Orthomyxoviruses

(Influenza virus)
The influenza pandemic of 1918-1919 killed
more people than the World War I (WWI), at
somewhere between 50 and 100 million
people. This was caused by the deadly strain
subtype H1N1 influenza type A virus. It has
been cited as the most devastating epidemic
in recorded world history. More people died
of influenza in a single year than in four-years
of the Black Death Bubonic Plague from 1347
to 1351.
 Orthomyxoviruses
• Major cause of respiratory disease. Influenza (flu) can
cause mild to severe illness, and has been responsible
for millions of deaths worldwide.
• ss negative-sense RNA. The antisense RNA genome
occurs in eight separate segments containing 10 genes.
• The envelope contains viral haemagglutinin (HA) and
neuraminidase (NA) proteins.
• Genetic reassortment of Influenzavirus is common. The
segmented viral genome allows a mixture of genome
segments from two strains, when a single cell is
infected by 2 different strains.
Influenza virus
 Classification
• Antigenic differences exhibited by two of the internal
structural proteins: nucleocapsid (NP) and matrix (M)
proteins, are used to divide influenza viruses into types AC.
NP antigens are stable and exhibit no serologic cross
reactivity.
• Surface glycoproteins: HA and NA, are used to subtype the
viruses. These two antigens are variable. These Ags are
responsible for immunity to infection.
• So far, 15 subtypes for HA (H1-H15); and 9
subtypes for NA (N1-N9) have been recovered from birds,
animals and humans.
• In humans, there are 4 HA (H1-3,H5) and 2 NA (N1-2).
 Function of HA
• Haemagglutinin = agglutinate erythrocytes
under certain conditions.
• HA binds virus particles to susceptible cells,
and is the major Ag against neutralising Abs.
 Function of NA

