Respiratory syncytial virus
(E) Influenza C virus
Answers
 1. D
 2. E
 3. A
 4. E
 5. C
 6. B
 7. D
 8. B
 9. C
10. C
11. A
12. D
13. D
14. A
15. D
16. A
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DM, Howley PM (editors-in-chief) Fields Virology, 5th ed. 
 Lippincott Williams & Wilkins, 2007.
Carroll_CH39_p565-p578.indd 578 5/22/15 5:31 PM
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	Section IV: Virology
	39. Orthomyxoviruses (Influenza Viruses)
	Properties of Orthomyxoviruses
	Influenza Virus Infections in Humans
	Chapter Summary
	Review Questions