• Functions at the end of viral replication cycle. It is a sialidase

that removes sialic acid from glycoconjugates.
• Facilitates release of virus particles from infected cell surfaces
during the budding process. And prevent self-aggregation of
virions by removing sialic acid residues from viral glycoproteins.
Also may help the virus to slide through the mucin layer in resp
T to reach the target epithelial cells.
 Influenza virus Replication
Expert Reviews in Molecular Medicine 2001 Cambridge University Press
• (a) The virus binds to cell-surface sialic acid receptors on the surface of
the host cell and (b) is internalised into endosomes, by receptor-mediated
encytosis. (c) Fusion btw viral envelope and cell membrane, and
uncoating events, (d) Low pH is required by the virus-mediated
membrane fusion to release of the viral genome (RNPs) into the
cytoplasm. The vRNPs are then imported into the nucleus for (e)
replication. (f) mRNAs are produced from viral nucleocapsids. Positive-
sense viral messenger RNAs (mRNAs) are exported out of the nucleus into
the cytoplasm for (g) protein synthesis. Cellular functions are more
involved. Protein synthesis requires cellular transcripts and RNA
polymerase II, which explains why influenza virus is inhibited by drugs
that block cellular transcription. (h) Some of the proteins are imported
into the nucleus to assist in viral RNA replication and (i) vRNP assembly,
which also occur in the nucleus. (j) Late in infection, the vRNPs form and
leave the nucleus, and (k) progeny viruses assemble and (l) bud from the
plasma membrane.
• The sites of action of anti-viral drugs are shown in red, italic text.
Abbreviations used: cRNA (+), positive-sense complementary RNA; HA,
haemagglutinin; M1, matrix protein; M2, tetrameric ion channel; mRNA
(+), positive-sense messenger RNA; NA, neuraminidase; NP,
nucleoprotein; NS1, a non-structural protein, NS2, a viral protein; pols,
polymerases; vRNA (-), negative-sense genomic RNA
 Pathogenesis & Pathology
• Spreads from person to person by airborne droplets, or
contaminated hands and surfaces.
• Viral NA lowers the viscosity of the mucous film in the resp T,
exposing the cellular surface receptors and promoting the
spread of virus-containing fluid to lower resp T. Within short
time, many resp cells are infected and eventually killed.
• Interferon is effective against influenza virus and attributes to
host recovery.
• 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 in the
epith lowers its resistance to secondary bacterial invaders esp
staphylococci, streptococci and Haemophilus influenzae.
 Antigenic Drift & Shift
• Antigenic variants confer selective advantage over
the parental virus in the presence of Ab against the
original strain.
• The 2 surface Ags undergo antigenic variation
independent of each other.
• Antigenic drift = Minor changes, a gradual change in
antigenicity due to point mutations that affect major
antigenic sites on the glycoprotein.
• Antigenic shift = Major changes, an abrupt change
due to genetic reassortment with an unrelated
strain, which results in the appearance of a new
subtype.
 Clinical findings
• Uncomplicated Influenza : Abrupt symptoms include
chills, headache, dry cough, muscular aches. These
may be induced by influenza A or B. In contrast,
influenza C causes a common cold illness, Coryza.
• Pneumonia : complications occur only in the elderly
and debilitated. Influenza infection enhances the
susceptibility of patients to bacterial superinfection,
due to loss of ciliary clearance, dysfunction of
phagocytic cells.
• Reye’s Syndrome : an acute encephalopathy of
children and adolescents (2-16yrs)
 Immunity
• Is long-lived and subtype specific.
• Abs to HA and NA are important. Resistance to initiation of
infection is related to Ab vs. HA, whereas severity of disease
and ability to transmit virus to contacts are associated with
Abs vs. NA.
• Local secretory IgA Abs is probably important in preventing
infection. Serum Abs are also protective and persist for years.
Abs modify the course of illness – person with low titres of
Abs may experience mild form of illness.
• Cell-mediated immune response is probably important for
clearance of an infection. Cytotoxic T lymphocyte response is
cross-reactive ie. able to lyse cells infected by any subtype of
virus, and is directed against both internal proteins (NP, M)
and the surface glycoproteins.
 Epidemiology
• Periodic outbreaks appear because of antigenic
changes in one or both surface glycoproteins of the
virus.
• Only influenza A viruses circulate in animals and
avians. Antigenic shift ?
• The recent strain in avian influenza A virus (H5N1) in
1997, reported in Hong Kong. The source was
domestic poultry. At present, there is no vaccine
against this strain.
 Prevention & Control by Vaccines
• A) Inactivated Viral Vaccines:
• Parenteral use;usually contain 1 or 2 type A and a type B
viruses, isolated from previous winter’s outbreaks.
• Strains are grown in embryonated eggs and the virus is
harvested from egg allantoic fluid.
• Vaccines are either whole virus (WV), subvirion (SV), or
surface Ag (SAg) preparations. WV=contains intact, inactivated
virus; SV=purified virus disrupted with detergents; SAg
contains purified HA and NA glycoproteins.
• Sometimes called “flu shot” or “flu jab”.
 Prevention & Control by Vaccines
• B) Live Attenuated Influenza Vaccine
• Contains live but attenuated (weakened) vaccine. It is sprayed
into nostril.

• For both types of vaccines, it will take up to 2 weeks to

develop protection after vaccination.
• The synthetic drugs amantadine and rimantadine
hydrochloride effectively prevent infection and illness caused
by type A, but not by type B, viruses. The drugs interfere with
virus uncoating and transport by blocking the transmembrane
M2 ion channel (see fig of replication).
Paramyxoviruses
 Paramyxoviruses
• The World Health Organisation (WHO) estimates that
acute respiratory infections and pneumonia are
responsible every year worlwide for the deaths of 4
million children under 5 years of age.
• Paramyxoviruses are the major respiratory pathogens
in this age group.
• Reinfections are common throughout childhood.
• All members of the Paramyxoviridae family initiate
infection via the resp T.
• Transmission is by person-to-person contact or by
large-droplet aerosols.
 General Structure
• Enveloped. Viral genome
is linear, negative sense
ss RNA. Non-segmented
genome, hence all
members are
antigenically stable.
• Haemagglutinin
glycoprotein HN
proteins are important
for viral attachment.
 Pathogenesis of Parainfluenza Infections

• Parainfluenza virus replication in

immunocompromised appears to be limited to
respiratory epithelia. Viraemia is rare. The result is
“common cold” syndrome.
• Infection may spread to larynx and upper trachea,
resulting in croup. Croup is characterised by resp
obstruction due to swelling of larynx and related
structures.
• Viral shedding is about 1 week after onset of illness.
Some immunocompromised children experience
persistent shedding.
 Clinical findings & Lab diagnosis
• Primary infections in children usually result in rhinitis,
pharyngitis, often with fever.
• Severe illness associated with Parainfluenza Type 3 may
occur in infants.
• Common complication is otitis media.
• Lab: Ag detection – immunofluorescence test; isolation
of virus-containing specimens; and serological by
detecting specific IgM Ab.
• Parainfluenza viruses are troublesome in hospitals.
Contact isolation is necessary to prevent outbreaks.
• Antiviral ribavirin is used to treat immunocompromised
with lower resp T disease.
Togaviruses
 Toga Viruses
• Structure
• Classification
• Multiplication
• Clinical manifestations
• Epidemiology
• Diagnosis
• Control
 Togaviridiae
• Rubivirus-rubella
• Alphavirus- Equine Encephalitis, Sindbis
• Pestivirus- animal pathogens
– bovine viral diarrhea, hog cholera
 Rubella: Structure
• enveloped
• icosahedral
• ss RNA sense
• 40-80 nm
• 30 nm core
• hemaglutinin peplomers + ssRNA
 Rubella: Classification
• Family Togaviridae
• genus Rubivirus only member
• single serotype
• three structural polypeptides

Unlike other Togaviruses

rubella is not arthropod
borne
 Rubella: Multiplication
• RNA is capped and polyadenylated
• serves as mRNA -> nonstructural proteins
• sense RNA -> antisense RNA
• Antisense RNA template for progeny RNA
• antisense RNA--> mRNA -> structural proteins
• mature at intracytoplasmic membranes
 Rubella: Clinical manifestations
Postnatal
• rash
• lymphadenopathy
• low grade fever
Congenital
• stillbirth
• spontaneous abortion
• birth defects
 Congential Rubella
• Ocular- cataracts, retinitis, glucoma
,microphthalmaia
• Heart defects- patent ductus arteriosis
• Deafness- cochelar deafness, central auditory
imperception
• CNS- mental retardation, encephalitis,
microcephaly
• Other- hepatitis, pneumonitis
 Rubella: Pathogenesis
• respiratory secretions -direct contact, droplet
• multiplies in cells of respiratory system
• extends to lymph nodes, spleen
 Rubella: Epidemiology
• worldwide
• vaccines licenced 1969
• no new epidemics
• incidence ~ 100 /year

Congential rubella occurs in

unvaccinated susceptible young
women
 Rubella: Host defenses
• interferon
• cell mediate immunity
• neutralizing antibodies
• hemagglutinin inhibiting antibodies
asymptomatic reinfection possible
 Rubella: Diagnosis
• Clinical manifestations- rash,
lymphadenopathy
• Isolate virus respiratory tract
• Detect Rubella IgM
 Diagnosis: Congenital Rubella
• isolate virus - urine, CSF, blood
• maternal circulating IgG- lasts 6 months
• Detect fetal or neonate IgM
 Rubella: Control
• live attentuated rubella vaccine
– mumps-measles-rubella combination
• subcutaneous
• 15 months of age
• asymptomatic in children
• mild symptoms in adults
 Rubella: Control Strategies
• 10-20% young women not immunized
• Therefore immunize
– college students
– health care personnel
– military personnel
– after childbirth, miscarriage or abortion
Alphavirus

Encephalitis
Alphaviruses are arthropod borne
(arboviruses)
 Alphavirus: Structure
• icosahedral 40-50 nm
• enveloped
• attachment glycoprotein
• ss RNA, sense, monopartite
 Alphavirus: Classification
• common envelope glycoprotein
• common capsid antigenic sites
• 26 antigenic types
 Alphavirus: Multiplication
• RNA is capped and polyadenylated
• serves as mRNA -> nonstructural proteins
• sense RNA -> antisense RNA
• Antisense RNA template for progeny RNA
• antisense RNA--> mRNA -> structural proteins
• mature at intracytoplasmic membranes
 Subgenomic mRNA
• sense strand -> antisense strand
• 3’ one-third of antisense strand -> mRNA
• mRNA -> structural proteins
Alphavirus: Clinical manifestations
• Encephalitis viruses
– fever, malaise, headache and/or encephalitis
• Arthritis viruses
– fever, rash, arthralgia, arthritis
 Alphavirus: Epidemiology
• mosquito-vertebrate-mosquito cycles
• geographically restricted
• epizootics- Venezuelan equine enchephalitis
• urban epidemics- chikungunya virus
• seasonal
 Alphavirus: Diagnosis
• clincal manifestations
• known exposure
• isolate virus
• detect IgM
 Alphavirus: Control
• reduce mosquito populations
• vaccinate vertebrate hosts- horses
• vaccine humans at high risk of exposure
Arthropod-borne Viruses

An Overview
 Arthropod-borne Viruses

Arthropod-borne viruses (arboviruses) are viruses that can be transmitted

to man by arthropod vectors. The WHO definition is as follows
“Viruses maintained in nature principally, or to an important
extent, through biological transmission between susceptible vertebrate hosts
by haematophagus arthropods or through transovarian and possibly venereal
transmission in arthropods.”

Arboviruses belong to three families

1. Togaviruses e.g. EEE, WEE, and VEE

2. Bunyaviruses e.g. Sandfly Fever, Rift Valley Fever, Crimean-Congo
Haemorrhagic Fever
3. Flaviviruses e.g. Yellow Fever, dengue, Japanese Encephalitis
 Transmission Cycles

• Man - arthropod -man

– e.g. dengue, urban yellow fever.
– Reservoir may be in either man or arthropod vector.
– In the latter transovarial transmission may take place.
• Animal - arthropod vector - man
– e.g. Japanese encephalitis, EEE, WEE, jungle yellow fever.
– The reservoir is in an animal.
– The virus is maintained in nature in a transmission cycle involving
the arthropod vector and animal. Man becomes infected
incidentally.
• Both cycles may be seen with some arboviruses such as yellow fever.
Man-Arthropod-Man Cycle
Animal-Arthropod-Man Cycle
 Arthropod Vectors

Mosquitoes
Japanese encephalitis, dengue, yellow fever, St. Louis
encephalitis, EEE, WEE, VEE etc.
Ticks
Crimean-Congo haemorrhagic fever, various tick-borne
encephalitides etc.
Sandflies
Sicilian sandfly fever, Rift valley fever.
Examples of Arthropod Vectors

Aedes Aegyti
Assorted Ticks

Culex Mosquito Phlebotmine Sandfly

 Animal Reservoirs

In many cases, the actual reservoir is not known. The

following animals are implicated as reservoirs
Birds Japanese encephalitis, St Louis encephalitis,
EEE, WEE
Pigs Japanese encephalitis
Monkeys Yellow Fever
Rodents VEE, Russian Spring-Summer encephalitis
 Diseases Caused

• Fever and rash - this is usually a non-specific illness

resembling a number of other viral illnesses such as
influenza, rubella, and enterovirus infections. The patients
may go on to develop encephalitis or haemorrhagic fever.

• Encephalitis - e.g. EEE, WEE, St Louis encephalitis,

Japanese encephalitis.
• Haemorrhagic fever - e.g. yellow fever, dengue, Crimean-
Congo haemorrhagic fever.
 Diagnosis

• Serology - usually used to make a diagnosis of arbovirus

infections.
• Culture - a number of cell lines may be used, including
mosquito cell lines. However, it is rarely carried out since
many of the pathogens are group 3 or 4 pathogens.
• Direct detection tests - e.g detection of antigen and nucleic
acids are available but again there are safety issues.
 Prevention

• Surveillance - of disease and vector populations

• Control of vector - pesticides, elimination of breeding
grounds
• Personal protection - screening of houses, bed nets, insect
repellants
• Vaccination - available for a number of arboviral infections
e.g. Yellow fever, Japanese encephalitis, Russian tick-
borne encephalitis
 Japanese Encephalitis

• First discovered and originally restricted to Japan. Now large scale

epidemics occur in China, India and other parts of Asia.
• Flavivirus, transmitted by culex mosquitoes.
• The virus is maintained in nature in a transmission cycle involving
mosquitoes, birds and pigs.
• Most human infections are subclinical: the inapparent to clinical cases
is 300:1
• In clinical cases, a life-threatening encephalitis occurs.
• The disease is usually diagnosed by serology. No specific therapy is
available.
• Since Culex has a flight range of 20km, all local control measures will
fail. An effective vaccine is available.
 Yellow Fever (1)

• Flavivirus, mainly found in West Africa and S America

• Yellow fever occurs in 2 major forms: urban and jungle (sylvatic)
yellow fever. Jungle YF is the natural reservoir of the disease in a cycle
involving nonhuman primates and forest mosquitoes. Man may
become incidentally infected on venturing into jungle areas.
• The urban form is transmitted between humans by the Aedes aegypti
mosquito
• Classically Yellow Fever presents with chills, fever, and headache.
Generalized myalgias and GI complaints (N+V).
• Some patients may experience an asymptomatic infection or a mild
undifferentiated febrile illness.
 Yellow Fever (2)

• After a period of 3 to 4 days, the more severely ill patients with a

classical YF course will develop bradycardia (Faget's sign),
jaundice, and haemorrhagic manifestations.
• 50% of patients with frank YF will develop fatal disease
characterized by severe haemorrhagic manifestations, oliguria and
hypotension.
• Diagnosis is usually made by serology
• There is no specific antiviral treatment
• An effective live attenuated vaccine is available against yellow
fever and is used for persons living in or traveling to endemic areas.
 Dengue (1)

• Dengue is the biggest arbovirus problem in the world today with

over 2 million cases per year. Dengue is found in SE Asia, Africa
and the Caribbean and S America.
• Flavivirus, 4 serotypes, transmitted by Aedes mosquitoes which
reside in water-filled containers.
• Human infections arise from a human-mosquitoe-human cycle
• Classically, dengue presents with a high fever, lymphadenopathy,
myalgia, bone and joint pains, headache, and a maculopapular rash.
• Severe cases may present with haemorrhagic fever and shock with
a mortality of 5-10%. (Dengue haemorrhagic fever or Dengue
shock syndrome.)
Distribution of Dengue
 Dengue (2)

• Dengue haemorrhagic fever and shock syndrome appear most

often in patients previously infected by a different serotype of
dengue, thus suggesting an immunopathological mechanism.
• Diagnosis is made by serology.
• No specific antiviral therapy is available.
• Prevention of dengue in endemic areas depends on mosquito
eradication. The population should remove all containers from
their premises which may serve as vessels for egg deposition.
• A live attenuated vaccine is being tried in Thailand with
encouraging results.
 Zika Virus

• Zika virus is a flavivirus that is primarily transmitted by Aedes

mosquitoes. It can also be sexually transmitted and possibly via
blood transfusions.
• Most infections are asymptomatic. When symptoms are present,
they are usually mild and resemble dengue.
• The distribution of zika virus is similar to Dengue, being found
mainly in tropical areas of Asia, Africa and America.
• Zika virus was first reported to be associated with microcephaly
and Guillain-Barré syndrome by Brazil in 2015.
• The risk of an infected pregnant women giving birth to a live or
dead baby with congenital abnormalities including microcephaly is
in the region of around 4-5% (based on US data)
Zika Virus Infections Worldwide